GATK gCNV Calling pipeline error
REQUIRED for all errors and issues:
a) GATK version used: gatk-4.3.0.0
b) Exact command used:
$GATK/gatk GermlineCNVCaller \
--run-mode COHORT \
-L $OUT/scatter_MODY/temp_0001_of_191/scattered.interval_list \
-I $OUT/MDT227/MDT227.readcounts.tsv \
-I $OUT/MDT228/MDT228.readcounts.tsv \
-I $OUT/MDT229/MDT229.readcounts.tsv \
-I $OUT/MDT230/MDT230.readcounts.tsv \
-I $OUT/MDT232/MDT232.readcounts.tsv \
-I $OUT/MDT233/MDT233.readcounts.tsv \
-I $OUT/MDT234/MDT234.readcounts.tsv \
-I $OUT/MDT235/MDT235.readcounts.tsv \
-I $OUT/MDT236/MDT236.readcounts.tsv \
-I $OUT/MDTB_021/MDTB_021.readcounts.tsv \
-I $OUT/MDT032/MDT032.readcounts.tsv \
-I $OUT/MDT033/MDT033.readcounts.tsv \
-I $OUT/MDT034/MDT034.readcounts.tsv \
-I $OUT/MDT035/MDT035.readcounts.tsv \
-I $OUT/MDT036/MDT036.readcounts.tsv \
-I $OUT/MDT088/MDT088.readcounts.tsv \
-I $OUT/MDT089/MDT089.readcounts.tsv \
-I $OUT/MDT090/MDT090.readcounts.tsv \
-I $OUT/MDT091/MDT091.readcounts.tsv \
-I $OUT/MDT092/MDT092.readcounts.tsv \
-I $OUT/MDT093/MDT093.readcounts.tsv \
-I $OUT/MDT087/MDT087.readcounts.tsv \
-I $OUT/MDT095/MDT095.readcounts.tsv \
-I $OUT/MDT096/MDT096.readcounts.tsv \
-I $OUT/MDT097/MDT097.readcounts.tsv \
-I $OUT/MDT098/MDT098.readcounts.tsv \
-I $OUT/MDT099/MDT099.readcounts.tsv \
-I $OUT/MDT100/MDT100.readcounts.tsv \
-I $OUT/MDT101/MDT101.readcounts.tsv \
-I $OUT/MDT102/MDT102.readcounts.tsv \
-I $OUT/MDT103/MDT103.readcounts.tsv \
-I $OUT/MDT104/MDT104.readcounts.tsv \
-I $OUT/MDT106/MDT106.readcounts.tsv \
-I $OUT/MDT107/MDT107.readcounts.tsv \
-I $OUT/MDT109/MDT109.readcounts.tsv \
-I $OUT/MDT110/MDT110.readcounts.tsv \
-I $OUT/MDT111/MDT111.readcounts.tsv \
-I $OUT/MDT112/MDT112.readcounts.tsv \
-I $OUT/MDT113/MDT113.readcounts.tsv \
-I $OUT/MDT114/MDT114.readcounts.tsv \
-I $OUT/MDT115/MDT115.readcounts.tsv \
-I $OUT/MDT116/MDT116.readcounts.tsv \
-I $OUT/MDT117/MDT117.readcounts.tsv \
-I $OUT/MDT118/MDT118.readcounts.tsv \
-I $OUT/MDT119/MDT119.readcounts.tsv \
-I $OUT/MDT120/MDT120.readcounts.tsv \
-I $OUT/MDT121/MDT121.readcounts.tsv \
-I $OUT/MDT122/MDT122.readcounts.tsv \
-I $OUT/MDT123/MDT123.readcounts.tsv \
-I $OUT/MDT124/MDT124.readcounts.tsv \
-I $OUT/MDT125/MDT125.readcounts.tsv \
-I $OUT/MDT126/MDT126.readcounts.tsv \
-I $OUT/MDT127/MDT127.readcounts.tsv \
-I $OUT/MDT128/MDT128.readcounts.tsv \
-I $OUT/MDT129/MDT129.readcounts.tsv \
-I $OUT/MDT131/MDT131.readcounts.tsv \
-I $OUT/MDT132/MDT132.readcounts.tsv \
-I $OUT/MDT133/MDT133.readcounts.tsv \
-I $OUT/MDT134/MDT134.readcounts.tsv \
-I $OUT/MDT135/MDT135.readcounts.tsv \
-I $OUT/MDT136/MDT136.readcounts.tsv \
-I $OUT/MDT137/MDT137.readcounts.tsv \
-I $OUT/MDT138/MDT138.readcounts.tsv \
-I $OUT/MDT139/MDT139.readcounts.tsv \
-I $OUT/MDT140/MDT140.readcounts.tsv \
-I $OUT/MDT141/MDT141.readcounts.tsv \
-I $OUT/MDT142/MDT142.readcounts.tsv \
-I $OUT/MDT143/MDT143.readcounts.tsv \
-I $OUT/MDT144/MDT144.readcounts.tsv \
-I $OUT/MDT145/MDT145.readcounts.tsv \
-I $OUT/MDT146/MDT146.readcounts.tsv \
-I $OUT/MDT147/MDT147.readcounts.tsv \
-I $OUT/MDT148/MDT148.readcounts.tsv \
-I $OUT/MDT149/MDT149.readcounts.tsv \
-I $OUT/MDT150/MDT150.readcounts.tsv \
-I $OUT/MDT155/MDT155.readcounts.tsv \
-I $OUT/MDT156/MDT156.readcounts.tsv \
-I $OUT/MDT157/MDT157.readcounts.tsv \
-I $OUT/MDT159/MDT159.readcounts.tsv \
-I $OUT/MDT162/MDT162.readcounts.tsv \
-I $OUT/MDT163/MDT163.readcounts.tsv \
-I $OUT/MDT164/MDT164.readcounts.tsv \
-I $OUT/MDT165/MDT165.readcounts.tsv \
-I $OUT/MDT166/MDT166.readcounts.tsv \
-I $OUT/MDT167/MDT167.readcounts.tsv \
-I $OUT/MDT168/MDT168.readcounts.tsv \
-I $OUT/MDT169/MDT169.readcounts.tsv \
-I $OUT/MDT171/MDT171.readcounts.tsv \
-I $OUT/MDT172/MDT172.readcounts.tsv \
-I $OUT/MDT173/MDT173.readcounts.tsv \
-I $OUT/MDT175/MDT175.readcounts.tsv \
-I $OUT/MDT176/MDT176.readcounts.tsv \
-I $OUT/MDT180/MDT180.readcounts.tsv \
-I $OUT/MDT181/MDT181.readcounts.tsv \
-I $OUT/MDT182/MDT182.readcounts.tsv \
-I $OUT/MDT183/MDT183.readcounts.tsv \
-I $OUT/MDT184/MDT184.readcounts.tsv \
-I $OUT/MDT186/MDT186.readcounts.tsv \
-I $OUT/MDT187/MDT187.readcounts.tsv \
-I $OUT/MDT188/MDT188.readcounts.tsv \
-I $OUT/MDT189/MDT189.readcounts.tsv \
-I $OUT/MDT190/MDT190.readcounts.tsv \
-I $OUT/MDT191/MDT191.readcounts.tsv \
-I $OUT/MDT197/MDT197.readcounts.tsv \
-I $OUT/MDT201/MDT201.readcounts.tsv \
-I $OUT/MDT202/MDT202.readcounts.tsv \
-I $OUT/MDT206/MDT206.readcounts.tsv \
-I $OUT/MDT209/MDT209.readcounts.tsv \
-I $OUT/MDT210/MDT210.readcounts.tsv \
-I $OUT/MDT211/MDT211.readcounts.tsv \
-I $OUT/MDT212/MDT212.readcounts.tsv \
-I $OUT/MDT213/MDT213.readcounts.tsv \
-I $OUT/MDT214/MDT214.readcounts.tsv \
-I $OUT/MDT215/MDT215.readcounts.tsv \
-I $OUT/MDT216/MDT216.readcounts.tsv \
-I $OUT/MDT217/MDT217.readcounts.tsv \
-I $OUT/MDT219/MDT219.readcounts.tsv \
-I $OUT/MDT220/MDT220.readcounts.tsv \
-I $OUT/MDT221/MDT221.readcounts.tsv \
-I $OUT/MDT222/MDT222.readcounts.tsv \
-I $OUT/MDT223/MDT223.readcounts.tsv \
-I $OUT/MDT224/MDT224.readcounts.tsv \
--contig-ploidy-calls $OUT/MODY_cohort_ploidy-calls \
--annotated-intervals $OUT/hg19_1-22-X-Y-M.annotated.tsv \
--interval-merging-rule OVERLAPPING_ONLY \
--output $OUT/MODY_cohort_CNV_Call \
--output-prefix MODY_cohort_CNV_Call \
--verbosity DEBUG
c) Entire program log:
ssertionError: Sample (MDT227) does not have ploidy metadata for contig (chr1)
17:50:13.322 INFO GermlineCNVCaller - Shutting down engine
I'm doing this for germline CNV calling
I refered https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants page for my command
But there's some error like above.
Please help
Heejun Jang
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