mitochondria_m2_wdl: MitochondriaPipeline Issues
Hey everyone,
i'm student of the ExBio Lab of TUM & new to using GATK. I'm having issues with running the Mitochondrial Pipeline locally.
Versions:
Cromwell: cromwell-51.jar
GATK: gatk.4.1.8.0
Command:
"java -jar cromwell-51.jar run ./mitochondria_m2_wdl/MitochondriaPipeline.wdl --inputs ./mitochondria_m2_wdl/ExampleInputsMitochondriaPipeline.json"
Output:
"Call input and runtime attributes evaluation failed for SubsetBamToChrM:
Failed to evaluate input 'disk_size' (reason 1 of 1): ValueEvaluator[IdentifierLookup]: No suitable input for 'ref_size' amongst {gatk_override,....}
Failed to evaluate input 'ref_size' (reason 1 of 1): java.lang.IllegalArgumentException: Could not build the path "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict". It may refer to a filesystem not supported by this instance of Cromwell. Supported filesystems are: HTTP, LinuxFileSystem."
As suggested in the docs, in the inputs.json file i'm providing the bam (& bai) file and also a reference fasta (&.fa.fai) file.
Apparently the pipeline is complaining about the gs:// default paths (for e.g. ref_dict ) in the inputs.json that it shouldn't require or need.
Is there anything else (other than of course the inputs.json file) that I should edit for the pipeline to work?
Any suggestions are much apprechiated,
Thanks!
-
Hi Valentin
I think the first error is associated with your second error. The workflow attempts to automatically predict the amount of disk size a user needs when running on the cloud so it does some calculations to obtain the size of the input files. However its having trouble getting the size of the input files because of the second error. You aren't running on the cloud but the workflow is setup to still do this regardless.
Failed to evaluate input 'disk_size' (reason 1 of 1): ValueEvaluator[IdentifierLookup]:
No suitable input for 'ref_size' amongst {gatk_override,....}In the second error cromwell is again having trouble with the input file because your command is running the workflow locally so its expecting input files from your local file system however the inputs you provided are from a google bucket (gs://) so its having trouble interpreting or finding the file.
Failed to evaluate input 'ref_size' (reason 1 of 1): java.lang.IllegalArgumentException:
Could not build the path "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict".
It may refer to a filesystem not supported by this instance of Cromwell.
Supported filesystems are: HTTP, LinuxFileSystem."If you plan on running the workflow locally you'll need to download all the files to your local computer and update the file paths in the input json.
-
Thanks Beri,
So ALL files in the inputs.json need to be downloaded, that's something i wasn't aware of. However in the various google cloud buckets mentioned in the tutorials I could find the needed mitochondrial fasta.ann, fasta.bwt, chrM.dict ,..., files. Also in none of these buckets I found shifted files.
Where or in which google cloud bucket could i find these files?
Thanks a lot.
-
Hi Valentin,
You'll find the files in the gs://gcp-public-data--broad-references/hg30/v0/chrM bucket.
-
Hi Beri ,
thanks for the quick help! Now running the pipeline my stderr.background file looks as follows:
"
INFO: Failed to detect whether we are running on Google Compute Engine.
10:21:45.788 INFO PrintReads - ------------------------------------------------------------
10:21:45.788 INFO PrintReads - The Genome Analysis Toolkit (GATK) v4.1.7.0
10:21:45.788 INFO PrintReads - For support and documentation go to https://software.broadinstitute.org/gatk/
10:21:45.789 INFO PrintReads - Executing as root@dc8377224dad on Linux v5.3.0-59-generic amd64
10:21:45.789 INFO PrintReads - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03
10:21:45.789 INFO PrintReads - Start Date/Time: August 5, 2020 10:21:45 AM UTC
10:21:45.789 INFO PrintReads - ------------------------------------------------------------
10:21:45.789 INFO PrintReads - ------------------------------------------------------------
10:21:45.789 INFO PrintReads - HTSJDK Version: 2.21.2
10:21:45.789 INFO PrintReads - Picard Version: 2.21.9
10:21:45.789 INFO PrintReads - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:21:45.789 INFO PrintReads - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:21:45.789 INFO PrintReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:21:45.789 INFO PrintReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:21:45.790 INFO PrintReads - Deflater: IntelDeflater
10:21:45.790 INFO PrintReads - Inflater: IntelInflater
10:21:45.790 INFO PrintReads - GCS max retries/reopens: 20
10:21:45.790 INFO PrintReads - Requester pays: disabled
10:21:45.790 INFO PrintReads - Initializing engine
10:21:46.084 INFO PrintReads - Shutting down engine
[August 5, 2020 10:21:46 AM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2162163712
***********************************************************************A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "chrM" is not valid for this input.
***********************************************************************
"
How do I fix this User error, as I don't know which of my inputs could be badly formed? I've seen this error in Biostar issues, but not when running the mitochondrial pipeline.
Thanks for the great help.
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That error is coming from one of the GATK tools (PrintReads), you may want to look through the gatk forum for a solution like this thread: https://gatk.broadinstitute.org/hc/en-us/community/posts/360057802492
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Thanks Beri,
indeed the thread solved that problem. What now came to me that the bam file (SRA ID: SRR4420337) i am trying to use has no read groups declared, and no @RG line in it's header.
This is probably the cause for :
"
09:35:13.257 INFO Mutect2 - ------------------------------------------------------------
09:35:13.257 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.1.7.0
09:35:13.257 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
09:35:13.257 INFO Mutect2 - Executing as root@9cf1fc8169e7 on Linux v5.3.0-59-generic amd64
09:35:13.257 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03
09:35:13.258 INFO Mutect2 - Start Date/Time: August 26, 2020 9:35:12 AM UTC
09:35:13.258 INFO Mutect2 - ------------------------------------------------------------
09:35:13.258 INFO Mutect2 - ------------------------------------------------------------
09:35:13.258 INFO Mutect2 - HTSJDK Version: 2.21.2
09:35:13.258 INFO Mutect2 - Picard Version: 2.21.9
09:35:13.258 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
09:35:13.258 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:35:13.258 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:35:13.258 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:35:13.258 INFO Mutect2 - Deflater: IntelDeflater
09:35:13.258 INFO Mutect2 - Inflater: IntelInflater
09:35:13.259 INFO Mutect2 - GCS max retries/reopens: 20
09:35:13.259 INFO Mutect2 - Requester pays: disabled
09:35:13.259 INFO Mutect2 - Initializing engine
09:35:13.753 INFO IntervalArgumentCollection - Processing 1120 bp from intervals
09:35:13.759 INFO Mutect2 - Done initializing engine
09:35:13.776 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
09:35:13.793 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
09:35:13.862 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
09:35:13.862 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
09:35:13.863 INFO IntelPairHmm - Available threads: 160
09:35:13.863 INFO IntelPairHmm - Requested threads: 4
09:35:13.863 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
09:35:13.865 INFO Mutect2 - Shutting down engine
[August 26, 2020 9:35:13 AM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2287468544
java.lang.IllegalArgumentException: samples cannot be empty
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:727)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel.<init>(ReferenceConfidenceModel.java:119)
at org.broadinstitute.hellbender.tools.walkers.mutect.SomaticReferenceConfidenceModel.<init>(SomaticReferenceConfidenceModel.java:37)
at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.<init>(Mutect2Engine.java:145)
at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2.onTraversalStart(Mutect2.java:261)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1046)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR"
Now I know that picard has this utility to AddOrReplaceReadgroups, which however hasn't worked out for me. Do you know of any other way to solve this?
Thanks a lot.
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Hi Valentin, read groups are necessary for using GATK, you can find more information here: https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups. We have a tool AddOrReplaceReadGroups that can help you add them: https://gatk.broadinstitute.org/hc/en-us/articles/360047217751-AddOrReplaceReadGroups-Picard-
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Greetings, I'm trying to run the MitochondriaPipeline:4.1.8.0 on AnVIL using CRAM files from AnVIL_GTEx_V8_hg38. The error I get is that the .bai index file does not exist. Any help is greatly appreciated. See the following error:
2021/03/22 14:29:39 Starting container setup.
2021/03/22 14:29:42 Done container setup.
2021/03/22 14:29:46 Starting localization.
2021/03/22 14:29:58 Localization script execution started...
2021/03/22 14:29:58 Localizing input gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -> /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta
2021/03/22 14:30:42 Localizing input gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict -> /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict
2021/03/22 14:30:42 Localizing input gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai -> /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai
Copying gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict...
/ [0 files][ 0.0 B/568.1 KiB]
/ [1 files][568.1 KiB/568.1 KiB]
Copying gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai...
/ [1 files][568.1 KiB/725.2 KiB]
/ [2 files][725.2 KiB/725.2 KiB]
Operation completed over 2 objects/725.2 KiB.
2021/03/22 14:30:43 Localizing input gs://fc-secure-cfb8308a-9e6f-48fb-949b-644874909598/ee690d7f-44d9-40de-bcfb-d15fea591e84/MitochondriaPipeline/86253698-8eae-47bd-a025-c4f11505c275/call-SubsetBamToChrM/script -> /cromwell_root/script
2021/03/22 14:30:45 Localization script execution complete.
2021/03/22 14:30:50 Done localization.
2021/03/22 14:30:51 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint=/bin/bash us.gcr.io/broad-gatk/gatk@sha256:192fedf9b9d65809da4a2954030269e3f311d296e6b5e4c6c7deec12c7fe84b2 /cromwell_root/script
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.c329fc7e
14:31:04.261 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
14:31:05.354 INFO PrintReads - ------------------------------------------------------------
14:31:05.354 INFO PrintReads - The Genome Analysis Toolkit (GATK) v4.1.7.0
14:31:05.354 INFO PrintReads - For support and documentation go to https://software.broadinstitute.org/gatk/
14:31:05.354 INFO PrintReads - Executing as root@0fea9a618abd on Linux v5.4.89+ amd64
14:31:05.355 INFO PrintReads - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03
14:31:05.355 INFO PrintReads - Start Date/Time: March 22, 2021 2:31:03 PM UTC
14:31:05.355 INFO PrintReads - ------------------------------------------------------------
14:31:05.355 INFO PrintReads - ------------------------------------------------------------
14:31:05.357 INFO PrintReads - HTSJDK Version: 2.21.2
14:31:05.357 INFO PrintReads - Picard Version: 2.21.9
14:31:05.358 INFO PrintReads - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:31:05.358 INFO PrintReads - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:31:05.358 INFO PrintReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:31:05.359 INFO PrintReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:31:05.359 INFO PrintReads - Deflater: IntelDeflater
14:31:05.359 INFO PrintReads - Inflater: IntelInflater
14:31:05.359 INFO PrintReads - GCS max retries/reopens: 20
14:31:05.360 INFO PrintReads - Requester pays: disabled
14:31:05.360 INFO PrintReads - Initializing engine
14:31:07.556 INFO PrintReads - Shutting down engine
[March 22, 2021 2:31:07 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=48758784
code: 400
message: Bucket is requester pays bucket but no user project provided.
reason: required
location: null
retryable: false
com.google.cloud.storage.StorageException: Bucket is requester pays bucket but no user project provided.
at com.google.cloud.storage.spi.v1.HttpStorageRpc.translate(HttpStorageRpc.java:229)
at com.google.cloud.storage.spi.v1.HttpStorageRpc.get(HttpStorageRpc.java:439)
at com.google.cloud.storage.StorageImpl$5.call(StorageImpl.java:242)
at com.google.cloud.storage.StorageImpl$5.call(StorageImpl.java:239)
at shaded.cloud_nio.com.google.api.gax.retrying.DirectRetryingExecutor.submit(DirectRetryingExecutor.java:105)
at shaded.cloud_nio.com.google.cloud.RetryHelper.run(RetryHelper.java:76)
at shaded.cloud_nio.com.google.cloud.RetryHelper.runWithRetries(RetryHelper.java:50)
at com.google.cloud.storage.StorageImpl.get(StorageImpl.java:238)
at com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider.checkAccess(CloudStorageFileSystemProvider.java:736)
at java.nio.file.Files.exists(Files.java:2385)
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:497)
at org.broadinstitute.hellbender.engine.ReadsDataSource.<init>(ReadsDataSource.java:218)
at org.broadinstitute.hellbender.engine.ReadsDataSource.<init>(ReadsDataSource.java:175)
at org.broadinstitute.hellbender.engine.GATKTool.initializeReads(GATKTool.java:455)
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:704)
at org.broadinstitute.hellbender.engine.ReadWalker.onStartup(ReadWalker.java:50)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
Caused by: shaded.cloud_nio.com.google.api.client.googleapis.json.GoogleJsonResponseException: 400 Bad Request
{
"code" : 400,
"errors" : [ {
"domain" : "global",
"message" : "Bucket is requester pays bucket but no user project provided.",
"reason" : "required"
} ],
"message" : "Bucket is requester pays bucket but no user project provided."
}
at shaded.cloud_nio.com.google.api.client.googleapis.json.GoogleJsonResponseException.from(GoogleJsonResponseException.java:150)
at shaded.cloud_nio.com.google.api.client.googleapis.services.json.AbstractGoogleJsonClientRequest.newExceptionOnError(AbstractGoogleJsonClientRequest.java:113)
at shaded.cloud_nio.com.google.api.client.googleapis.services.json.AbstractGoogleJsonClientRequest.newExceptionOnError(AbstractGoogleJsonClientRequest.java:40)
at shaded.cloud_nio.com.google.api.client.googleapis.services.AbstractGoogleClientRequest$1.interceptResponse(AbstractGoogleClientRequest.java:451)
at shaded.cloud_nio.com.google.api.client.http.HttpRequest.execute(HttpRequest.java:1089)
at shaded.cloud_nio.com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:549)
at shaded.cloud_nio.com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:482)
at shaded.cloud_nio.com.google.api.client.googleapis.services.AbstractGoogleClientRequest.execute(AbstractGoogleClientRequest.java:599)
at com.google.cloud.storage.spi.v1.HttpStorageRpc.get(HttpStorageRpc.java:436)
... 20 more
Using GATK jar /root/gatk.jar defined in environment variable GATK_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 /root/gatk.jar PrintReads -R /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -L chrM --read-filter MateOnSameContigOrNoMappedMateReadFilter --read-filter MateUnmappedAndUnmappedReadFilter -I gs://fc-secure-ff8156a3-ddf3-42e4-9211-0fd89da62108/GTEx_Analysis_2017-06-05_v8_WGS_CRAM_files/GTEX-1117F-0003-SM-6WBT7.cram --read-index gs://fc-secure-ff8156a3-ddf3-42e4-9211-0fd89da62108/GTEx_Analysis_2017-06-05_v8_WGS_CRAM_files/GTEX-1117F-0003-SM-6WBT7.crai -O GTEX-1117F-0003-SM-6WBT7.bam
2021/03/22 14:31:09 Starting delocalization.
2021/03/22 14:31:10 Delocalization script execution started...
2021/03/22 14:31:10 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-secure-cfb8308a-9e6f-48fb-949b-644874909598/ee690d7f-44d9-40de-bcfb-d15fea591e84/MitochondriaPipeline/86253698-8eae-47bd-a025-c4f11505c275/call-SubsetBamToChrM/memory_retry_rc
2021/03/22 14:31:10 Delocalizing output /cromwell_root/rc -> gs://fc-secure-cfb8308a-9e6f-48fb-949b-644874909598/ee690d7f-44d9-40de-bcfb-d15fea591e84/MitochondriaPipeline/86253698-8eae-47bd-a025-c4f11505c275/call-SubsetBamToChrM/rc
2021/03/22 14:31:11 Delocalizing output /cromwell_root/stdout -> gs://fc-secure-cfb8308a-9e6f-48fb-949b-644874909598/ee690d7f-44d9-40de-bcfb-d15fea591e84/MitochondriaPipeline/86253698-8eae-47bd-a025-c4f11505c275/call-SubsetBamToChrM/stdout
2021/03/22 14:31:12 Delocalizing output /cromwell_root/stderr -> gs://fc-secure-cfb8308a-9e6f-48fb-949b-644874909598/ee690d7f-44d9-40de-bcfb-d15fea591e84/MitochondriaPipeline/86253698-8eae-47bd-a025-c4f11505c275/call-SubsetBamToChrM/stderr
2021/03/22 14:31:13 Delocalizing output /cromwell_root/GTEX-1117F-0003-SM-6WBT7.bai -> gs://fc-secure-cfb8308a-9e6f-48fb-949b-644874909598/ee690d7f-44d9-40de-bcfb-d15fea591e84/MitochondriaPipeline/86253698-8eae-47bd-a025-c4f11505c275/call-SubsetBamToChrM/GTEX-1117F-0003-SM-6WBT7.bai
Required file output '/cromwell_root/GTEX-1117F-0003-SM-6WBT7.bai' does not exist.
Update:
I fixed the error by adding "gtex-mt-snps" as the attribute for the requester_pays_project variable.
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I fixed the error by adding "gtex-mt-snps" as the attribute for the requester_pays_project variable.
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Thanks for sharing your fix!
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My pleasure Beri!
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I'm running the MitochondriaPipeline on a participant_set of 259 participant cram files within the AnVIL_GTEx_V8_hg38 workspace that I cloned to my workspace but I get the following error:
[
0:{
}"message":"Call input and runtime attributes evaluation failed for SubsetBamToChrM""causedBy":[]0:{}"message":"Failed to evaluate input 'disk_size' (reason 1 of 1): [Attempted 1 time(s)] - FileNotFoundException: gs://fc-secure-cfb8308a-9e6f-48fb-949b-644874909598/809ecf2f-12c2-41bc-86d1-9c5461c07eac/MitochondriaPipeline/ae5c7a96-3bee-4bf1-9d0e-ef808599c6b6/call-SubsetBamToChrM/1-MitochondriaPipeline_259_GTEx_breast_participants"]
For the SubsetBamToChrM Task Name, I used the participant_set name "1-MitochondriaPipeline_259_GTEx_breast_participants" as the basename attribute.
Googling the parts of this error finds a GATK comment page that suggests some data for one or more of the participants are not found. Apparently, at dbGaP only 207 of the 259 participants have cram files. Would that explain this error? How can I check if all 259 participant IDs have cram and cram_index files on Terra?
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