Unclear why Picard ValidateSamFile is producing an error
Answered
Dear all,
I am using Picard ValidateSamFile in a snakemake pipeline and the rule is erroring. While the pipeline is running, conda is installing the picard version 2.27.4 and all its dependencies (I made a yaml config file with the famous conda env export command).
This is the snakemake output:
Error in rule validate_sam:
jobid: 4
output: results/05_Validation/validatesamfile/ERR3343471_bwa_10X_realign_fix-mate_sorted_validate_bam.txt
log: results/11_Reports/validatesamfiles/ERR3343471_bwa_10X_realign_fix-mate_sorted_validate_bam.log (check log file(s) for error message)
conda-env: /Users/loictalignani/snakemake-models/shave/.snakemake/conda/6a4939c953ba582a2b9543a289dc2298
shell:
picard ValidateSamFile -I results/05_Validation/ERR3343471_bwa_10X_realign_fix-mate_sorted.bam -R resources/genomes/GCA_018104305.1_AalbF3_genomic.fasta -O results/05_Validation/validatesamfile/ERR3343471_bwa_10X_realign_fix-mate_sorted_validate_bam.txt --VERBOSITY ERROR > results/11_Reports/validatesamfiles/ERR3343471_bwa_10X_realign_fix-mate_sorted_validate_bam.log 2>&1
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job validate_sam since they might be corrupted:
results/05_Validation/validatesamfile/ERR3343471_bwa_10X_realign_fix-mate_sorted_validate_bam.txt
Job failed, going on with independent jobs.
Exiting because a job execution failed. Look above for error message
When I'm looking at the log, I can't find anything wrong, except that Picard tells me that I didn't provide a GCS but no file is produced.
07:27:36.054 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/loictalignani/snakemake-models/shave/.snakemake/conda/6a4939c953ba582a2b9543a289dc2298/share/picard-2.27.4-0/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib
[Tue Nov 15 07:27:36 CET 2022] ValidateSamFile --INPUT results/05_Validation/ERR3343471_bwa_10X_realign_fix-mate_sorted.bam --OUTPUT results/05_Validation/validatesamfile/ERR3343471_bwa_10X_realign_fix-mate_sorted_validate_bam.txt --VERBOSITY ERROR --REFERENCE_SEQUENCE resources/genomes/GCA_018104305.1_AalbF3_genomic.fasta --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --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 15 07:27:36 CET 2022] Executing as loictalignani@MBP-Loic.local on Mac OS X 12.4 x86_64; OpenJDK 64-Bit Server VM 11.0.15+10-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.27.4-SNAPSHOT
[Tue Nov 15 07:27:37 CET 2022] picard.sam.ValidateSamFile done. Elapsed time: 0,03 minutes.
Runtime.totalMemory()=575668224
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Thank you in advance for your help.
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Hi LOIC TALIGNANI,
Thank you for writing into the GATK forum so that we can assist you with this question!
I don't see any overt errors with your ValidateSamFile command, however, it does look like it only ran for 0,03 minutes, which is very short. In addition, the log does not show any of the normal output while GATK is running in the middle.
I'm not familiar with snakemate, so I don't know what you are referring to with the rule erroring. I think there might be an error message somewhere in the snakemate logs you are missing, potentially a problem with the initialization of the command. Could you check if there is any other error messages you are missing?
Best,
Genevieve
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Hello Genevieve,
Thank you for your answer.Indeed, 0.03 seconds is very very short.
Unfortunately, I don't have any other log that would show a possible problem, and snakemake automatically cleans up the generated files if the command produces an error.
I will test the same command directly under bash and let you know. -
I tried to run the same command in a shell and you can see below the .txt produced by the command:
ERROR::MISSING_PLATFORM_VALUE:Read name ERR3343471, A platform (PL) attribute was not found for read group
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 2709, Read name ERR3343471.92021, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 7122, Read name ERR3343471.50013, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 7727, Read name ERR3343471.23829, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 24924, Read name ERR3343471.163429, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 24951, Read name ERR3343471.33530, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 24978, Read name ERR3343471.80939, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 24981, Read name ERR3343471.88186, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 24991, Read name ERR3343471.99648, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 24995, Read name ERR3343471.100587, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 25011, Read name ERR3343471.127817, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 25014, Read name ERR3343471.130157, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 25024, Read name ERR3343471.139017, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 25026, Read name ERR3343471.141762, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 25049, Read name ERR3343471.169892, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 25054, Read name ERR3343471.174099, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 25057, Read name ERR3343471.174705, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 25081, Read name ERR3343471.200491, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 25082, Read name ERR3343471.202076, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 25144, Read name ERR3343471.45927, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 25275, Read name ERR3343471.179718, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 26014, Read name ERR3343471.159539, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 29917, Read name ERR3343471.88359, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 32164, Read name ERR3343471.206745, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 35702, Read name ERR3343471.85076, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 35757, Read name ERR3343471.16800, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 35760, Read name ERR3343471.51543, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 35763, Read name ERR3343471.100177, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 35766, Read name ERR3343471.128895, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 35781, Read name ERR3343471.4411, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 35784, Read name ERR3343471.4921, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 35785, Read name ERR3343471.21722, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 35918, Read name ERR3343471.159416, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 35989, Read name ERR3343471.74630, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 37083, Read name ERR3343471.138288, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 37096, Read name ERR3343471.138715, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 37102, Read name ERR3343471.50100, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 37108, Read name ERR3343471.156228, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 37111, Read name ERR3343471.205433, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 37966, Read name ERR3343471.15356, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38009, Read name ERR3343471.74285, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38010, Read name ERR3343471.80752, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38012, Read name ERR3343471.83423, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38016, Read name ERR3343471.93601, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38018, Read name ERR3343471.176108, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38022, Read name ERR3343471.198807, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38029, Read name ERR3343471.42638, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38031, Read name ERR3343471.76000, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38034, Read name ERR3343471.101355, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38038, Read name ERR3343471.130843, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38039, Read name ERR3343471.143509, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38041, Read name ERR3343471.173673, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38044, Read name ERR3343471.194464, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38129, Read name ERR3343471.198864, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38150, Read name ERR3343471.29772, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38299, Read name ERR3343471.80680, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 38318, Read name ERR3343471.74450, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 39051, Read name ERR3343471.22140, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 39197, Read name ERR3343471.9394, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 39312, Read name ERR3343471.173242, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 40844, Read name ERR3343471.92194, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 40911, Read name ERR3343471.65167, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 41712, Read name ERR3343471.175518, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 43577, Read name ERR3343471.138391, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 44478, Read name ERR3343471.165889, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 49952, Read name ERR3343471.50360, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 55147, Read name ERR3343471.27495, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 55178, Read name ERR3343471.75683, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 63697, Read name ERR3343471.156539, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67061, Read name ERR3343471.185700, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67292, Read name ERR3343471.116655, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67326, Read name ERR3343471.147285, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67380, Read name ERR3343471.189410, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67399, Read name ERR3343471.203385, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67433, Read name ERR3343471.34254, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67474, Read name ERR3343471.87023, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67564, Read name ERR3343471.162265, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67622, Read name ERR3343471.198626, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67723, Read name ERR3343471.48661, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67729, Read name ERR3343471.80811, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67736, Read name ERR3343471.132751, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67741, Read name ERR3343471.155949, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 67745, Read name ERR3343471.188743, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 68129, Read name ERR3343471.102549, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 68393, Read name ERR3343471.25768, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 68677, Read name ERR3343471.172644, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 70090, Read name ERR3343471.186681, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 70556, Read name ERR3343471.207181, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 72631, Read name ERR3343471.125408, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 72701, Read name ERR3343471.162346, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 74193, Read name ERR3343471.158555, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 75099, Read name ERR3343471.118611, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 75365, Read name ERR3343471.57136, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 75421, Read name ERR3343471.21369, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 77775, Read name ERR3343471.23914, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 78720, Read name ERR3343471.99405, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 78724, Read name ERR3343471.138131, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 78998, Read name ERR3343471.45070, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 79394, Read name ERR3343471.640, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 79397, Read name ERR3343471.24975, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped
Maximum output of [100] errors reached.I haven't used ValidateSamFile yet and I don't know if the result is correct, but it seems to me that the job is done correctly.
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Yes, it looks like these errors you got by running it in bash are helpful enough to determine what you need in your file. Glad it is working! If you're not familiar with read groups, take a look at this article: https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
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Ok, thanks a lot.
So command is working correctly - Unfortunately this does not explain why it generates an error in my snakemake pipeline.
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Well, these are errors with your bam file, so I think the snakemate pipeline is incorrectly deleting the text file.
(ERROR::MISSING_PLATFORM_VALUE:Read name ERR3343471, A platform (PL) attribute was not found for read group)
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