Hello,

I am trying to run ASEReadCounter (GATK_4_2_1_0) using the following command:

    gatk ASEReadCounter \\
            -R ${params.genome}  \\
            -V ${params.vcf_infile}  \\
            -O final_results_ASEReadCounter_counts \\
            -I ${params.bam_infile}

and I used this command for different sample before and worked perfectly. below I copied the log message. would you please let me know what the problem could be?

BTW, bam file and vcf files have similar chromosome notation.

Error executing process > 'ASEReadCounter (1)'

Caused by:
  Process `ASEReadCounter (1)` terminated with an error exit status (2)

Command executed:

  gatk ASEReadCounter \
      -R /hpc/diaggen/users/Behzad/bam/STAR/hg38_genome/GRCh38.p13.genome.fa  \
      -V /hpc/diaggen/users/Behzad/bam/NF/main/deve/github/final/test2/github/merged/4a/d7b565c5fef4ef6fedbe5cb12d1b98/final_results_rmats/MA/vcf/file1chr.vcf.gz  \
      -O final_results_ASEReadCounter_counts \
      -I /hpc/diaggen/users/Behzad/PMRBM000AWB_MAE_AS/PMRBM000AWB_BHKY7TDSX2Aligned.out.sorted2.bam

Command exit status:
  2

Command output:
  (empty)

Command error:
  11:37:17.177 INFO  ASEReadCounter - ------------------------------------------------------------
  11:37:17.178 INFO  ASEReadCounter - HTSJDK Version: 2.24.1
  11:37:17.178 INFO  ASEReadCounter - Picard Version: 2.27.1
  11:37:17.178 INFO  ASEReadCounter - Built for Spark Version: 2.4.5
  11:37:17.178 INFO  ASEReadCounter - HTSJDK Defaults.COMPRESSION_LEVEL : 2
  11:37:17.178 INFO  ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
  11:37:17.178 INFO  ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
  11:37:17.178 INFO  ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
  11:37:17.179 INFO  ASEReadCounter - Deflater: IntelDeflater
  11:37:17.179 INFO  ASEReadCounter - Inflater: IntelInflater
  11:37:17.179 INFO  ASEReadCounter - GCS max retries/reopens: 20
  11:37:17.179 INFO  ASEReadCounter - Requester pays: disabled
  11:37:17.179 INFO  ASEReadCounter - Initializing engine
  11:37:18.369 INFO  FeatureManager - Using codec VCFCodec to read file file:///hpc/diaggen/users/Behzad/bam/NF/main/deve/github/final/test2/github/merged/4a/d7b565c5fef4ef6fedbe5cb12d1b98/final_results_rmats/MA/vcf/file1chr.vcf.gz
  11:37:18.667 INFO  ASEReadCounter - Shutting down engine
  [October 24, 2022 11:37:18 AM GMT] org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter done. Elapsed time: 0.04 minutes.
  Runtime.totalMemory()=2201485312
  ***********************************************************************
  
  A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found.
    reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, 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, KQ759759.1, ML143376.1, KN538364.1, ML143355.1, ML143348.1, ML143347.1, ML143346.1, ML143352.1, KQ759762.1, ML143375.1, KQ031383.1, KN538369.1, ML143342.1, ML143350.1, ML143362.1, JH159136.1, ML143357.1, ML143385.1, ML143378.1, ML143382.1, ML143383.1, ML143384.1, JH159137.1, ML143356.1, ML143364.1, ML143365.1, KZ208923.1, KZ208924.1, KQ031387.1, KV766195.1, KZ208916.1, ML143363.1, KN538360.1, KZ208920.1, KZ208906.1, KN196484.1, KN196476.1, KQ983257.1, KN196479.1, KV575245.1, KZ208917.1, KZ208911.1, KN196473.1, KZ559108.1, KN196487.1, KQ759760.1, KN196475.1, KV880766.1, KV880767.1, KQ090016.1, ML143374.1, KV880764.1, KN538361.1, KN196474.1, ML143360.1, KZ559109.1, ML143359.1, KQ090022.1, KV766194.1, KN196478.1, KZ559104.1, KN196480.1, ML143370.1, KQ090028.1, KN196483.1, KN196481.1, KN538363.1, KN538362.1, KQ031385.1, KV766192.1, KQ031386.1, KQ031388.1, KN538365.1, KN538366.1, KN538367.1, ML143361.1, KN538370.1, KN538373.1, KZ559113.1, KV880765.1, KV766196.1, KN538371.1, KQ031384.1, KN538372.1, KQ090021.1, ML143371.1, KN196482.1, KZ559115.1, KZ208914.1, KZ208922.1, ML143373.1, ML143369.1, ML143366.1, ML143367.1, ML143372.1, ML143380.1, ML143377.1, ML143345.1, KQ458386.1, ML143358.1, KV575244.1, ML143381.1, KZ559100.1, ML143379.1, ML143354.1, ML143351.1, ML143353.1, ML143344.1, ML143349.1, KZ208912.1, ML143341.1, KZ208915.1, KV880768.1, KN196472.1, GL383545.1, GL383546.1, KI270824.1, KI270825.1, KQ090020.1, GL383547.1, KN538368.1, KI270826.1, KI270827.1, KZ559111.1, KI270829.1, KI270830.1, KI270831.1, KI270832.1, KI270902.1, KI270903.1, KZ559110.1, KI270927.1, GL877875.1, GL383549.1, GL383550.2, KQ090023.1, GL877876.1, GL383552.1, KI270904.1, GL383553.2, KI270835.1, GL383551.1, KI270837.1, KI270833.1, KI270834.1, KI270836.1, KZ208918.1, KZ559112.1, KI270838.1, KI270839.1, KI270840.1, KI270841.1, KI270842.1, KI270843.1, KQ090024.1, KQ090025.1, KI270844.1, KI270845.1, KI270846.1, KI270847.1, KZ208919.1, ML143368.1, KI270852.1, KI270848.1, GL383554.1, KI270906te/Time: October 24, 2022 11:37:16 AM GMT
  11:37:17.177 INFO  ASEReadCounter - ------------------------------------------------------------
  11:37:17.177 INFO  ASEReadCounter - ------------------------------------------------------------
  11:37:17.178 INFO  ASEReadCounter - HTSJDK Version: 2.24.1
  11:37:17.178 INFO  ASEReadCounter - Picard Version: 2.27.1
  11:37:17.178 INFO  ASEReadCounter - Built for Spark Version: 2.4.5
  11:37:17.178 INFO  ASEReadCounter - HTSJDK Defaults.COMPRESSION_LEVEL : 2
  11:37:17.178 INFO  ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
  11:37:17.178 INFO  ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
  11:37:17.178 INFO  ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
  11:37:17.179 INFO  ASEReadCounter - Deflater: IntelDeflater
  11:37:17.179 INFO  ASEReadCounter - Inflater: IntelInflater
  11:37:17.179 INFO  ASEReadCounter - GCS max retries/reopens: 20
  11:37:17.179 INFO  ASEReadCounter - Requester pays: disabled
  11:37:17.179 INFO  ASEReadCounter - Initializing engine
  11:37:18.369 INFO  FeatureManager - Using codec VCFCodec to read file file:///hpc/diaggen/users/Behzad/bam/NF/main/deve/github/final/test2/github/merged/4a/d7b565c5fef4ef6fedbe5cb12d1b98/final_results_rmats/MA/vcf/file1chr.vcf.gz
  11:37:18.667 INFO  ASEReadCounter - Shutting down engine
  [October 24, 2022 11:37:18 AM GMT] org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter done. Elapsed time: 0.04 minutes.
  Runtime.totalMemory()=2201485312
  ***********************************************************************
  
  A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found.
    reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, 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, KQ759759.1, ML143376.1, KN538364.1, ML143355.1, ML143348.1, ML143347.1, ML143346.1, ML143352.1, KQ759762.1, ML143375.1, KQ031383.1, KN538369.1, ML143342.1, ML143350.1, ML143362.1, JH159136.1, ML143357.1, ML143385.1, ML143378.1, ML143382.1, ML143383.1, ML143384.1, JH159137.1, ML143356.1, ML143364.1, ML143365.1, KZ208923.1, KZ208924.1, KQ031387.1, KV766195.1, KZ208916.1, ML143363.1, KN538360.1, KZ208920.1, KZ208906.1, KN196484.1, KN196476.1, KQ983257.1, KN196479.1, KV575245.1, KZ208917.1, KZ208911.1, KN196473.1, KZ559108.1, KN196487.1, KQ759760.1, KN196475.1, KV880766.1, KV880767.1, KQ090016.1, ML143374.1, KV880764.1, KN538361.1, KN196474.1, ML143360.1, KZ559109.1, ML143359.1, KQ090022.1, KV766194.1, KN196478.1, KZ559104.1, KN196480.1, ML143370.1, KQ090028.1, KN196483.1, KN196481.1, KN538363.1, KN538362.1, KQ031385.1, KV766192.1, KQ031386.1, KQ031388.1, KN538365.1, KN538366.1, KN538367.1, ML143361.1, KN538370.1, KN538373.1, KZ559113.1, KV880765.1, KV766196.1, KN538371.1, KQ031384.1, KN538372.1, KQ090021.1, ML143371.1, KN196482.1, KZ559115.1, KZ208914.1, KZ208922.1, ML143373.1, ML143369.1, ML143366.1, ML143367.1, ML143372.1, ML143380.1, ML143377.1, ML143345.1, KQ458386.1, ML143358.1, KV575244.1, ML143381.1, KZ559100.1, ML143379.1, ML143354.1, ML143351.1, ML143353.1, ML143344.1, ML143349.1, KZ208912.1, ML143341.1, KZ208915.1, KV880768.1, KN196472.1, GL383545.1, GL383546.1, KI270824.1, KI270825.1, KQ090020.1, GL383547.1, KN538368.1, KI270826.1, KI270827.1, KZ559111.1, KI270829.1, KI270830.1, KI270831.1, KI270832.1, KI270902.1, KI270903.1, KZ559110.1, KI270927.1, GL877875.1, GL383549.1, GL383550.2, KQ090023.1, GL877876.1, GL383552.1, KI270904.1, GL383553.2, KI270835.1, GL383551.1, KI270837.1, KI270833.1, KI270834.1, KI270836.1, KZ208918.1, KZ559112.1, KI270838.1, KI270839.1, KI270840.1, KI270841.1, KI270842.1, KI270843.1, KQ090024.1, KQ090025.1, KI270844.1, KI270845.1, KI270846.1, KI270847.1, KZ208919.1, ML143368.1, KI270852.1, KI270848.1, GL383554.1, KI270906.1, GL383555.2, KI270851.1, KI270849.1, KI270905.1, KI270850.1, KQ031389.1, KI270853.1, GL383556.1, GL383557.1, KI270855.1, KQ031390.1, KI270856.1, KQ090027.1, KQ090026.1, KZ208921.1, KI270854.1, KI270909.1, KV766197.1, KZ559114.1, GL383563.3, KI270861.1, GL383564.2, GL000258.2, KI270860.1, KI270907.1, KI270862.1, GL383565.1, KI270908.1, KV766198.1, KI270910.1, GL383566.1, JH159146.1, JH159147.1, JH159148.1, KI270857.1, KI270858.1, KI270859.1, KZ559116.1, GL383567.1, GL383568.1, GL383569.1, GL383570.1, GL383571.1, GL383572.1, KI270863.1, KI270864.1, KQ458385.1, KI270912.1, KI270911.1, KV575254.1, KV575246.1, KV575256.1, KV575253.1, KV575252.1, KV575255.1, KV575259.1, KI270917.1, KI270918.1, KI270919.1, KV575247.1, KV575248.1, KV575250.1, KV575249.1, KV575257.1, KI270920.1, KI270921.1, KI270922.1, KI270923.1, KI270929.1, KI270930.1, KI270931.1, KI270932.1, KI270933.1, KI270882.1, KI270883.1, KI270884.1, KI270885.1, KI270886.1, KI270887.1, KI270888.1, KV575258.1, KV575251.1, KV575260.1, KI270889.1, KI270890.1, GL000209.2, KI270891.1, KI270914.1, KI270915.1, KI270916.1, GL949746.1, GL949747.2, GL949748.2, GL949749.2, GL949750.2, GL949751.2, GL949752.1, GL949753.2, GL383573.1, GL383574.1, GL383575.2, KI270866.1, GL383576.1, KI270867.1, KI270865.1, KI270938.1, KI270868.1, KI270760.1, KI270762.1, GL383518.1, KI270759.1, KI270766.1, GL383519.1, KI270761.1, KQ458382.1, GL383520.2, KI270763.1, KQ458383.1, KI270765.1, KI270764.1, KQ983255.1, KQ458384.1, KV880763.1, KZ208904.1, KZ208905.1, KI270892.1, GL383577.2, KI270869.1, KI270870.1, KI270871.1, GL383578.2, GL383579.2, GL383580.2, GL383581.2, KI270872.1, KI270873.1, KI270874.1, GL383582.2, GL383583.2, KI270875.1, KI270876.1, KI270877.1, KI270878.1, KI270879.1, KB663609.1, KI270928.1, KN196485.1, KN196486.1, KQ458387.1, KQ458388.1, KQ759761.1, KI270769.1, KI270767.1, GL383521.1, KI270772.1, GL383522.1, KI270770.1, KI270893.1, KI270894.1, GL582966.2, KI270773.1, KI270776.1, KI270768.1, KI270774.1, KI270771.1, KI270775.1, KQ983256.1, KZ208907.1, KZ208908.1, JH636055.2, GL383526.1, KI270779.1, KI270777.1, KI270782.1, KI270783.1, KI270778.1, KI270895.1, KZ208909.1, KI270780.1, KI270924.1, ML143343.1, KI270781.1, KI270934.1, KZ559105.1, KI270935.1, KZ559101.1, KI270936.1, KZ559102.1, KI270937.1, KZ559103.1, KI270784.1, KQ983258.1, KV766193.1, GL383527.1, KI270790.1, GL383528.1, KI270787.1, GL000257.2, KI270785.1, KQ090013.1, KI270786.1, KI270788.1, KI270789.1, KI270896.1, KI270925.1, KQ090014.1, KQ090015.1, GL383532.1, KI270897.1, GL383531.1, GL949742.1, GL339449.2, KI270795.1, KI270791.1, GL383530.1, KI270898.1, KI270792.1, KI270796.1, KI270793.1, KI270794.1, KN196477.1, KV575243.1, KZ208910.1, KQ090017.1, GL383533.1, KB021644.2, KI270797.1, KI270798.1, KI270799.1, KI270800.1, KI270801.1, KI270802.1, KI270758.1, GL000250.2, GL000251.2, GL000252.2, GL000253.2, GL000254.2, GL000255.2, GL000256.2, KI270804.1, KI270806.1, GL383534.2, KI270805.1, KI270899.1, KI270809.1, KI270803.1, KI270807.1, KZ559106.1, KZ208913.1, KI270808.1, KI270811.1, KI270814.1, KI270810.1, KI270812.1, KI270815.1, KI270813.1, KI270816.1, KI270818.1, KI270817.1, KI270900.1, KI270819.1, KI270901.1, KI270820.1, KI270926.1, KZ559107.1, KI270821.1, KI270822.1, GL383539.1, GL383540.1, GL383541.1, GL383542.1, KI270823.1, KQ090018.1, KQ090019.1, KI270880.1, KI270881.1, KI270913.1, KV766199.1, 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]
    features contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT]
  
  ***********************************************************************
  Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
  Using GATK jar /gatk/gatk-package-4.2.6.1-local.jar
  Running:
      java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.2.6.1-local.jar ASEReadCounter -R /hpc/diaggen/users/Behzad/bam/STAR/hg38_genome/GRCh38.p13.genome.fa -V /hpc/diaggen/users/Behzad/bam/NF/main/deve/github/final/test2/github/merged/4a/d7b565c5fef4ef6fedbe5cb12d1b98/final_results_rmats/MA/vcf/file1chr.vcf.gz -O final_results_ASEReadCounter_counts -I /hpc/diaggen/users/Behzad/PMRBM000AWB_MAE_AS/PMRBM000AWB_BHKY7TDSX2Aligned.out.sorted2.bam

Work dir:
  /hpc/diaggen/users/Behzad/bam/NF/main/deve/github/final/test2/Richard/work/85/eabd071fe58233cb1200266590b7e1

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

WARN: Killing pending tasks (1)