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no output #484

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akulan1 opened this issue Nov 14, 2024 · 12 comments
Open

no output #484

akulan1 opened this issue Nov 14, 2024 · 12 comments

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@akulan1
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akulan1 commented Nov 14, 2024

Hi,
We have 10x data from a cell village and I am trying to identify donors in the village using donor assignment. I have the 10x bam file, barcodes.tsv, gtf and vcf files.

Step 1: I ran Drop-seq_tools-2.5.1/TagReadWithGeneFunction on the bam file
Step 2: Drop-seq_tools-2.5.1/AssignCellsToSamples - outputs: V1_possorted_genome_bam_tagged.bam.donor_assignments.txt is empty (just header) and the *donor_assignments.vcf is not generated at all.

Here’s the command I am using:

/home/akulan/Drop-seq_tools-2.5.1/AssignCellsToSamples -m 24g -INPUT_BAM V1_possorted_genome_bam_tagged.bam -CELL_BC_FILE /data/GBMAD/McMahon-Claudia_SC_083024/V1_outs_090624/V1_filtered_feature_bc_matrix/barcodes.tsv.gz -VCF /data/akulan/gsa_may2024/PLINK_130524_0118/GSA_051324_scClaudiaV1labelled_chrAdded_snpsOnly.vcf.gz -OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.txt -VCF_OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.vcf.gz -CELL_BARCODE_TAG CB -LOCUS_FUNCTION_LIST INTRONIC -IGNORED_CHROMOSOMES null -IGNORED_CHROMOSOMES chrX -IGNORED_CHROMOSOMES chrY -IGNORED_CHROMOSOMES chrM

Any suggestions will be greatly appreciated.

Thank you very much.

Regards,
Nirmala
@jamesnemesh
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Could you please attach the log file the program generated when it ran?

@jamesnemesh jamesnemesh reopened this Nov 14, 2024
@akulan1
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akulan1 commented Nov 14, 2024

[akulan@cn2877 V1_outs_090624]$ /home/akulan/Drop-seq_tools-2.5.1/AssignCellsToSamples -m 24g -INPUT_BAM V1_possorted_genome_bam_tagged.bam -CELL_BC_FILE /data/GBMAD/McMahon-Claudia_SC_083024/V1_outs_090624/V1_filtered_feature_bc_matrix/barcodes.tsv.gz -VCF /data/akulan/gsa_may2024/PLINK_130524_0118/GSA_051324_scClaudiaV1labelled_chrAdded_snpsOnly.vcf.gz -OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.txt -VCF_OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.vcf.gz -CELL_BARCODE_TAG CB -LOCUS_FUNCTION_LIST INTRONIC -IGNORED_CHROMOSOMES null -IGNORED_CHROMOSOMES chrX -IGNORED_CHROMOSOMES chrY -IGNORED_CHROMOSOMES chrM
[Thu Nov 14 12:50:13 EST 2024] AssignCellsToSamples --INPUT_BAM V1_possorted_genome_bam_tagged.bam --VCF /data/akulan/gsa_may2024/PLINK_130524_0118/GSA_051324_scClaudiaV1labelled_chrAdded_snpsOnly.vcf.gz --OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.txt --VCF_OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.vcf.gz --CELL_BARCODE_TAG CB --CELL_BC_FILE /data/GBMAD/McMahon-Claudia_SC_083024/V1_outs_090624/V1_filtered_feature_bc_matrix/barcodes.tsv.gz --IGNORED_CHROMOSOMES chrX --IGNORED_CHROMOSOMES chrY --IGNORED_CHROMOSOMES chrM --LOCUS_FUNCTION_LIST CODING --LOCUS_FUNCTION_LIST UTR --LOCUS_FUNCTION_LIST INTRONIC --MOLECULAR_BARCODE_TAG XM --FUNCTION_TAG XF --EDIT_DISTANCE 1 --READ_MQ 10 --GQ_THRESHOLD 30 --RETAIN_MONOMORPIC_SNPS false --FRACTION_SAMPLES_PASSING 0.5 --ADD_MISSING_VALUES true --DNA_MODE false --SNP_LOG_RATE 1000 --GENE_NAME_TAG gn --GENE_STRAND_TAG gs --GENE_FUNCTION_TAG gf --STRAND_STRATEGY SENSE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Nov 14 12:50:13 EST 2024] Executing as akulan@cn2877 on Linux 4.18.0-425.19.2.el8_7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_372-b07; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.5.1(0edbe6e_1673302695)
INFO 2024-11-14 12:50:13 AssignCellsToSamples Number of contigs in common: 25.
Contigs only in BAM INPUT(S): GL000008.2, GL000009.2, GL000194.1, GL000195.1, GL000205.2, GL000208.1, GL000213.1, GL000214.1, GL000216.2, GL000218.1, GL000219.1, GL000220.1, GL000221.1, GL000224.1, GL000225.1, GL000226.1, KI270302.1, KI270303.1, KI270304.1, KI270305.1, KI270310.1, KI270311.1, KI270312.1, KI270315.1, KI270316.1, KI270317.1, KI270320.1, KI270322.1, KI270329.1, KI270330.1, KI270333.1, KI270334.1, KI270335.1, KI270336.1, KI270337.1, KI270338.1, KI270340.1, KI270362.1, KI270363.1, KI270364.1, KI270366.1, KI270371.1, KI270372.1, KI270373.1, KI270374.1, KI270375.1, KI270376.1, KI270378.1, KI270379.1, KI270381.1, KI270382.1, KI270383.1, KI270384.1, KI270385.1, KI270386.1, KI270387.1, KI270388.1, KI270389.1, KI270390.1, KI270391.1, KI270392.1, KI270393.1, KI270394.1, KI270395.1, KI270396.1, KI270411.1, KI270412.1, KI270414.1, KI270417.1, KI270418.1, KI270419.1, KI270420.1, KI270422.1, KI270423.1, KI270424.1, KI270425.1, KI270429.1, KI270435.1, KI270438.1, KI270442.1, KI270448.1, KI270465.1, KI270466.1, KI270467.1, KI270468.1, KI270507.1, KI270508.1, KI270509.1, KI270510.1, KI270511.1, KI270512.1, KI270515.1, KI270516.1, KI270517.1, KI270518.1, KI270519.1, KI270521.1, KI270522.1, KI270528.1, KI270529.1, KI270530.1, KI270538.1, KI270539.1, KI270544.1, KI270548.1, KI270579.1, KI270580.1, KI270581.1, KI270582.1, KI270583.1, KI270584.1, KI270587.1, KI270588.1, KI270589.1, KI270590.1, KI270591.1, KI270593.1, KI270706.1, KI270707.1, KI270708.1, KI270709.1, KI270710.1, KI270711.1, KI270712.1, KI270713.1, KI270714.1, KI270715.1, KI270716.1, KI270717.1, KI270718.1, KI270719.1, KI270720.1, KI270721.1, KI270722.1, KI270723.1, KI270724.1, KI270725.1, KI270726.1, KI270727.1, KI270728.1, KI270729.1, KI270730.1, KI270731.1, KI270732.1, KI270733.1, KI270734.1, KI270735.1, KI270736.1, KI270737.1, KI270738.1, KI270739.1, KI270740.1, KI270741.1, KI270742.1, KI270743.1, KI270744.1, KI270745.1, KI270746.1, KI270747.1, KI270748.1, KI270749.1, KI270750.1, KI270751.1, KI270752.1, KI270753.1, KI270754.1, KI270755.1, KI270756.1, KI270757.1
Contigs only in GSA_051324_scClaudiaV1labelled_chrAdded_snpsOnly.vcf.gz: 0, chrXY

INFO 2024-11-14 12:50:13 AssignCellsToSamples Genotype Quality [GQ] not found in header. Disabling GQ_THRESHOLD parameter
INFO 2024-11-14 12:50:13 AssignCellsToSamples Found 192 samples in VCF and requested sample list out of 192 requested
INFO 2024-11-14 12:50:13 AssignCellsToSamples Found 192 samples in VCF and requested sample list out of 192 requested
INFO 2024-11-14 12:50:13 AssignCellsToSamples Genotype Quality Filter disabled. Enabling A/T, C/G SNP Filter to eliminate potential allele flipping variants
INFO 2024-11-14 12:50:13 AssignCellsToSamples Scanning VCF to find potential SNP sites
12:50:29 [main] WARN com.intel.gkl.compression.IntelInflater - Zero Bytes Written : 0
INFO 2024-11-14 12:50:29 AssignCellsToSamples Found [540716] potential SNP sites to query.
INFO 2024-11-14 12:50:29 AssignCellsToSamples Found 192 samples in VCF and requested sample list out of 192 requested
INFO 2024-11-14 12:50:29 AssignCellsToSamples Genotype Quality Filter disabled. Enabling A/T, C/G SNP Filter to eliminate potential allele flipping variants
INFO 2024-11-14 12:50:29 AssignCellsToSamples Found 9527 cell barcodes in file
INFO 2024-11-14 12:50:33 SNPUMIBasePileupIterator Processed 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:10,420,040
INFO 2024-11-14 12:50:36 SNPUMIBasePileupIterator Processed 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:23,961,864
INFO 2024-11-14 12:50:40 SNPUMIBasePileupIterator Processed 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr1:32,334,649
INFO 2024-11-14 12:50:43 SNPUMIBasePileupIterator Processed 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr1:43,775,018
INFO 2024-11-14 12:50:46 SNPUMIBasePileupIterator Processed 5,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 3s. Last read position: chr1:53,208,900
INFO 2024-11-14 12:50:49 SNPUMIBasePileupIterator Processed 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: chr1:86,743,295
INFO 2024-11-14 12:50:52 SNPUMIBasePileupIterator Processed 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr1:116,988,401
INFO 2024-11-14 12:50:56 SNPUMIBasePileupIterator Processed 8,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: chr1:154,978,941
INFO 2024-11-14 12:50:59 SNPUMIBasePileupIterator Processed 9,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: chr1:175,010,074
INFO 2024-11-14 12:51:02 SNPUMIBasePileupIterator Processed 10,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: chr1:213,008,012
INFO 2024-11-14 12:51:05 SNPUMIBasePileupIterator Processed 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr1:240,138,229
INFO 2024-11-14 12:51:08 SNPUMIBasePileupIterator Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 3s. Last read position: chr10:17,235,360
INFO 2024-11-14 12:51:11 SNPUMIBasePileupIterator Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: chr10:59,852,647
INFO 2024-11-14 12:51:15 SNPUMIBasePileupIterator Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: chr10:79,813,763
INFO 2024-11-14 12:51:18 SNPUMIBasePileupIterator Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: chr10:109,865,009
INFO 2024-11-14 12:51:21 SNPUMIBasePileupIterator Processed 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: chr11:840,341
INFO 2024-11-14 12:51:24 SNPUMIBasePileupIterator Processed 17,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: chr11:17,075,479
INFO 2024-11-14 12:51:27 SNPUMIBasePileupIterator Processed 18,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: chr11:57,528,765
INFO 2024-11-14 12:51:31 SNPUMIBasePileupIterator Processed 19,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 3s. Last read position: chr11:65,120,661
INFO 2024-11-14 12:51:34 SNPUMIBasePileupIterator Processed 20,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 3s. Last read position: chr11:65,855,099
INFO 2024-11-14 12:51:37 SNPUMIBasePileupIterator Processed 21,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: chr11:75,404,770
INFO 2024-11-14 12:51:40 SNPUMIBasePileupIterator Processed 22,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 3s. Last read position: chr11:115,377,422
INFO 2024-11-14 12:51:43 SNPUMIBasePileupIterator Processed 23,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: chr12:6,534,856
INFO 2024-11-14 12:51:47 SNPUMIBasePileupIterator Processed 24,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 3s. Last read position: chr12:22,687,216
INFO 2024-11-14 12:51:50 SNPUMIBasePileupIterator Processed 25,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: chr12:49,185,247
INFO 2024-11-14 12:51:53 SNPUMIBasePileupIterator Processed 26,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 3s. Last read position: chr12:56,117,197
INFO 2024-11-14 12:51:56 SNPUMIBasePileupIterator Processed 27,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 3s. Last read position: chr12:66,858,941
INFO 2024-11-14 12:52:00 SNPUMIBasePileupIterator Processed 28,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 3s. Last read position: chr12:98,600,002
INFO 2024-11-14 12:52:03 SNPUMIBasePileupIterator Processed 29,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 3s. Last read position: chr12:117,190,405
INFO 2024-11-14 12:52:06 SNPUMIBasePileupIterator Processed 30,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: chr12:130,875,968
INFO 2024-11-14 12:52:09 SNPUMIBasePileupIterator Processed 31,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 3s. Last read position: chr13:30,465,856
INFO 2024-11-14 12:52:12 SNPUMIBasePileupIterator Processed 32,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 3s. Last read position: chr13:71,775,301
INFO 2024-11-14 12:52:16 SNPUMIBasePileupIterator Processed 33,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 3s. Last read position: chr14:21,256,802
INFO 2024-11-14 12:52:19 SNPUMIBasePileupIterator Processed 34,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 3s. Last read position: chr14:45,129,830
INFO 2024-11-14 12:52:22 SNPUMIBasePileupIterator Processed 35,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 3s. Last read position: chr14:68,935,205
INFO 2024-11-14 12:52:25 SNPUMIBasePileupIterator Processed 36,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: chr14:100,259,391
INFO 2024-11-14 12:52:28 SNPUMIBasePileupIterator Processed 37,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 3s. Last read position: chr15:28,216,278
INFO 2024-11-14 12:52:31 SNPUMIBasePileupIterator Processed 38,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 3s. Last read position: chr15:48,879,572
INFO 2024-11-14 12:52:35 SNPUMIBasePileupIterator Processed 39,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 3s. Last read position: chr15:67,177,620
INFO 2024-11-14 12:52:38 SNPUMIBasePileupIterator Processed 40,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 3s. Last read position: chr15:80,121,813
INFO 2024-11-14 12:52:41 SNPUMIBasePileupIterator Processed 41,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: chr16:1,321,764
INFO 2024-11-14 12:52:44 SNPUMIBasePileupIterator Processed 42,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: chr16:8,849,016
INFO 2024-11-14 12:52:48 SNPUMIBasePileupIterator Processed 43,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 3s. Last read position: chr16:29,525,973
INFO 2024-11-14 12:52:51 SNPUMIBasePileupIterator Processed 44,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 3s. Last read position: chr16:69,192,821
INFO 2024-11-14 12:52:54 SNPUMIBasePileupIterator Processed 45,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 3s. Last read position: chr16:89,561,314
INFO 2024-11-14 12:52:57 SNPUMIBasePileupIterator Processed 46,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 3s. Last read position: chr17:5,432,876
INFO 2024-11-14 12:53:00 SNPUMIBasePileupIterator Processed 47,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 3s. Last read position: chr17:16,382,091
INFO 2024-11-14 12:53:04 SNPUMIBasePileupIterator Processed 48,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: chr17:36,943,554
INFO 2024-11-14 12:53:07 SNPUMIBasePileupIterator Processed 49,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 3s. Last read position: chr17:44,040,172
INFO 2024-11-14 12:53:10 SNPUMIBasePileupIterator Processed 50,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 3s. Last read position: chr17:58,897,020
INFO 2024-11-14 12:53:13 SNPUMIBasePileupIterator Processed 51,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 3s. Last read position: chr17:75,173,629
INFO 2024-11-14 12:53:17 SNPUMIBasePileupIterator Processed 52,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 3s. Last read position: chr18:673,096
INFO 2024-11-14 12:53:20 SNPUMIBasePileupIterator Processed 53,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 3s. Last read position: chr18:36,798,449
INFO 2024-11-14 12:53:23 SNPUMIBasePileupIterator Processed 54,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 3s. Last read position: chr18:80,146,458
INFO 2024-11-14 12:53:26 SNPUMIBasePileupIterator Processed 55,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 3s. Last read position: chr19:4,657,941
INFO 2024-11-14 12:53:29 SNPUMIBasePileupIterator Processed 56,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 3s. Last read position: chr19:10,557,332
INFO 2024-11-14 12:53:33 SNPUMIBasePileupIterator Processed 57,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 3s. Last read position: chr19:17,862,165
INFO 2024-11-14 12:53:36 SNPUMIBasePileupIterator Processed 58,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 3s. Last read position: chr19:35,654,589
INFO 2024-11-14 12:53:39 SNPUMIBasePileupIterator Processed 59,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 3s. Last read position: chr19:43,508,055
INFO 2024-11-14 12:53:42 SNPUMIBasePileupIterator Processed 60,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 3s. Last read position: chr19:49,490,259
INFO 2024-11-14 12:53:46 SNPUMIBasePileupIterator Processed 61,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 3s. Last read position: chr19:55,386,666
INFO 2024-11-14 12:53:49 SNPUMIBasePileupIterator Processed 62,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 3s. Last read position: chr2:10,045,286
INFO 2024-11-14 12:53:52 SNPUMIBasePileupIterator Processed 63,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 3s. Last read position: chr2:37,146,896
INFO 2024-11-14 12:53:55 SNPUMIBasePileupIterator Processed 64,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 3s. Last read position: chr2:61,514,639
INFO 2024-11-14 12:53:58 SNPUMIBasePileupIterator Processed 65,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 3s. Last read position: chr2:85,559,060
INFO 2024-11-14 12:54:01 SNPUMIBasePileupIterator Processed 66,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 3s. Last read position: chr2:119,567,968
INFO 2024-11-14 12:54:04 SNPUMIBasePileupIterator Processed 67,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 3s. Last read position: chr2:163,717,648
INFO 2024-11-14 12:54:08 SNPUMIBasePileupIterator Processed 68,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 3s. Last read position: chr2:193,513,824
INFO 2024-11-14 12:54:11 SNPUMIBasePileupIterator Processed 69,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 3s. Last read position: chr2:216,122,098
INFO 2024-11-14 12:54:14 SNPUMIBasePileupIterator Processed 70,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 3s. Last read position: chr2:231,708,571
INFO 2024-11-14 12:54:17 SNPUMIBasePileupIterator Processed 71,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 3s. Last read position: chr20:4,780,299
INFO 2024-11-14 12:54:20 SNPUMIBasePileupIterator Processed 72,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 3s. Last read position: chr20:37,241,353
INFO 2024-11-14 12:54:24 SNPUMIBasePileupIterator Processed 73,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 3s. Last read position: chr20:62,308,698
INFO 2024-11-14 12:54:27 SNPUMIBasePileupIterator Processed 74,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 3s. Last read position: chr21:31,666,479
INFO 2024-11-14 12:54:30 SNPUMIBasePileupIterator Processed 75,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 3s. Last read position: chr22:20,785,244
INFO 2024-11-14 12:54:33 SNPUMIBasePileupIterator Processed 76,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 3s. Last read position: chr22:37,678,523
INFO 2024-11-14 12:54:36 SNPUMIBasePileupIterator Processed 77,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 3s. Last read position: chr22:46,684,662
INFO 2024-11-14 12:54:39 SNPUMIBasePileupIterator Processed 78,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 3s. Last read position: chr3:23,919,269
INFO 2024-11-14 12:54:42 SNPUMIBasePileupIterator Processed 79,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 3s. Last read position: chr3:47,677,808
INFO 2024-11-14 12:54:46 SNPUMIBasePileupIterator Processed 80,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 3s. Last read position: chr3:57,064,600
INFO 2024-11-14 12:54:49 SNPUMIBasePileupIterator Processed 81,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 3s. Last read position: chr3:108,211,363
INFO 2024-11-14 12:54:52 SNPUMIBasePileupIterator Processed 82,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 3s. Last read position: chr3:136,727,284
INFO 2024-11-14 12:54:55 SNPUMIBasePileupIterator Processed 83,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 3s. Last read position: chr3:174,138,688
INFO 2024-11-14 12:54:58 SNPUMIBasePileupIterator Processed 84,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 3s. Last read position: chr3:197,951,298
INFO 2024-11-14 12:55:01 SNPUMIBasePileupIterator Processed 85,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 3s. Last read position: chr4:39,454,618
INFO 2024-11-14 12:55:04 SNPUMIBasePileupIterator Processed 86,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 3s. Last read position: chr4:77,020,631
INFO 2024-11-14 12:55:08 SNPUMIBasePileupIterator Processed 87,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 3s. Last read position: chr4:107,908,571
INFO 2024-11-14 12:55:11 SNPUMIBasePileupIterator Processed 88,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 3s. Last read position: chr4:151,103,033
INFO 2024-11-14 12:55:14 SNPUMIBasePileupIterator Processed 89,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 3s. Last read position: chr5:1,489,772
INFO 2024-11-14 12:55:17 SNPUMIBasePileupIterator Processed 90,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 3s. Last read position: chr5:43,289,701
INFO 2024-11-14 12:55:20 SNPUMIBasePileupIterator Processed 91,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 3s. Last read position: chr5:77,691,348
INFO 2024-11-14 12:55:23 SNPUMIBasePileupIterator Processed 92,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 3s. Last read position: chr5:110,288,828
INFO 2024-11-14 12:55:26 SNPUMIBasePileupIterator Processed 93,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 3s. Last read position: chr5:138,851,771
INFO 2024-11-14 12:55:30 SNPUMIBasePileupIterator Processed 94,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 3s. Last read position: chr5:157,292,488
INFO 2024-11-14 12:55:33 SNPUMIBasePileupIterator Processed 95,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 3s. Last read position: chr5:179,623,140
INFO 2024-11-14 12:55:36 SNPUMIBasePileupIterator Processed 96,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 3s. Last read position: chr6:21,741,070
INFO 2024-11-14 12:55:39 SNPUMIBasePileupIterator Processed 97,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 3s. Last read position: chr6:33,275,976
INFO 2024-11-14 12:55:43 SNPUMIBasePileupIterator Processed 98,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 3s. Last read position: chr6:38,676,027
INFO 2024-11-14 12:55:46 SNPUMIBasePileupIterator Processed 99,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 3s. Last read position: chr6:73,281,886
INFO 2024-11-14 12:55:49 SNPUMIBasePileupIterator Processed 100,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 3s. Last read position: chr6:100,730,742
INFO 2024-11-14 12:55:52 SNPUMIBasePileupIterator Processed 101,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 3s. Last read position: chr6:132,815,086
INFO 2024-11-14 12:55:55 SNPUMIBasePileupIterator Processed 102,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 3s. Last read position: chr6:160,019,960
INFO 2024-11-14 12:55:58 SNPUMIBasePileupIterator Processed 103,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 3s. Last read position: chr7:7,637,914
INFO 2024-11-14 12:56:01 SNPUMIBasePileupIterator Processed 104,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 3s. Last read position: chr7:42,237,180
INFO 2024-11-14 12:56:05 SNPUMIBasePileupIterator Processed 105,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 3s. Last read position: chr7:74,500,223
INFO 2024-11-14 12:56:08 SNPUMIBasePileupIterator Processed 106,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 3s. Last read position: chr7:99,459,170
INFO 2024-11-14 12:56:11 SNPUMIBasePileupIterator Processed 107,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 3s. Last read position: chr7:128,541,801
INFO 2024-11-14 12:56:14 SNPUMIBasePileupIterator Processed 108,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 3s. Last read position: chr7:151,597,580
INFO 2024-11-14 12:56:17 SNPUMIBasePileupIterator Processed 109,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 3s. Last read position: chr8:30,544,589
INFO 2024-11-14 12:56:20 SNPUMIBasePileupIterator Processed 110,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 3s. Last read position: chr8:66,922,374
INFO 2024-11-14 12:56:23 SNPUMIBasePileupIterator Processed 111,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 3s. Last read position: chr8:98,045,379
INFO 2024-11-14 12:56:26 SNPUMIBasePileupIterator Processed 112,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 3s. Last read position: chr8:140,585,091
INFO 2024-11-14 12:56:30 SNPUMIBasePileupIterator Processed 113,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 3s. Last read position: chr9:19,121,019
INFO 2024-11-14 12:56:33 SNPUMIBasePileupIterator Processed 114,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 3s. Last read position: chr9:65,206,826
INFO 2024-11-14 12:56:36 SNPUMIBasePileupIterator Processed 115,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 3s. Last read position: chr9:100,430,835
INFO 2024-11-14 12:56:39 SNPUMIBasePileupIterator Processed 116,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 3s. Last read position: chr9:125,240,858
INFO 2024-11-14 12:56:42 SNPUMIBasePileupIterator Processed 117,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 3s. Last read position: chr9:133,351,009
INFO 2024-11-14 12:56:45 SNPUMIBasePileupIterator Processed 118,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chrM:2,979
INFO 2024-11-14 12:56:48 SNPUMIBasePileupIterator Processed 119,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 2s. Last read position: chrM:8,623
INFO 2024-11-14 12:56:50 SNPUMIBasePileupIterator Processed 120,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 2s. Last read position: chrM:11,804
INFO 2024-11-14 12:56:53 SNPUMIBasePileupIterator Processed 121,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 2s. Last read position: chrX:12,977,018
INFO 2024-11-14 12:56:56 SNPUMIBasePileupIterator Processed 122,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 3s. Last read position: chrX:56,729,560
INFO 2024-11-14 12:56:59 SNPUMIBasePileupIterator Processed 123,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 3s. Last read position: chrX:102,641,033
INFO 2024-11-14 12:57:02 SNPUMIBasePileupIterator Processed 124,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 2s. Last read position: chrX:140,731,984
INFO 2024-11-14 12:57:05 SNPUMIBasePileupIterator Processed 125,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 2s. Last read position: GL000220.1:154,604
INFO 2024-11-14 12:57:08 SNPUMIBasePileupIterator Processed 126,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: /
INFO 2024-11-14 12:57:10 SNPUMIBasePileupIterator Processed 127,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 2s. Last read position: /
INFO 2024-11-14 12:57:12 SNPUMIBasePileupIterator Processed 128,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: /
INFO 2024-11-14 12:57:15 SNPUMIBasePileupIterator Processed 129,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: /
INFO 2024-11-14 12:57:17 SNPUMIBasePileupIterator Processed 130,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: /
INFO 2024-11-14 12:57:18 AssignCellsToSamples Processed [0] SNPs in BAM + VCF
INFO 2024-11-14 12:57:18 AssignCellsToSamples Finished!
[Thu Nov 14 12:57:18 EST 2024] org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.sampleassignment.AssignCellsToSamples done. Elapsed time: 7.08 minutes.
Runtime.totalMemory()=1258815488
[akulan@cn2877 V1_outs_090624]$

@jamesnemesh
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Hi, thank you for submitting the log.

You mentioned this is 10x data. In your command, you set the cell barcode tag correctly via --CELL_BARCODE_TAG CB. However, the molecular barcode tag is not set (perhaps you lost it while cutting/pasting from the cookbook?). In the log, the default value is shown as --MOLECULAR_BARCODE_TAG XM. Since the 10x format uses UB as their tag value, the program can't find any reads with set UB values. This results in all reads being discarded, and the program is then unable to find overlaps between reads that satisfy all conditions and overlap SNP sites in the VCF.

It looks like you're very close - just set the MOLECULAR_BARCODE_TAG to UB and try again!

@akulan1
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akulan1 commented Nov 14, 2024

When I use the --MOLECULAR_BARCODE_TAG UB, I am getting an error

[akulan@cn2878 V1_outs_090624]$ /home/akulan/Drop-seq_tools-2.5.1/AssignCellsToSamples -m 24g -INPUT_BAM V1_possorted_genome_bam_tagged.bam -CELL_BC_FILE /data/GBMAD/McMahon-Claudia_SC_083024/V1_outs_090624/V1_filtered_feature_bc_matrix/barcodes.tsv.gz -VCF /data/akulan/gsa_may2024/PLINK_130524_0118/GSA_051324_scClaudiaV1labelled_chrAdded_snpsOnly.vcf.gz -OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.txt -VCF_OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.vcf.gz -CELL_BARCODE_TAG CB -MOLECULAR_BARCODE_TAG UB, -LOCUS_FUNCTION_LIST INTRONIC -IGNORED_CHROMOSOMES null -IGNORED_CHROMOSOMES chrX -IGNORED_CHROMOSOMES chrY -IGNORED_CHROMOSOMES chrM
[Tue Nov 12 20:16:20 EST 2024] AssignCellsToSamples --INPUT_BAM V1_possorted_genome_bam_tagged.bam --VCF /data/akulan/gsa_may2024/PLINK_130524_0118/GSA_051324_scClaudiaV1labelled_chrAdded_snpsOnly.vcf.gz --OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.txt --VCF_OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.vcf.gz --CELL_BARCODE_TAG CB --MOLECULAR_BARCODE_TAG UB, --CELL_BC_FILE /data/GBMAD/McMahon-Claudia_SC_083024/V1_outs_090624/V1_filtered_feature_bc_matrix/barcodes.tsv.gz --IGNORED_CHROMOSOMES chrX --IGNORED_CHROMOSOMES chrY --IGNORED_CHROMOSOMES chrM --LOCUS_FUNCTION_LIST CODING --LOCUS_FUNCTION_LIST UTR --LOCUS_FUNCTION_LIST INTRONIC --FUNCTION_TAG XF --EDIT_DISTANCE 1 --READ_MQ 10 --GQ_THRESHOLD 30 --RETAIN_MONOMORPIC_SNPS false --FRACTION_SAMPLES_PASSING 0.5 --ADD_MISSING_VALUES true --DNA_MODE false --SNP_LOG_RATE 1000 --GENE_NAME_TAG gn --GENE_STRAND_TAG gs --GENE_FUNCTION_TAG gf --STRAND_STRATEGY SENSE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Tue Nov 12 20:16:20 EST 2024] Executing as akulan@cn2878 on Linux 4.18.0-425.19.2.el8_7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_372-b07; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.5.1(0edbe6e_1673302695)
INFO 2024-11-12 20:16:20 AssignCellsToSamples Number of contigs in common: 25.
Contigs only in BAM INPUT(S): GL000008.2, GL000009.2, GL000194.1, GL000195.1, GL000205.2, GL000208.1, GL000213.1, GL000214.1, GL000216.2, GL000218.1, GL000219.1, GL000220.1, GL000221.1, GL000224.1, GL000225.1, GL000226.1, KI270302.1, KI270303.1, KI270304.1, KI270305.1, KI270310.1, KI270311.1, KI270312.1, KI270315.1, KI270316.1, KI270317.1, KI270320.1, KI270322.1, KI270329.1, KI270330.1, KI270333.1, KI270334.1, KI270335.1, KI270336.1, KI270337.1, KI270338.1, KI270340.1, KI270362.1, KI270363.1, KI270364.1, KI270366.1, KI270371.1, KI270372.1, KI270373.1, KI270374.1, KI270375.1, KI270376.1, KI270378.1, KI270379.1, KI270381.1, KI270382.1, KI270383.1, KI270384.1, KI270385.1, KI270386.1, KI270387.1, KI270388.1, KI270389.1, KI270390.1, KI270391.1, KI270392.1, KI270393.1, KI270394.1, KI270395.1, KI270396.1, KI270411.1, KI270412.1, KI270414.1, KI270417.1, KI270418.1, KI270419.1, KI270420.1, KI270422.1, KI270423.1, KI270424.1, KI270425.1, KI270429.1, KI270435.1, KI270438.1, KI270442.1, KI270448.1, KI270465.1, KI270466.1, KI270467.1, KI270468.1, KI270507.1, KI270508.1, KI270509.1, KI270510.1, KI270511.1, KI270512.1, KI270515.1, KI270516.1, KI270517.1, KI270518.1, KI270519.1, KI270521.1, KI270522.1, KI270528.1, KI270529.1, KI270530.1, KI270538.1, KI270539.1, KI270544.1, KI270548.1, KI270579.1, KI270580.1, KI270581.1, KI270582.1, KI270583.1, KI270584.1, KI270587.1, KI270588.1, KI270589.1, KI270590.1, KI270591.1, KI270593.1, KI270706.1, KI270707.1, KI270708.1, KI270709.1, KI270710.1, KI270711.1, KI270712.1, KI270713.1, KI270714.1, KI270715.1, KI270716.1, KI270717.1, KI270718.1, KI270719.1, KI270720.1, KI270721.1, KI270722.1, KI270723.1, KI270724.1, KI270725.1, KI270726.1, KI270727.1, KI270728.1, KI270729.1, KI270730.1, KI270731.1, KI270732.1, KI270733.1, KI270734.1, KI270735.1, KI270736.1, KI270737.1, KI270738.1, KI270739.1, KI270740.1, KI270741.1, KI270742.1, KI270743.1, KI270744.1, KI270745.1, KI270746.1, KI270747.1, KI270748.1, KI270749.1, KI270750.1, KI270751.1, KI270752.1, KI270753.1, KI270754.1, KI270755.1, KI270756.1, KI270757.1
Contigs only in GSA_051324_scClaudiaV1labelled_chrAdded_snpsOnly.vcf.gz: 0, chrXY

INFO 2024-11-12 20:16:20 AssignCellsToSamples Genotype Quality [GQ] not found in header. Disabling GQ_THRESHOLD parameter
INFO 2024-11-12 20:16:20 AssignCellsToSamples Found 192 samples in VCF and requested sample list out of 192 requested
INFO 2024-11-12 20:16:20 AssignCellsToSamples Found 192 samples in VCF and requested sample list out of 192 requested
INFO 2024-11-12 20:16:20 AssignCellsToSamples Genotype Quality Filter disabled. Enabling A/T, C/G SNP Filter to eliminate potential allele flipping variants
INFO 2024-11-12 20:16:20 AssignCellsToSamples Scanning VCF to find potential SNP sites
20:16:35 [main] WARN com.intel.gkl.compression.IntelInflater - Zero Bytes Written : 0
INFO 2024-11-12 20:16:35 AssignCellsToSamples Found [540716] potential SNP sites to query.
INFO 2024-11-12 20:16:35 AssignCellsToSamples Found 192 samples in VCF and requested sample list out of 192 requested
INFO 2024-11-12 20:16:35 AssignCellsToSamples Genotype Quality Filter disabled. Enabling A/T, C/G SNP Filter to eliminate potential allele flipping variants
INFO 2024-11-12 20:16:35 AssignCellsToSamples Found 9527 cell barcodes in file
[Tue Nov 12 20:16:35 EST 2024] org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.sampleassignment.AssignCellsToSamples done. Elapsed time: 0.26 minutes.
Runtime.totalMemory()=7886340096
Exception in thread "main" java.lang.IllegalArgumentException: String tag does not have length() == 2: UB,
at htsjdk.samtools.SAMTag.makeBinaryTag(SAMTag.java:125)
at htsjdk.samtools.SAMTagUtil.makeBinaryTag(SAMTagUtil.java:186)
at org.broadinstitute.dropseqrna.utils.readiterators.RequiredTagPredicate.(RequiredTagPredicate.java:39)
at org.broadinstitute.dropseqrna.utils.readiterators.MissingTagFilteringIterator.(MissingTagFilteringIterator.java:39)
at org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.SNPUMIBasePileupIterator.(SNPUMIBasePileupIterator.java:112)
at org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.sampleassignment.AssignCellsToSamples.prepareIterator(AssignCellsToSamples.java:900)
at org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.sampleassignment.AssignCellsToSamples.doWork(AssignCellsToSamples.java:263)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at org.broadinstitute.dropseqrna.cmdline.DropSeqMain.main(DropSeqMain.java:42)
[akulan@cn2878 V1_outs_090624]$

@jamesnemesh
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You set the tag name to be:
MOLECULAR_BARCODE_TAG UB,
you want
MOLECULAR_BARCODE_TAG UB

The warning was because you set a BAM tag name to be 3 characters long, and bam tags are by definition length 2.

@akulan1
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akulan1 commented Nov 14, 2024

It works! But, I get only one output V1_possorted_genome_bam_tagged.bam.donor_assignments.txt.

I don't get the V1_possorted_genome_bam_tagged.bam.donor_assignments.vcf.gz. This is not there. Why is this missing?

@jamesnemesh
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Log file please.

@akulan1
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akulan1 commented Nov 14, 2024

Sorry, here it is.

[akulan@cn2877 V1_outs_090624]$ /home/akulan/Drop-seq_tools-2.5.1/AssignCellsToSamples -m 24g -INPUT_BAM V1_possorted_genome_bam_tagged.bam -CELL_BC_FILE /data/GBMAD/McMahon-Claudia_SC_083024/V1_outs_090624/V1_filtered_feature_bc_matrix/barcodes.tsv.gz -VCF /data/akulan/gsa_may2024/PLINK_130524_0118/GSA_051324_scClaudiaV1labelled_chrAdded_snpsOnly.vcf.gz -OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.txt -VCF_OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.vcf.gz -CELL_BARCODE_TAG CB -MOLECULAR_BARCODE_TAG UB -LOCUS_FUNCTION_LIST INTRONIC -IGNORED_CHROMOSOMES null -IGNORED_CHROMOSOMES chrX -IGNORED_CHROMOSOMES chrY -IGNORED_CHROMOSOMES chrM
[Thu Nov 14 15:25:31 EST 2024] AssignCellsToSamples --INPUT_BAM V1_possorted_genome_bam_tagged.bam --VCF /data/akulan/gsa_may2024/PLINK_130524_0118/GSA_051324_scClaudiaV1labelled_chrAdded_snpsOnly.vcf.gz --OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.txt --VCF_OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.vcf.gz --CELL_BARCODE_TAG CB --MOLECULAR_BARCODE_TAG UB --CELL_BC_FILE /data/GBMAD/McMahon-Claudia_SC_083024/V1_outs_090624/V1_filtered_feature_bc_matrix/barcodes.tsv.gz --IGNORED_CHROMOSOMES chrX --IGNORED_CHROMOSOMES chrY --IGNORED_CHROMOSOMES chrM --LOCUS_FUNCTION_LIST CODING --LOCUS_FUNCTION_LIST UTR --LOCUS_FUNCTION_LIST INTRONIC --FUNCTION_TAG XF --EDIT_DISTANCE 1 --READ_MQ 10 --GQ_THRESHOLD 30 --RETAIN_MONOMORPIC_SNPS false --FRACTION_SAMPLES_PASSING 0.5 --ADD_MISSING_VALUES true --DNA_MODE false --SNP_LOG_RATE 1000 --GENE_NAME_TAG gn --GENE_STRAND_TAG gs --GENE_FUNCTION_TAG gf --STRAND_STRATEGY SENSE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Nov 14 15:25:31 EST 2024] Executing as akulan@cn2877 on Linux 4.18.0-425.19.2.el8_7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_372-b07; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.5.1(0edbe6e_1673302695)
INFO 2024-11-14 15:25:32 AssignCellsToSamples Number of contigs in common: 25.
Contigs only in BAM INPUT(S): GL000008.2, GL000009.2, GL000194.1, GL000195.1, GL000205.2, GL000208.1, GL000213.1, GL000214.1, GL000216.2, GL000218.1, GL000219.1, GL000220.1, GL000221.1, GL000224.1, GL000225.1, GL000226.1, KI270302.1, KI270303.1, KI270304.1, KI270305.1, KI270310.1, KI270311.1, KI270312.1, KI270315.1, KI270316.1, KI270317.1, KI270320.1, KI270322.1, KI270329.1, KI270330.1, KI270333.1, KI270334.1, KI270335.1, KI270336.1, KI270337.1, KI270338.1, KI270340.1, KI270362.1, KI270363.1, KI270364.1, KI270366.1, KI270371.1, KI270372.1, KI270373.1, KI270374.1, KI270375.1, KI270376.1, KI270378.1, KI270379.1, KI270381.1, KI270382.1, KI270383.1, KI270384.1, KI270385.1, KI270386.1, KI270387.1, KI270388.1, KI270389.1, KI270390.1, KI270391.1, KI270392.1, KI270393.1, KI270394.1, KI270395.1, KI270396.1, KI270411.1, KI270412.1, KI270414.1, KI270417.1, KI270418.1, KI270419.1, KI270420.1, KI270422.1, KI270423.1, KI270424.1, KI270425.1, KI270429.1, KI270435.1, KI270438.1, KI270442.1, KI270448.1, KI270465.1, KI270466.1, KI270467.1, KI270468.1, KI270507.1, KI270508.1, KI270509.1, KI270510.1, KI270511.1, KI270512.1, KI270515.1, KI270516.1, KI270517.1, KI270518.1, KI270519.1, KI270521.1, KI270522.1, KI270528.1, KI270529.1, KI270530.1, KI270538.1, KI270539.1, KI270544.1, KI270548.1, KI270579.1, KI270580.1, KI270581.1, KI270582.1, KI270583.1, KI270584.1, KI270587.1, KI270588.1, KI270589.1, KI270590.1, KI270591.1, KI270593.1, KI270706.1, KI270707.1, KI270708.1, KI270709.1, KI270710.1, KI270711.1, KI270712.1, KI270713.1, KI270714.1, KI270715.1, KI270716.1, KI270717.1, KI270718.1, KI270719.1, KI270720.1, KI270721.1, KI270722.1, KI270723.1, KI270724.1, KI270725.1, KI270726.1, KI270727.1, KI270728.1, KI270729.1, KI270730.1, KI270731.1, KI270732.1, KI270733.1, KI270734.1, KI270735.1, KI270736.1, KI270737.1, KI270738.1, KI270739.1, KI270740.1, KI270741.1, KI270742.1, KI270743.1, KI270744.1, KI270745.1, KI270746.1, KI270747.1, KI270748.1, KI270749.1, KI270750.1, KI270751.1, KI270752.1, KI270753.1, KI270754.1, KI270755.1, KI270756.1, KI270757.1
Contigs only in GSA_051324_scClaudiaV1labelled_chrAdded_snpsOnly.vcf.gz: 0, chrXY

INFO 2024-11-14 15:25:32 AssignCellsToSamples Genotype Quality [GQ] not found in header. Disabling GQ_THRESHOLD parameter
INFO 2024-11-14 15:25:32 AssignCellsToSamples Found 192 samples in VCF and requested sample list out of 192 requested
INFO 2024-11-14 15:25:32 AssignCellsToSamples Found 192 samples in VCF and requested sample list out of 192 requested
INFO 2024-11-14 15:25:32 AssignCellsToSamples Genotype Quality Filter disabled. Enabling A/T, C/G SNP Filter to eliminate potential allele flipping variants
INFO 2024-11-14 15:25:32 AssignCellsToSamples Scanning VCF to find potential SNP sites
15:25:48 [main] WARN com.intel.gkl.compression.IntelInflater - Zero Bytes Written : 0
INFO 2024-11-14 15:25:48 AssignCellsToSamples Found [540716] potential SNP sites to query.
INFO 2024-11-14 15:25:48 AssignCellsToSamples Found 192 samples in VCF and requested sample list out of 192 requested
INFO 2024-11-14 15:25:48 AssignCellsToSamples Genotype Quality Filter disabled. Enabling A/T, C/G SNP Filter to eliminate potential allele flipping variants
INFO 2024-11-14 15:25:48 AssignCellsToSamples Found 9527 cell barcodes in file
INFO 2024-11-14 15:25:50 SNPUMIBasePileupIterator Seen many non-increasing record positions. Printing Read-names as well.
INFO 2024-11-14 15:25:53 SNPUMIBasePileupIterator Processed 1,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 4s. Last read position: chr1:10,419,893. Last read name: VH01243:131:AACMHYHHV:1:1504:56822:52267
INFO 2024-11-14 15:25:57 SNPUMIBasePileupIterator Processed 2,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 4s. Last read position: chr1:23,795,214. Last read name: VH01243:131:AACMHYHHV:1:1601:21564:7096
INFO 2024-11-14 15:26:01 SNPUMIBasePileupIterator Processed 3,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 4s. Last read position: chr1:32,334,073. Last read name: VH01243:131:AACMHYHHV:1:2210:38663:33430
INFO 2024-11-14 15:26:06 SNPUMIBasePileupIterator Processed 4,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 4s. Last read position: chr1:43,172,150. Last read name: VH01243:131:AACMHYHHV:1:2608:64074:39678
INFO 2024-11-14 15:26:10 SNPUMIBasePileupIterator Processed 5,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 4s. Last read position: chr1:52,419,696. Last read name: VH01243:131:AACMHYHHV:2:2612:58431:44979
INFO 2024-11-14 15:26:14 SNPUMIBasePileupIterator Processed 6,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 4s. Last read position: chr1:84,690,313. Last read name: VH01243:131:AACMHYHHV:2:1614:72254:45395
INFO 2024-11-14 15:26:18 SNPUMIBasePileupIterator Processed 7,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 4s. Last read position: chr1:114,610,448. Last read name: VH01243:131:AACMHYHHV:1:2313:61783:37803
INFO 2024-11-14 15:26:22 SNPUMIBasePileupIterator Processed 8,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 4s. Last read position: chr1:154,206,922. Last read name: VH01243:131:AACMHYHHV:2:1305:38095:31916
INFO 2024-11-14 15:26:26 SNPUMIBasePileupIterator Processed 9,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 4s. Last read position: chr1:173,856,883. Last read name: VH01243:131:AACMHYHHV:1:1107:59549:50904
INFO 2024-11-14 15:26:30 SNPUMIBasePileupIterator Processed 10,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: chr1:211,360,054. Last read name: VH01243:131:AACMHYHHV:1:1409:61007:28697
INFO 2024-11-14 15:26:34 SNPUMIBasePileupIterator Processed 11,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 4s. Last read position: chr1:235,161,174. Last read name: VH01243:131:AACMHYHHV:1:1109:26298:17622
INFO 2024-11-14 15:26:38 SNPUMIBasePileupIterator Processed 12,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 3s. Last read position: chr10:15,257,523. Last read name: VH01243:131:AACMHYHHV:1:2106:71099:37311
INFO 2024-11-14 15:26:42 SNPUMIBasePileupIterator Processed 13,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 4s. Last read position: chr10:50,080,757. Last read name: VH01243:131:AACMHYHHV:2:1307:73693:27561
INFO 2024-11-14 15:26:47 SNPUMIBasePileupIterator Processed 14,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 4s. Last read position: chr10:78,035,675. Last read name: VH01243:131:AACMHYHHV:1:1203:20125:4786
INFO 2024-11-14 15:26:51 SNPUMIBasePileupIterator Processed 15,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: chr10:102,697,375. Last read name: VH01243:131:AACMHYHHV:2:1505:32149:6888
INFO 2024-11-14 15:26:55 SNPUMIBasePileupIterator Processed 16,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 4s. Last read position: chr11:810,282. Last read name: VH01243:131:AACMHYHHV:2:1610:41295:55637
INFO 2024-11-14 15:26:59 SNPUMIBasePileupIterator Processed 17,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 4s. Last read position: chr11:14,520,334. Last read name: VH01243:131:AACMHYHHV:1:1408:59719:2950
INFO 2024-11-14 15:27:03 SNPUMIBasePileupIterator Processed 18,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 4s. Last read position: chr11:47,164,649. Last read name: VH01243:131:AACMHYHHV:2:1506:40140:47023
INFO 2024-11-14 15:27:08 SNPUMIBasePileupIterator Processed 19,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 4s. Last read position: chr11:64,244,499. Last read name: VH01243:131:AACMHYHHV:1:2407:20674:35853
INFO 2024-11-14 15:27:12 SNPUMIBasePileupIterator Processed 20,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 4s. Last read position: chr11:65,502,701. Last read name: VH01243:131:AACMHYHHV:1:2307:9994:36005
INFO 2024-11-14 15:27:16 SNPUMIBasePileupIterator Processed 21,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 4s. Last read position: chr11:74,976,862. Last read name: VH01243:131:AACMHYHHV:2:1402:13516:21920
INFO 2024-11-14 15:27:21 SNPUMIBasePileupIterator Processed 22,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 4s. Last read position: chr11:108,122,644. Last read name: VH01243:131:AACMHYHHV:1:2114:50175:14498
INFO 2024-11-14 15:27:25 SNPUMIBasePileupIterator Processed 23,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 4s. Last read position: chr12:869,286. Last read name: VH01243:131:AACMHYHHV:1:2314:36958:42783
INFO 2024-11-14 15:27:29 SNPUMIBasePileupIterator Processed 24,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 4s. Last read position: chr12:15,903,292. Last read name: VH01243:131:AACMHYHHV:2:1514:75606:17584
INFO 2024-11-14 15:27:33 SNPUMIBasePileupIterator Processed 25,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 4s. Last read position: chr12:49,127,962. Last read name: VH01243:131:AACMHYHHV:2:2512:44552:54729
INFO 2024-11-14 15:27:38 SNPUMIBasePileupIterator Processed 26,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 4s. Last read position: chr12:55,896,311. Last read name: VH01243:131:AACMHYHHV:1:1205:25559:47440
INFO 2024-11-14 15:27:42 SNPUMIBasePileupIterator Processed 27,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 4s. Last read position: chr12:57,239,123. Last read name: VH01243:131:AACMHYHHV:2:1609:14671:15653
INFO 2024-11-14 15:27:47 SNPUMIBasePileupIterator Processed 28,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 4s. Last read position: chr12:93,792,039. Last read name: VH01243:131:AACMHYHHV:2:2612:46748:40719
INFO 2024-11-14 15:27:51 SNPUMIBasePileupIterator Processed 29,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 4s. Last read position: chr12:112,405,315. Last read name: VH01243:131:AACMHYHHV:2:1306:18856:43085
INFO 2024-11-14 15:27:55 SNPUMIBasePileupIterator Processed 30,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 4s. Last read position: chr12:123,135,608. Last read name: VH01243:131:AACMHYHHV:1:2611:20087:15388
INFO 2024-11-14 15:27:59 SNPUMIBasePileupIterator Processed 31,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 4s. Last read position: chr13:28,661,111. Last read name: VH01243:131:AACMHYHHV:1:1405:63544:1170
INFO 2024-11-14 15:28:03 SNPUMIBasePileupIterator Processed 32,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 4s. Last read position: chr13:49,040,648. Last read name: VH01243:131:AACMHYHHV:1:1412:20276:46588
INFO 2024-11-14 15:28:07 SNPUMIBasePileupIterator Processed 33,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 3s. Last read position: chr13:110,720,440. Last read name: VH01243:131:AACMHYHHV:2:2205:66308:47137
INFO 2024-11-14 15:28:12 SNPUMIBasePileupIterator Processed 34,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 4s. Last read position: chr14:34,434,383. Last read name: VH01243:131:AACMHYHHV:1:2607:41408:25081
INFO 2024-11-14 15:28:16 SNPUMIBasePileupIterator Processed 35,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 4s. Last read position: chr14:60,155,228. Last read name: VH01243:131:AACMHYHHV:1:2607:25711:55921
INFO 2024-11-14 15:28:20 SNPUMIBasePileupIterator Processed 36,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 4s. Last read position: chr14:90,403,952. Last read name: VH01243:131:AACMHYHHV:2:1605:20598:32370
INFO 2024-11-14 15:28:24 SNPUMIBasePileupIterator Processed 37,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 4s. Last read position: chr14:103,590,519. Last read name: VH01243:131:AACMHYHHV:1:1509:58583:48008
INFO 2024-11-14 15:28:28 SNPUMIBasePileupIterator Processed 38,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 4s. Last read position: chr15:43,485,465. Last read name: VH01243:131:AACMHYHHV:2:2107:42052:36137
INFO 2024-11-14 15:28:32 SNPUMIBasePileupIterator Processed 39,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 4s. Last read position: chr15:63,584,245. Last read name: VH01243:131:AACMHYHHV:2:2111:38890:36535
INFO 2024-11-14 15:28:37 SNPUMIBasePileupIterator Processed 40,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 4s. Last read position: chr15:74,010,222. Last read name: VH01243:131:AACMHYHHV:1:2605:52258:1435
INFO 2024-11-14 15:28:47 SNPUMIBasePileupIterator Processed 41,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 10s. Last read position: chr15:92,830,943. Last read name: VH01243:131:AACMHYHHV:2:1404:21034:23718
INFO 2024-11-14 15:28:52 SNPUMIBasePileupIterator Processed 42,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 4s. Last read position: chr16:1,965,059. Last read name: VH01243:131:AACMHYHHV:1:1406:26923:53498
INFO 2024-11-14 15:28:56 SNPUMIBasePileupIterator Processed 43,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 4s. Last read position: chr16:21,243,753. Last read name: VH01243:131:AACMHYHHV:1:1601:66498:42290
INFO 2024-11-14 15:29:00 SNPUMIBasePileupIterator Processed 44,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 3s. Last read position: chr16:53,893,199. Last read name: VH01243:131:AACMHYHHV:2:1113:63601:15085
INFO 2024-11-14 15:29:04 SNPUMIBasePileupIterator Processed 45,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 4s. Last read position: chr16:81,492,038. Last read name: VH01243:131:AACMHYHHV:2:2413:54228:4654
INFO 2024-11-14 15:29:08 SNPUMIBasePileupIterator Processed 46,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 4s. Last read position: chr17:1,364,966. Last read name: VH01243:131:AACMHYHHV:2:1308:59624:19061
INFO 2024-11-14 15:29:16 SNPUMIBasePileupIterator Processed 47,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 7s. Last read position: chr17:7,578,367. Last read name: VH01243:131:AACMHYHHV:2:2201:61461:8819
INFO 2024-11-14 15:29:20 SNPUMIBasePileupIterator Processed 48,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 4s. Last read position: chr17:17,726,485. Last read name: VH01243:131:AACMHYHHV:1:2208:55894:54331
INFO 2024-11-14 15:29:24 SNPUMIBasePileupIterator Processed 49,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 4s. Last read position: chr17:38,850,151. Last read name: VH01243:131:AACMHYHHV:1:2108:24404:47080
INFO 2024-11-14 15:29:32 SNPUMIBasePileupIterator Processed 50,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 7s. Last read position: chr17:45,637,582. Last read name: VH01243:131:AACMHYHHV:2:2402:46085:37898
INFO 2024-11-14 15:29:36 SNPUMIBasePileupIterator Processed 51,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 4s. Last read position: chr17:61,135,051. Last read name: VH01243:131:AACMHYHHV:2:2213:45650:40568
INFO 2024-11-14 15:29:40 SNPUMIBasePileupIterator Processed 52,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 4s. Last read position: chr17:75,898,906. Last read name: VH01243:131:AACMHYHHV:1:2602:26506:52400
INFO 2024-11-14 15:29:44 SNPUMIBasePileupIterator Processed 53,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 4s. Last read position: chr18:3,621,868. Last read name: VH01243:131:AACMHYHHV:2:2604:16186:40151
INFO 2024-11-14 15:29:48 SNPUMIBasePileupIterator Processed 54,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 4s. Last read position: chr18:44,934,392. Last read name: VH01243:131:AACMHYHHV:1:1209:47600:18512
INFO 2024-11-14 15:29:53 SNPUMIBasePileupIterator Processed 55,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 4s. Last read position: chr19:1,014,351. Last read name: VH01243:131:AACMHYHHV:2:1310:19405:25990
INFO 2024-11-14 15:29:57 SNPUMIBasePileupIterator Processed 56,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 4s. Last read position: chr19:5,630,684. Last read name: VH01243:131:AACMHYHHV:1:2203:33815:25517
INFO 2024-11-14 15:30:01 SNPUMIBasePileupIterator Processed 57,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 4s. Last read position: chr19:10,829,099. Last read name: VH01243:131:AACMHYHHV:2:2602:41370:25952
INFO 2024-11-14 15:30:06 SNPUMIBasePileupIterator Processed 58,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 4s. Last read position: chr19:17,862,188. Last read name: VH01243:131:AACMHYHHV:2:2607:18269:44089
INFO 2024-11-14 15:30:10 SNPUMIBasePileupIterator Processed 59,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 4s. Last read position: chr19:35,745,970. Last read name: VH01243:131:AACMHYHHV:2:2502:38587:47515
INFO 2024-11-14 15:30:15 SNPUMIBasePileupIterator Processed 60,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 4s. Last read position: chr19:43,553,083. Last read name: VH01243:131:AACMHYHHV:2:1305:59984:31916
INFO 2024-11-14 15:30:19 SNPUMIBasePileupIterator Processed 61,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 4s. Last read position: chr19:49,490,265. Last read name: VH01243:131:AACMHYHHV:2:2513:68448:36024
INFO 2024-11-14 15:30:28 SNPUMIBasePileupIterator Processed 62,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 8s. Last read position: chr19:55,386,623. Last read name: VH01243:131:AACMHYHHV:1:2510:45953:48595
INFO 2024-11-14 15:30:32 SNPUMIBasePileupIterator Processed 63,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 4s. Last read position: chr2:9,584,079. Last read name: VH01243:131:AACMHYHHV:1:2504:23912:5127
INFO 2024-11-14 15:30:36 SNPUMIBasePileupIterator Processed 64,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 4s. Last read position: chr2:33,224,701. Last read name: VH01243:131:AACMHYHHV:2:1405:16906:26141
INFO 2024-11-14 15:30:41 SNPUMIBasePileupIterator Processed 65,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 4s. Last read position: chr2:58,583,572. Last read name: VH01243:131:AACMHYHHV:1:2607:27888:16941
INFO 2024-11-14 15:30:45 SNPUMIBasePileupIterator Processed 66,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 4s. Last read position: chr2:84,906,485. Last read name: VH01243:131:AACMHYHHV:1:1609:39477:27959
INFO 2024-11-14 15:30:49 SNPUMIBasePileupIterator Processed 67,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 3s. Last read position: chr2:117,520,714. Last read name: VH01243:131:AACMHYHHV:1:2108:74053:35494
INFO 2024-11-14 15:30:53 SNPUMIBasePileupIterator Processed 68,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 4s. Last read position: chr2:159,369,422. Last read name: VH01243:131:AACMHYHHV:2:2507:73580:31423
INFO 2024-11-14 15:30:57 SNPUMIBasePileupIterator Processed 69,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 4s. Last read position: chr2:189,032,763. Last read name: VH01243:131:AACMHYHHV:1:1608:23666:24835
INFO 2024-11-14 15:31:01 SNPUMIBasePileupIterator Processed 70,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 4s. Last read position: chr2:212,113,291. Last read name: VH01243:131:AACMHYHHV:1:2110:14634:32351
INFO 2024-11-14 15:31:06 SNPUMIBasePileupIterator Processed 71,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 4s. Last read position: chr2:231,461,719. Last read name: VH01243:131:AACMHYHHV:1:2308:41957:42707
INFO 2024-11-14 15:31:11 SNPUMIBasePileupIterator Processed 72,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 4s. Last read position: chr20:2,658,760. Last read name: VH01243:131:AACMHYHHV:1:1201:26260:47383
INFO 2024-11-14 15:31:15 SNPUMIBasePileupIterator Processed 73,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 4s. Last read position: chr20:35,740,325. Last read name: VH01243:131:AACMHYHHV:1:2304:66119:21049
INFO 2024-11-14 15:31:19 SNPUMIBasePileupIterator Processed 74,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 4s. Last read position: chr20:59,032,265. Last read name: VH01243:131:AACMHYHHV:1:2110:59264:19799
INFO 2024-11-14 15:31:23 SNPUMIBasePileupIterator Processed 75,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 4s. Last read position: chr21:25,943,580. Last read name: VH01243:131:AACMHYHHV:1:1207:43681:15578
INFO 2024-11-14 15:31:27 SNPUMIBasePileupIterator Processed 76,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 4s. Last read position: chr22:19,113,904. Last read name: VH01243:131:AACMHYHHV:1:1401:55137:46342
INFO 2024-11-14 15:31:32 SNPUMIBasePileupIterator Processed 77,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 4s. Last read position: chr22:32,498,651. Last read name: VH01243:131:AACMHYHHV:1:2206:59283:39280
INFO 2024-11-14 15:31:36 SNPUMIBasePileupIterator Processed 78,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 4s. Last read position: chr22:42,618,986. Last read name: VH01243:131:AACMHYHHV:2:2110:47146:6093
INFO 2024-11-14 15:31:41 SNPUMIBasePileupIterator Processed 79,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 4s. Last read position: chr3:17,393,235. Last read name: VH01243:131:AACMHYHHV:1:1505:16186:11110
INFO 2024-11-14 15:31:45 SNPUMIBasePileupIterator Processed 80,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 4s. Last read position: chr3:40,940,346. Last read name: VH01243:131:AACMHYHHV:2:1501:66290:17319
INFO 2024-11-14 15:31:50 SNPUMIBasePileupIterator Processed 81,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 4s. Last read position: chr3:51,993,883. Last read name: VH01243:131:AACMHYHHV:1:1206:56197:35361
INFO 2024-11-14 15:31:54 SNPUMIBasePileupIterator Processed 82,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 4s. Last read position: chr3:99,676,508. Last read name: VH01243:131:AACMHYHHV:2:2511:10581:22166
INFO 2024-11-14 15:31:58 SNPUMIBasePileupIterator Processed 83,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 4s. Last read position: chr3:129,169,652. Last read name: VH01243:131:AACMHYHHV:1:2105:28229:46247
INFO 2024-11-14 15:32:03 SNPUMIBasePileupIterator Processed 84,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 4s. Last read position: chr3:160,417,783. Last read name: VH01243:131:AACMHYHHV:2:1209:44173:38939
INFO 2024-11-14 15:32:06 SNPUMIBasePileupIterator Processed 85,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 3s. Last read position: chr3:194,486,638. Last read name: VH01243:131:AACMHYHHV:2:2608:70399:24229
INFO 2024-11-14 15:32:11 SNPUMIBasePileupIterator Processed 86,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 4s. Last read position: chr4:17,813,077. Last read name: VH01243:131:AACMHYHHV:2:1204:13497:20954
INFO 2024-11-14 15:32:20 SNPUMIBasePileupIterator Processed 87,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 9s. Last read position: chr4:62,105,612. Last read name: VH01243:131:AACMHYHHV:2:1601:52258:37974
INFO 2024-11-14 15:32:24 SNPUMIBasePileupIterator Processed 88,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 4s. Last read position: chr4:98,900,168. Last read name: VH01243:131:AACMHYHHV:2:2103:12229:31499
INFO 2024-11-14 15:32:29 SNPUMIBasePileupIterator Processed 89,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 4s. Last read position: chr4:139,084,164. Last read name: VH01243:131:AACMHYHHV:1:1613:27832:47137
INFO 2024-11-14 15:32:33 SNPUMIBasePileupIterator Processed 90,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 4s. Last read position: chr4:180,997,851. Last read name: VH01243:131:AACMHYHHV:1:2604:42298:8289
INFO 2024-11-14 15:32:37 SNPUMIBasePileupIterator Processed 91,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 3s. Last read position: chr5:33,857,911. Last read name: VH01243:131:AACMHYHHV:1:1210:51103:45603
INFO 2024-11-14 15:32:41 SNPUMIBasePileupIterator Processed 92,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 3s. Last read position: chr5:70,279,429. Last read name: VH01243:131:AACMHYHHV:1:1111:64112:6244
INFO 2024-11-14 15:32:45 SNPUMIBasePileupIterator Processed 93,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 4s. Last read position: chr5:88,669,352. Last read name: VH01243:131:AACMHYHHV:2:1211:61650:47781
INFO 2024-11-14 15:32:49 SNPUMIBasePileupIterator Processed 94,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 4s. Last read position: chr5:132,952,413. Last read name: VH01243:131:AACMHYHHV:2:2403:30729:55259
INFO 2024-11-14 15:32:54 SNPUMIBasePileupIterator Processed 95,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 4s. Last read position: chr5:150,444,331. Last read name: VH01243:131:AACMHYHHV:2:1211:43908:9444
INFO 2024-11-14 15:32:58 SNPUMIBasePileupIterator Processed 96,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 4s. Last read position: chr5:172,408,451. Last read name: VH01243:131:AACMHYHHV:1:2204:37375:47288
INFO 2024-11-14 15:33:02 SNPUMIBasePileupIterator Processed 97,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 4s. Last read position: chr6:7,408,336. Last read name: VH01243:131:AACMHYHHV:1:1410:14084:40132
INFO 2024-11-14 15:33:06 SNPUMIBasePileupIterator Processed 98,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 3s. Last read position: chr6:30,724,214. Last read name: VH01243:131:AACMHYHHV:1:2402:62237:36895
INFO 2024-11-14 15:33:15 SNPUMIBasePileupIterator Processed 99,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 8s. Last read position: chr6:34,424,674. Last read name: VH01243:131:AACMHYHHV:1:2607:6984:25574
INFO 2024-11-14 15:33:19 SNPUMIBasePileupIterator Processed 100,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 4s. Last read position: chr6:44,250,123. Last read name: VH01243:131:AACMHYHHV:2:2604:44230:33165
INFO 2024-11-14 15:33:23 SNPUMIBasePileupIterator Processed 101,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 4s. Last read position: chr6:75,240,300. Last read name: VH01243:131:AACMHYHHV:1:1612:59889:19818
INFO 2024-11-14 15:33:27 SNPUMIBasePileupIterator Processed 102,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 4s. Last read position: chr6:113,861,482. Last read name: VH01243:131:AACMHYHHV:2:2606:44021:55334
INFO 2024-11-14 15:33:32 SNPUMIBasePileupIterator Processed 103,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 4s. Last read position: chr6:144,095,074. Last read name: VH01243:131:AACMHYHHV:1:2102:41598:18493
INFO 2024-11-14 15:33:36 SNPUMIBasePileupIterator Processed 104,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 3s. Last read position: chr7:2,538,327. Last read name: VH01243:131:AACMHYHHV:2:2211:19992:17149
INFO 2024-11-14 15:33:40 SNPUMIBasePileupIterator Processed 105,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 4s. Last read position: chr7:23,522,883. Last read name: VH01243:131:AACMHYHHV:1:1306:49835:52248
INFO 2024-11-14 15:33:44 SNPUMIBasePileupIterator Processed 106,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 4s. Last read position: chr7:54,752,381. Last read name: VH01243:131:AACMHYHHV:2:1411:67085:49617
INFO 2024-11-14 15:33:48 SNPUMIBasePileupIterator Processed 107,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 4s. Last read position: chr7:84,148,441. Last read name: VH01243:131:AACMHYHHV:2:2110:64623:23794
INFO 2024-11-14 15:33:53 SNPUMIBasePileupIterator Processed 108,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 4s. Last read position: chr7:102,531,354. Last read name: VH01243:131:AACMHYHHV:2:1404:26714:30988
INFO 2024-11-14 15:33:56 SNPUMIBasePileupIterator Processed 109,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 3s. Last read position: chr7:134,891,457. Last read name: VH01243:131:AACMHYHHV:1:2207:43624:15710
INFO 2024-11-14 15:34:01 SNPUMIBasePileupIterator Processed 110,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 4s. Last read position: chr8:8,840,207. Last read name: VH01243:131:AACMHYHHV:2:1303:37621:18266
INFO 2024-11-14 15:34:05 SNPUMIBasePileupIterator Processed 111,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 4s. Last read position: chr8:42,405,555. Last read name: VH01243:131:AACMHYHHV:1:1112:58261:16751
INFO 2024-11-14 15:34:09 SNPUMIBasePileupIterator Processed 112,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 4s. Last read position: chr8:73,483,814. Last read name: VH01243:131:AACMHYHHV:1:1604:74394:30344
INFO 2024-11-14 15:34:14 SNPUMIBasePileupIterator Processed 113,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 4s. Last read position: chr8:103,229,862. Last read name: VH01243:131:AACMHYHHV:2:2310:11509:46531
INFO 2024-11-14 15:34:19 SNPUMIBasePileupIterator Processed 114,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 4s. Last read position: chr8:144,450,127. Last read name: VH01243:131:AACMHYHHV:2:2412:35803:54426
INFO 2024-11-14 15:34:23 SNPUMIBasePileupIterator Processed 115,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 4s. Last read position: chr9:21,854,858. Last read name: VH01243:131:AACMHYHHV:2:2205:58072:36516
INFO 2024-11-14 15:34:27 SNPUMIBasePileupIterator Processed 116,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 4s. Last read position: chr9:78,272,265. Last read name: VH01243:131:AACMHYHHV:1:2510:44002:29303
INFO 2024-11-14 15:34:31 SNPUMIBasePileupIterator Processed 117,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 4s. Last read position: chr9:110,244,782. Last read name: VH01243:131:AACMHYHHV:2:1502:41901:43634
INFO 2024-11-14 15:34:35 SNPUMIBasePileupIterator Processed 118,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 4s. Last read position: chr9:127,449,306. Last read name: VH01243:131:AACMHYHHV:1:1209:68562:43559
INFO 2024-11-14 15:34:40 SNPUMIBasePileupIterator Processed 119,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 4s. Last read position: chr9:136,840,895. Last read name: VH01243:131:AACMHYHHV:1:1111:18099:24267
INFO 2024-11-14 15:34:43 SNPUMIBasePileupIterator Processed 120,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 3s. Last read position: chrM:5,364. Last read name: VH01243:131:AACMHYHHV:1:2501:46445:36024
INFO 2024-11-14 15:34:46 SNPUMIBasePileupIterator Processed 121,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 2s. Last read position: chrM:8,981. Last read name: VH01243:131:AACMHYHHV:1:2206:73807:25706
INFO 2024-11-14 15:34:49 SNPUMIBasePileupIterator Processed 122,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 2s. Last read position: chrM:14,055. Last read name: VH01243:131:AACMHYHHV:1:1103:19292:40454
INFO 2024-11-14 15:34:52 SNPUMIBasePileupIterator Processed 123,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 2s. Last read position: chrX:19,359,665. Last read name: VH01243:131:AACMHYHHV:2:1608:63260:47459
INFO 2024-11-14 15:34:55 SNPUMIBasePileupIterator Processed 124,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 2s. Last read position: chrX:71,300,986. Last read name: VH01243:131:AACMHYHHV:2:1513:28930:50052
INFO 2024-11-14 15:34:58 SNPUMIBasePileupIterator Processed 125,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 3s. Last read position: chrX:108,610,972. Last read name: VH01243:131:AACMHYHHV:1:1306:69376:51226
INFO 2024-11-14 15:35:01 SNPUMIBasePileupIterator Processed 126,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 2s. Last read position: chrX:154,365,223. Last read name: VH01243:131:AACMHYHHV:2:1103:43605:52532
INFO 2024-11-14 15:35:03 SNPUMIBasePileupIterator Processed 127,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 2s. Last read position: /. Last read name: VH01243:131:AACMHYHHV:1:2611:24518:16562
INFO 2024-11-14 15:35:06 SNPUMIBasePileupIterator Processed 128,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 2s. Last read position: /. Last read name: VH01243:131:AACMHYHHV:2:1511:55932:45774
INFO 2024-11-14 15:35:08 SNPUMIBasePileupIterator Processed 129,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 2s. Last read position: /. Last read name: VH01243:131:AACMHYHHV:1:2410:21318:29227
INFO 2024-11-14 15:35:10 SNPUMIBasePileupIterator Processed 130,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 2s. Last read position: /. Last read name: VH01243:131:AACMHYHHV:1:1105:56651:10220
INFO 2024-11-14 15:35:13 SNPUMIBasePileupIterator Processed 131,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 2s. Last read position: /. Last read name: VH01243:131:AACMHYHHV:1:2402:46786:8648
INFO 2024-11-14 15:35:18 AssignCellsToSamples Processed [1000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:20 AssignCellsToSamples Processed [2000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:20 AssignCellsToSamples Processed [3000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:21 AssignCellsToSamples Processed [4000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:21 AssignCellsToSamples Processed [5000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:22 AssignCellsToSamples Processed [6000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:22 AssignCellsToSamples Processed [7000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:23 AssignCellsToSamples Processed [8000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:23 AssignCellsToSamples Processed [9000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:24 AssignCellsToSamples Processed [10000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:24 AssignCellsToSamples Processed [11000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:25 AssignCellsToSamples Processed [12000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:25 AssignCellsToSamples Processed [13000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:26 AssignCellsToSamples Processed [14000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:26 AssignCellsToSamples Processed [15000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:27 AssignCellsToSamples Processed [16000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:28 AssignCellsToSamples Processed [17000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:28 AssignCellsToSamples Processed [18000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:29 AssignCellsToSamples Processed [19000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:29 AssignCellsToSamples Processed [20000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:30 AssignCellsToSamples Processed [21000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:30 AssignCellsToSamples Processed [22000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:31 AssignCellsToSamples Processed [23000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:31 AssignCellsToSamples Processed [24000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:31 AssignCellsToSamples Processed [25000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:32 AssignCellsToSamples Processed [26000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:32 AssignCellsToSamples Processed [27000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:33 AssignCellsToSamples Processed [28000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:33 AssignCellsToSamples Processed [29000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:34 AssignCellsToSamples Processed [30000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:34 AssignCellsToSamples Processed [31000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:36 AssignCellsToSamples Processed [32000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:37 AssignCellsToSamples Processed [33000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:37 AssignCellsToSamples Processed [34000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:38 AssignCellsToSamples Processed [35000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:38 AssignCellsToSamples Processed [36000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:39 AssignCellsToSamples Processed [37000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:39 AssignCellsToSamples Processed [38000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:40 AssignCellsToSamples Processed [39000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:41 AssignCellsToSamples Processed [40000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:41 AssignCellsToSamples Processed [41000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:41 AssignCellsToSamples Processed [42000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:42 AssignCellsToSamples Processed [43000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:43 AssignCellsToSamples Processed [44000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:43 AssignCellsToSamples Processed [45000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:43 AssignCellsToSamples Processed [46000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:44 AssignCellsToSamples Processed [47000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:45 AssignCellsToSamples Processed [48000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:45 AssignCellsToSamples Processed [49000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:46 AssignCellsToSamples Processed [50000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:46 AssignCellsToSamples Processed [51000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:46 AssignCellsToSamples Processed [52000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:47 AssignCellsToSamples Processed [53000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:48 AssignCellsToSamples Processed [54000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:49 AssignCellsToSamples Processed [55000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:49 AssignCellsToSamples Processed [56000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:49 AssignCellsToSamples Processed [57000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:50 AssignCellsToSamples Processed [58000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:50 AssignCellsToSamples Processed [59000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:51 AssignCellsToSamples Processed [60000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:51 AssignCellsToSamples Processed [61000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:52 AssignCellsToSamples Processed [62000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:52 AssignCellsToSamples Processed [63000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:53 AssignCellsToSamples Processed [64000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:53 AssignCellsToSamples Processed [65000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:54 AssignCellsToSamples Processed [66000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:54 AssignCellsToSamples Processed [67000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:55 AssignCellsToSamples Processed [68000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:55 AssignCellsToSamples Processed [69000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:55 AssignCellsToSamples Processed [70000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:56 AssignCellsToSamples Processed [71000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:57 AssignCellsToSamples Processed [72000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:57 AssignCellsToSamples Processed [73000] SNPs in BAM + VCF
INFO 2024-11-14 15:35:58 AssignCellsToSamples Processed [74000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:03 AssignCellsToSamples Processed [75000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:03 AssignCellsToSamples Processed [76000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:04 AssignCellsToSamples Processed [77000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:04 AssignCellsToSamples Processed [78000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:05 AssignCellsToSamples Processed [79000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:05 AssignCellsToSamples Processed [80000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:06 AssignCellsToSamples Processed [81000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:07 AssignCellsToSamples Processed [82000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:08 AssignCellsToSamples Processed [83000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:09 AssignCellsToSamples Processed [84000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:09 AssignCellsToSamples Processed [85000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:10 AssignCellsToSamples Processed [86000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:10 AssignCellsToSamples Processed [87000] SNPs in BAM + VCF
INFO 2024-11-14 15:36:10 AssignCellsToSamples Processed [87189] SNPs in BAM + VCF
INFO 2024-11-14 15:36:12 AssignCellsToSamples Finished!
[Thu Nov 14 15:36:12 EST 2024] org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.sampleassignment.AssignCellsToSamples done. Elapsed time: 10.68 minutes.
Runtime.totalMemory()=10657726464
[akulan@cn2877 V1_outs_090624]$

@jamesnemesh
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Strange, everything in the log looks OK to me at first glance. Could you try using absolute paths instead of relative paths for the outputs? I don't have a strong opinion that will work, but we generally use all of our tools in workflows with absolute paths, so maybe there's a strange bug we never caught?

@akulan1
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akulan1 commented Nov 14, 2024

Thanks Jim giving the absolute paths worked and did get the vcf output!

@jamesnemesh
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@akulan1 I'm glad that fixed your issue!

@alecw Let's do some validation of relative and absolute paths for the outputs (especially the VCF) and see if there's an issue we can fix in the next release.

@alecw
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alecw commented Nov 18, 2024

I tried running AssignCellsToSamples with -VCF_OUTPUT V1_possorted_genome_bam_tagged.bam.donor_assignments.vcf.gz and it wrote files in the directory in which the program was invoked as expected. So there is something weird for @akulan1 that probably we can't debug.

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