jamesnemesh
commented
4 days ago Could you please attach the log file the program generated when it ran?
Open akulan1 opened 4 days ago
jamesnemesh
commented
4 days ago Could you please attach the log file the program generated when it ran?
akulan1
commented
4 days ago [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
commented
4 days ago 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
commented
4 days ago 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.
jamesnemesh
commented
4 days ago 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
commented
4 days ago 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
commented
4 days ago Log file please.
akulan1
commented
4 days ago 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
commented
4 days ago 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
commented
4 days ago Thanks Jim giving the absolute paths worked and did get the vcf output!
jamesnemesh
commented
4 days ago @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
commented
21 hours ago 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.
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