Hi All,
I am trying to use GATK unified genotyper with -L option. The command works fine with out option but failing with L option.
##################
@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:249250621 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo Sapien
@SQ SN:chr2 LN:243199373 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:a0d9851da00400dec1098a9255ac712e SP:Homo Sapien
@SQ SN:chr3 LN:198022430 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:641e4338fa8d52a5b781bd2a2c08d3c3 SP:Homo Sapien
@SQ SN:chr4 LN:191154276 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:23dccd106897542ad87d2765d28a19a1 SP:Homo Sapien
@SQ SN:chr5 LN:180915260 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:0740173db9ffd264d728f32784845cd7 SP:Homo Sapien
@SQ SN:chr6 LN:171115067 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1d3a93a248d92a729ee764823acbbc6b SP:Homo Sapien
@SQ SN:chr7 LN:159138663 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:618366e953d6aaad97dbe4777c29375e SP:Homo Sapien
@SQ SN:chr8 LN:146364022 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:96f514a9929e410c6651697bded59aec SP:Homo Sapien
@SQ SN:chr9 LN:141213431 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:3e273117f15e0a400f01055d9f393768 SP:Homo Sapien
@SQ SN:chr10 LN:135534747 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:988c28e000e84c26d552359af1ea2e1d SP:Homo Sapien
@SQ SN:chr11 LN:135006516 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Homo Sapien
@SQ SN:chr12 LN:133851895 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:51851ac0e1a115847ad36449b0015864 SP:Homo Sapien
@SQ SN:chr13 LN:115169878 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:283f8d7892baa81b510a015719ca7b0b SP:Homo Sapien
@SQ SN:chr14 LN:107349540 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:98f3cae32b2a2e9524bc19813927542e SP:Homo Sapien
@SQ SN:chr15 LN:102531392 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:e5645a794a8238215b2cd77acb95a078 SP:Homo Sapien
@SQ SN:chr16 LN:90354753 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Homo Sapien
@SQ SN:chr17 LN:81195210 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Homo Sapien
@SQ SN:chr18 LN:78077248 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Homo Sapien
@SQ SN:chr19 LN:59128983 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1aacd71f30db8e561810913e0b72636d SP:Homo Sapien
@SQ SN:chr20 LN:63025520 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Homo Sapien
@SQ SN:chr21 LN:48129895 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:2979a6085bfe28e3ad6f552f361ed74d SP:Homo Sapien
@SQ SN:chr22 LN:51304566 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:a718acaa6135fdca8357d5bfe94211dd SP:Homo Sapien
@SQ SN:chrX LN:155270560 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:7e0e2e580297b7764e31dbc80c2540dd SP:Homo Sapien
@SQ SN:chrY LN:59373566 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1e86411d73e6f00a10590f976be01623 SP:Homo Sapien
chr1 564490 564532 + target_1
chr1 564533 564534 + target_2
chr1 564672 564718 + target_3
chr1 564720 564721 + target_4
##########################################
This is second header I tried
@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:249250621 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr2 LN:243199373 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr3 LN:198022430 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr4 LN:191154276 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr5 LN:180915260 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr6 LN:171115067 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr7 LN:159138663 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr8 LN:146364022 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr9 LN:141213431 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr10 LN:135534747 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr11 LN:135006516 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr12 LN:133851895 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr13 LN:115169878 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr14 LN:107349540 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr15 LN:102531392 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr16 LN:90354753 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr17 LN:81195210 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr18 LN:78077248 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr19 LN:59128983 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr20 LN:63025520 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr21 LN:48129895 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr22 LN:51304566 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chrX LN:155270560 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chrY LN:59373566 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
chr1 564490 564532 + target_1
chr1 564533 564534 + target_2
chr1 564672 564718 + target_3
chr1 564720 564721 + target_4
#####################
I am not understanding the exact header format . I tried googling lot but didn't got how should be header
#############
This is error I am getting
INFO 17:05:07,240 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 17:05:30,725 ProgressMeter - done 1.47e+07 23.0 s 1.0 s 100.0% 23.0 s 0.0 s
INFO 17:05:30,726 ProgressMeter - Total runtime 23.49 secs, 0.39 min, 0.01 hours
INFO 17:05:30,728 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 332130 total reads (0.00%)
INFO 17:05:30,728 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter
INFO 17:05:30,728 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 17:05:30,729 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 17:05:30,730 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 17:05:30,730 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 17:05:30,730 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
INFO 17:05:30,731 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
INFO 17:05:31,962 GATKRunReport - Uploaded run statistics report to AWS S3
###########################
I am trying to use GATK unified genotyper with -L option. The command works fine with out option but failing with L option.
##################
@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:249250621 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo Sapien
@SQ SN:chr2 LN:243199373 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:a0d9851da00400dec1098a9255ac712e SP:Homo Sapien
@SQ SN:chr3 LN:198022430 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:641e4338fa8d52a5b781bd2a2c08d3c3 SP:Homo Sapien
@SQ SN:chr4 LN:191154276 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:23dccd106897542ad87d2765d28a19a1 SP:Homo Sapien
@SQ SN:chr5 LN:180915260 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:0740173db9ffd264d728f32784845cd7 SP:Homo Sapien
@SQ SN:chr6 LN:171115067 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1d3a93a248d92a729ee764823acbbc6b SP:Homo Sapien
@SQ SN:chr7 LN:159138663 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:618366e953d6aaad97dbe4777c29375e SP:Homo Sapien
@SQ SN:chr8 LN:146364022 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:96f514a9929e410c6651697bded59aec SP:Homo Sapien
@SQ SN:chr9 LN:141213431 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:3e273117f15e0a400f01055d9f393768 SP:Homo Sapien
@SQ SN:chr10 LN:135534747 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:988c28e000e84c26d552359af1ea2e1d SP:Homo Sapien
@SQ SN:chr11 LN:135006516 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Homo Sapien
@SQ SN:chr12 LN:133851895 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:51851ac0e1a115847ad36449b0015864 SP:Homo Sapien
@SQ SN:chr13 LN:115169878 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:283f8d7892baa81b510a015719ca7b0b SP:Homo Sapien
@SQ SN:chr14 LN:107349540 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:98f3cae32b2a2e9524bc19813927542e SP:Homo Sapien
@SQ SN:chr15 LN:102531392 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:e5645a794a8238215b2cd77acb95a078 SP:Homo Sapien
@SQ SN:chr16 LN:90354753 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Homo Sapien
@SQ SN:chr17 LN:81195210 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Homo Sapien
@SQ SN:chr18 LN:78077248 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Homo Sapien
@SQ SN:chr19 LN:59128983 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1aacd71f30db8e561810913e0b72636d SP:Homo Sapien
@SQ SN:chr20 LN:63025520 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Homo Sapien
@SQ SN:chr21 LN:48129895 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:2979a6085bfe28e3ad6f552f361ed74d SP:Homo Sapien
@SQ SN:chr22 LN:51304566 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:a718acaa6135fdca8357d5bfe94211dd SP:Homo Sapien
@SQ SN:chrX LN:155270560 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:7e0e2e580297b7764e31dbc80c2540dd SP:Homo Sapien
@SQ SN:chrY LN:59373566 AS:hg19 UR:file:/raid/references-and-indexes/hg19/hg19_lite/hg19_lite.fa M5:1e86411d73e6f00a10590f976be01623 SP:Homo Sapien
chr1 564490 564532 + target_1
chr1 564533 564534 + target_2
chr1 564672 564718 + target_3
chr1 564720 564721 + target_4
##########################################
This is second header I tried
@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:249250621 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr2 LN:243199373 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr3 LN:198022430 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr4 LN:191154276 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr5 LN:180915260 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr6 LN:171115067 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr7 LN:159138663 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr8 LN:146364022 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr9 LN:141213431 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr10 LN:135534747 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr11 LN:135006516 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr12 LN:133851895 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr13 LN:115169878 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr14 LN:107349540 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr15 LN:102531392 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr16 LN:90354753 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr17 LN:81195210 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr18 LN:78077248 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr19 LN:59128983 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr20 LN:63025520 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr21 LN:48129895 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chr22 LN:51304566 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chrX LN:155270560 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
@SQ SN:chrY LN:59373566 /mnt/idash/Genomics/data_ressources/references-and-indexes/hg19/hg19_lite/hg19_lite.fa
chr1 564490 564532 + target_1
chr1 564533 564534 + target_2
chr1 564672 564718 + target_3
chr1 564720 564721 + target_4
#####################
I am not understanding the exact header format . I tried googling lot but didn't got how should be header
#############
This is error I am getting
INFO 17:05:07,240 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 17:05:30,725 ProgressMeter - done 1.47e+07 23.0 s 1.0 s 100.0% 23.0 s 0.0 s
INFO 17:05:30,726 ProgressMeter - Total runtime 23.49 secs, 0.39 min, 0.01 hours
INFO 17:05:30,728 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 332130 total reads (0.00%)
INFO 17:05:30,728 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter
INFO 17:05:30,728 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 17:05:30,729 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 17:05:30,730 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 17:05:30,730 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 17:05:30,730 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
INFO 17:05:30,731 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
INFO 17:05:31,962 GATKRunReport - Uploaded run statistics report to AWS S3
###########################
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