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# createpanelrefs
  • m
    I'll try to steal some already processed data from sarek that way it'll be easier
  • m
    I think we can have realistically a release next week
  • r
    shared a GIF
  • a
    Hi! I'd like to create a PONs for Mutect2 using my normal samples, but I can’t find whether it’s possible to use the fastq files instead of the bams. It seems as explained in the docs that it is only possible to pass the bam or cram. Thank you!
    👀 1
    m
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  • j
    Hello all! Thank you for creating this module! Could someone give me some general guidelines for job submission on an HPC? I know everyone's environment is different but my first attempt failed when I just let slurm do whatever. I have 40 whole exome samples that I'm using to make a PON for mutect2.
    m
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    • 2
  • p
    Hi. I am trying to run this command:
  • p
    Copy code
    nextflow run nf-core/createpanelrefs -r dev  -profile singularity --input createpanelrefs_SLPD001_samplesheet.csv --tools germlinecnvcaller --genome GATK.GRCh38 --igenomes_base /data/ref/igenomes/ --outdir createpanelrefs_SLPD001_out
    With igenomes data downloaded fro aws as this:
  • p
    Copy code
    /data/ref/igenomes/Homo_sapiens/GATK/GRCh38/:
Annotation  Sequence
/data/ref/igenomes/Homo_sapiens/GATK/GRCh38/Sequence:
BWAIndex  BWAmem2Index  Chromosomes  dragmap  Length  WholeGenomeFasta
/data/ref/igenomes/Homo_sapiens/GATK/GRCh38/Annotation:
ASCAT  Control-FREEC  GATKBundle  GermlineResource  intervals  MSIsensor2  MSIsensorPro  NGSCheckMate  Sentieon
  • p
    I get this error:
    Copy code
    ERROR ~ Error executing process > 'NFCORE_CREATEPANELREFS:CREATEPANELREFS:GERMLINECNVCALLER_COHORT:GATK4_COLLECTREADCOUNTS (SLPD001)'

Caused by:
  Process `NFCORE_CREATEPANELREFS:CREATEPANELREFS:GERMLINECNVCALLER_COHORT:GATK4_COLLECTREADCOUNTS (SLPD001)` terminated with an error exit status (2)


Command executed:

  gatk --java-options "-Xmx9830M -XX:-UsePerfData" \
      CollectReadCounts \
      --input P2233_137_S2_L001_R1_001.bam \
      --intervals genome.interval_list \
      --output SLPD001.hdf5 \
      --reference Homo_sapiens_assembly38.fasta \
      --tmp-dir . \
      --format HDF5 --imr OVERLAPPING_ONLY
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CREATEPANELREFS:CREATEPANELREFS:GERMLINECNVCALLER_COHORT:GATK4_COLLECTREADCOUNTS":
      gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Using GATK jar /opt/conda/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-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 -Xmx9830M -XX:-UsePerfData -jar /opt/conda/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar CollectReadCounts --input P2233_137_S2_L001_R1_001.bam --intervals genome.interval_list --output SLPD001.hdf5 --reference Homo_sapiens_assembly38.fasta --tmp-dir . --format HDF5 --imr OVERLAPPING_ONLY
  09:28:39.258 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/conda/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
  09:28:39.669 INFO  CollectReadCounts - ------------------------------------------------------------
  09:28:39.674 INFO  CollectReadCounts - The Genome Analysis Toolkit (GATK) v4.6.2.0
  09:28:39.675 INFO  CollectReadCounts - For support and documentation go to <https://software.broadinstitute.org/gatk/>
  09:28:39.675 INFO  CollectReadCounts - Executing as peter@monod33.mbb.ki.se on Linux v4.18.0-553.53.1.el8_10.x86_64 amd64
  09:28:39.675 INFO  CollectReadCounts - Java runtime: OpenJDK 64-Bit Server VM v17.0.11-internal+0-adhoc..src
  09:28:39.676 INFO  CollectReadCounts - Start Date/Time: December 2, 2025 at 9:28:39 AM GMT
  09:28:39.676 INFO  CollectReadCounts - ------------------------------------------------------------
  09:28:39.676 INFO  CollectReadCounts - ------------------------------------------------------------
  09:28:39.677 INFO  CollectReadCounts - HTSJDK Version: 4.2.0
  09:28:39.678 INFO  CollectReadCounts - Picard Version: 3.4.0
  09:28:39.678 INFO  CollectReadCounts - Built for Spark Version: 3.5.0
  09:28:39.680 INFO  CollectReadCounts - HTSJDK Defaults.COMPRESSION_LEVEL : 2
  09:28:39.680 INFO  CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
  09:28:39.681 INFO  CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
  09:28:39.681 INFO  CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
  09:28:39.681 INFO  CollectReadCounts - Deflater: IntelDeflater
  09:28:39.681 INFO  CollectReadCounts - Inflater: IntelInflater
  09:28:39.681 INFO  CollectReadCounts - GCS max retries/reopens: 20
  09:28:39.681 INFO  CollectReadCounts - Requester pays: disabled
  09:28:39.682 INFO  CollectReadCounts - Initializing engine
  09:28:40.325 INFO  FeatureManager - Using codec IntervalListCodec to read file <file://genome.interval>_list
  09:28:49.587 INFO  IntervalArgumentCollection - Processing 3043969085 bp from intervals
  09:28:49.710 INFO  CollectReadCounts - Done initializing engine
  09:28:49.718 WARN  CollectReadCounts - Sequence dictionary in BAM does not match the master sequence dictionary.
  09:28:49.720 INFO  CollectReadCounts - Collecting read counts...
  09:28:49.721 INFO  ProgressMeter - Starting traversal
  09:28:49.721 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
  09:28:49.844 INFO  CollectReadCounts - Shutting down engine
  [December 2, 2025 at 9:28:49 AM GMT] org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts done. Elapsed time: 0.18 minutes.
  Runtime.totalMemory()=2088763392
  ***********************************************************************
  
  A USER ERROR has occurred: Contig chr1_KI270706v1_random not present in reads sequence dictionary
  
  ***********************************************************************
  Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Work dir:
  /datf/sl/users/ivana/BTB/raredisease/work/ef/f478d93adf8dfe766525651d998d6e

Container:  /datf/sl/users/ivana/BTB/raredisease/work/singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-ce-ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0-data.img
    This happens even though I removed all alignments to 'chr1_KI270706v1_random' from my bam files.
    m
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  • d
    createpanelrefs is also experiencing the issue described here for nf-core/rnaseq when running without using igenomes: https://github.com/nf-core/rnaseq/issues/1690 The workaround described there is a temp fix on the user end; add this to config file: 
    validation.ignoreParams = ["igenomes_base"]
    👀 1
    m
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  • f
    ❌ createpanelrefs/createpanelrefs/test_full failed 😿 Run Name big_booth_4 Duration 8h 4m 58s Status ❌ Failed Error Message
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    (more omitted..)
15:38:59.437 INFO  ProgressMeter -       chr12:87223728            464.2              10161430          21888.9
15:39:09.441 INFO  ProgressMeter -       chr12:87893586            464.4              10165030          21888.8
15:39:19.449 INFO  ProgressMeter -       chr12:88884727            464.6              10169430          21890.4
15:39:29.449 INFO  ProgressMeter -       chr12:89762698            464.7              10173550          21891.4
15:39:39.478 INFO  ProgressMeter -       chr12:90596435            464.9              10177530          21892.1
15:39:49.478 INFO  ProgressMeter -       chr12:91305121            465.1              10180900          21891.5
15:39:59.483 INFO  ProgressMeter -       chr12:92029896            465.2              10184590          21891.6
15:40:09.490 INFO  ProgressMeter -       chr12:92752742            465.4              10188300          21891.7
15:40:19.502 INFO  ProgressMeter -       chr12:93532336            465.6              10192260          21892.4
15:40:29.505 INFO  ProgressMeter -       chr12:94463985            465.7              10196600          21893.8
15:40:39.511 INFO  ProgressMeter -       chr12:95072513            465.9              10200090          21893.5
15:40:49.526 INFO  ProgressMeter -       chr12:95711298            466.1              10203660          21893.3
15:40:59.541 INFO  ProgressMeter -       chr12:96551243            466.2              10207680          21894.1
15:41:09.547 INFO  ProgressMeter -       chr12:97319239            466.4              10211450          21894.4
15:41:19.547 INFO  ProgressMeter -       chr12:98131117            466.6              10215420          21895.0
15:41:29.551 INFO  ProgressMeter -       chr12:98968423            466.7              10219510          21896.0
15:41:39.558 INFO  ProgressMeter -       chr12:99746594            466.9              10223370          21896.4
15:41:49.571 INFO  ProgressMeter -      chr12:100840323            467.1       ...
    Command Line
    Copy code
    nextflow run '<https://github.com/nf-core/createpanelrefs>' -name big_booth_4 -params-file '<https://api.cloud.seqera.io/ephemeral/TQcBY8Dklvqa-wbNE7fgjg.json>' -with-tower -r dev -profile test_full -resume eb25704c-0764-40b9-b2e1-076448793b8e -latest
    Apr 17, 2026 at 3:56 PM 🔗 View in Seqera Platform button
    🚫 1
  • f
    ❌ createpanelrefs/createpanelrefs/test_full failed 😿 Run Name big_booth_5 Duration 21h 55m 46s Status ❌ Failed Error Message
    Copy code
    (more omitted..)
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 -Xmx4915M -XX:-UsePerfData -jar /opt/conda/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar GenomicsDBImport --variant HCC1395N.vcf.gz --variant NA12878.vcf.gz --genomicsdb-workspace-path null --intervals genome.bed --tmp-dir .
06:02:35.686 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/conda/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
06:02:35.825 INFO  GenomicsDBImport - ------------------------------------------------------------
06:02:35.827 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.6.2.0
06:02:35.827 INFO  GenomicsDBImport - For support and documentation go to <https://software.broadinstitute.org/gatk/>
06:02:35.827 INFO  GenomicsDBImport - Executing as root@ip-172-31-21-134.eu-west-1.compute.internal on Linux v6.1.166-197.305.amzn2023.x86_64 amd64
06:02:35.827 INFO  GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v17.0.11-internal+0-adhoc..src
06:02:35.827 INFO  GenomicsDBImport - Start Date/Time: April 22, 2026 at 6:02:35 AM GMT
06:02:35.828 INFO  GenomicsDBImport - ------------------------------------------------------------
06:02:35.828 INFO  GenomicsDBImport - ------------------------------------------------------------
06:02:35.828 INFO  GenomicsDBImport - HTSJDK Version: 4.2.0
06:02:35.828 INFO  GenomicsDBImport - Picard Version: 3.4.0
06:02:35.828 INFO  GenomicsDBImport - Built for Spark Version: 3.5.0
06:02:35.830 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
06:02:35.830 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
06:02:35.830 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
06:02:35.830 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
06...
    Command Line
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    nextflow run '<https://github.com/nf-core/createpanelrefs>' -name big_booth_5 -params-file '<https://api.cloud.seqera.io/ephemeral/oqFFR8l_QIWW8GLEg6yLhw.json>' -with-tower -r dev -profile test_full -resume eb25704c-0764-40b9-b2e1-076448793b8e -latest
    Apr 22, 2026 at 6:02 AM 🔗 View in Seqera Platform button
  • r
    Don't like the failures, but I love the notifications 😆
    💯 1
  • m
    yeah, it looks amazing
  • j
    To me, it would be something to add to the template
  • m
    It is in, that will come with the new template
    ❤️ 1
  • m
  • m
    yeah, I am just trying things out, you know me
  • f
    ❌ createpanelrefs/test_full failed 😿 Run Name spontaneous_cantor Duration 24.7s Status ❌ Failed Error Message
    Copy code
    The following invalid input values have been detected:

* --input (<https://raw.githubusercontent.com/nf-core/test-datasets/createpanelrefs/csv/1.0/recal_cram_sarek.csv>): Validation of file failed:
	-> Entry 1: Error for field 'crai' (<s3://nf-core-awsmegatests/sarek/results-4bd2948f98c5bf7b785c91cf6708fffccab...ull_germline_aws/preprocessing/recalibrated/NA12878/NA12878.recal.cram.crai>): the file or directory '<s3://nf-core-awsmegatests/sarek/results-4bd2948f98c5bf7b785c91cf6708fffccab25467/test_full_germline_aws/preprocessing/recalibrated/NA12878/NA12878.recal.cram.crai>' does not exist (CRAM index file cannot contain spaces and must have extension '.crai')
	-> Entry 2: Error for field 'crai' (<s3://nf-core-awsmegatests/sarek/results-4bd2948f98c5bf7b785c91cf6708fffccab.../test_full_aws/preprocessing/recalibrated/HCC1395N/HCC1395N.recal.cram.crai>): the file or directory '<s3://nf-core-awsmegatests/sarek/results-4bd2948f98c5bf7b785c91cf6708fffccab25467/test_full_aws/preprocessing/recalibrated/HCC1395N/HCC1395N.recal.cram.crai>' does not exist (CRAM index file cannot contain spaces and must have extension '.crai')
    Command Line
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    nextflow run '<https://github.com/nf-core/createpanelrefs>' -name spontaneous_cantor -params-file '<https://api.cloud.seqera.io/ephemeral/KysJ0eSZPgGhAo2q9WsrXA.json>' -with-tower -r 8e82d2b5a0fa3cdf1c8ef0da536136d6584718dd -profile test_full
    May 19, 2026 at 3:41 PM
    🫠 1
  • f
    ❌ createpanelrefs/test_full failed 😿 Run Name pensive_mclean Duration 1h 5m 55s Status ❌ Failed Error Message
    Copy code
    (more omitted..)
14:40:08.675 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/conda/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
14:40:08.768 INFO  GenomicsDBImport - ------------------------------------------------------------
14:40:08.770 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.6.2.0
14:40:08.771 INFO  GenomicsDBImport - For support and documentation go to <https://software.broadinstitute.org/gatk/>
14:40:08.771 INFO  GenomicsDBImport - Executing as root@ip-172-31-28-229.eu-west-1.compute.internal on Linux v6.1.166-197.305.amzn2023.x86_64 amd64
14:40:08.771 INFO  GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v17.0.11-internal+0-adhoc..src
14:40:08.771 INFO  GenomicsDBImport - Start Date/Time: June 3, 2026 at 2:40:08 PM GMT
14:40:08.771 INFO  GenomicsDBImport - ------------------------------------------------------------
14:40:08.771 INFO  GenomicsDBImport - ------------------------------------------------------------
14:40:08.772 INFO  GenomicsDBImport - HTSJDK Version: 4.2.0
14:40:08.772 INFO  GenomicsDBImport - Picard Version: 3.4.0
14:40:08.772 INFO  GenomicsDBImport - Built for Spark Version: 3.5.0
14:40:08.774 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:40:08.774 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:40:08.774 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:40:08.774 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:40:08.774 INFO  GenomicsDBImport - Deflater: IntelDeflater
14:40:08.774 INFO  GenomicsDBImport - Inflater: IntelInflater
14:40:08.774 INFO  GenomicsDBImport - GCS max retries/reopens: 20
14:40:08.774 INFO  GenomicsDBImport - Requester pays: disabled
14:40:08.775 INFO  GenomicsDBImport - Initializing engine
14:40:09.114 INFO  FeatureManager - Using codec BEDCodec to read file file:///fusion/s3/nf-core-aw...
    Command Line
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    nextflow run '<https://github.com/nf-core/createpanelrefs>' -name pensive_mclean -params-file '<https://api.cloud.seqera.io/ephemeral/QTfJX5MCeHz-p8D1n8EKzQ.json>' -with-tower -r 4747dcb35ee6b1e24efcbe38b5e516375e186101 -profile test_full
    Jun 3, 2026 at 2:40 PM
    🚫 1
    m
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    • 1
  • f
    ✅ createpanelrefs/test_full completed successfully! 🎉 Run Name pensive_mclean_3 Duration 2h 37m 3s Status ✅ Success Tasks Cached: 54, Completed: 10, Failed: 1 Jun 4, 2026 at 10:52 AM
    🤩 1
    m
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    • 1
  • m
    <!here> WE FINALLY have a release: https://github.com/nf-core/createpanelrefs/releases/tag/1.0.0 It took only 3 years. Thanks to ALL of you: @Ram, @Francesco Lescai, @Anders Jemt, @Felix Lenner, @Daniel Mendoza, @Matthias De Smet, @Nicolas Vannieuwkerke, @Rike Hanssen...
    🎉 3
    extreme teamwork 4
    m
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  • f
    ❌ createpanelrefs/test_full failed 😿 Run Name festering_kimura Duration 1h 35m 46s Status ❌ Failed Error Message
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    9:26AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
9:31AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
9:36AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
9:41AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
9:46AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
9:51AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
9:56AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
10:01AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
10:06AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
10:11AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
10:12AM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 400, RequestID: Y4E355EKSA8MVC4W, HostID: iG0D2rsnSbTFiouBWDWA9j125BxUkXo6W9phx/pYCds1KhUUlog1fCAweVxvOlSKvweAuOv/0wY=, api error InvalidRequest: The specified copy source is larger than the maximum allowable size for a copy source: 5368709120" goid=257604 id=/s3/nf-core-awsmegatests/work/createpanelrefs/work-dev/ae/fdd3f3ded75cc20ee04d871b80ab4f/NA12878.bam length=26440892416 offset=0
10:12AM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=258023 id=/s3/nf-core-awsmegatests/work/createpanelrefs/work-dev/ae/fdd3f3ded75cc20ee04d871b80ab4f/NA12878.bam.d8j8i88ie12s76ka83r0.28856811520.d8j8gt8ie12s76ka80og.chk length=134217728 offset=0
10:12AM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=257607 id=/s3/nf-core-awsmegatests/work/createpanelrefs/work-dev/ae/fdd3f3ded75cc20ee04d871b80ab4f/NA12878.bam.d8j8h3oie12s76ka838g.26709327872.d8j8gt8ie12s76k...
    Command Line
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    nextflow run '<https://github.com/nf-core/createpanelrefs>' -name festering_kimura -params-file '<https://api.cloud.seqera.io/ephemeral/Vav4s96phov0bf8C7yWQbA.json>' -with-tower -r dev -profile test_full
    Jun 8, 2026 at 10:13 AM
    😭 2
  • f
    ✅ createpanelrefs/test_full completed successfully! 🎉 Run Name distraught_venter Duration 2h 36m 55s Status ✅ Success Tasks Completed: 64, Failed: 3 Jun 8, 2026 at 11:31 AM
    🎉 1
  • f
    ❌ createpanelrefs/test_full failed 😿 Run Name festering_kimura_2 Duration 1h 35m 36s Status ❌ Failed Error Message
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    12:32PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
12:32PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-0fc0777c66c2e4720 instance-type=c6id.8xlarge
12:32PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
12:37PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
12:42PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
12:47PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
12:52PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
12:57PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
1:02PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
1:07PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
1:10PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 400, RequestID: VRT6C6S5NXABG7B6, HostID: pCVeIRWjaW6fgRn2nEAT6TLLGujHiajNyriKWCQUIT0masJoC7fd8lK0j08nFTcA3ruCpotRyp4=, api error InvalidRequest: The specified copy source is larger than the maximum allowable size for a copy source: 5368709120" goid=188149 id=/s3/nf-core-awsmegatests/work/createpanelrefs/work-dev/26/2da35f670ba27e20c01f4b78248ea7/NA12878.bam length=40533753856 offset=0
1:10PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=188174 id=/s3/nf-core-awsmegatests/work/createpanelrefs/work-dev/26/2da35f670ba27e20c01f4b78248ea7/NA12878.bam.d8jbef807fsc75bk05q0.43754979328.d8jbcm807fsc75bk01qg.chk length=134217728 offset=0
1:10PM ERR [seqera-fusion] cannot upload part copy error="operation error S3: UploadPartCopy, https response error StatusCode: 0, RequestID: , HostID: , canceled, context canceled" goid=188154 id=/s3/nf-core-awsmegatests/work/createpanelrefs/work-dev/26/2da3...
    Command Line
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    nextflow run '<https://github.com/nf-core/createpanelrefs>' -name festering_kimura_2 -params-file '<https://api.cloud.seqera.io/ephemeral/7Rz29GBcHxkK5mmrCYNKIQ.json>' -with-tower -r 236c3d0eca4b5908f65b2f70bf4dbb937f742333 -profile test_full -resume a1706507-e102-4af8-a2dc-b1d524cb041c
    Jun 8, 2026 at 1:11 PM
    🚫 1
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    ❌ createpanelrefs/test_full failed 😿 Run Name admiring_brown Duration 18.8s Status ❌ Failed Error Message
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    Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/createpanelrefs>, projectDir: /.nextflow/assets/.repos/nf-core/createpanelrefs/clones/78e462842a0f2d4548e5886e8b9954b48cad1ce3, commitId: 78e462842a0f2d4548e5886e8b9954b48cad1ce3, revision: dev, startTime: 2026-11-02T10:14:40.626534332Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/createpanelrefs>' -name admiring_brown -params-file '<https://api.cloud.seqera.io/ephemeral/feW3J1NlyPykEoOmHZS91g.json>' -with-tower -r dev -profile test_full, nextflow: nextflow.NextflowMeta(version:26.04.7, build:13988, timestamp:08-10-2026 16:23 UTC, preview:nextflow.NextflowMeta$Preview@26864891, enable:nextflow.NextflowMeta$Features@5946e540, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/createpanelrefs/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?
    Command Line
    Copy code
    nextflow run '<https://github.com/nf-core/createpanelrefs>' -name admiring_brown -params-file '<https://api.cloud.seqera.io/ephemeral/feW3J1NlyPykEoOmHZS91g.json>' -with-tower -r dev -profile test_full
    Nov 2, 2026 at 10:15 AM
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    ✅ createpanelrefs/test_full completed successfully! 🎉 Run Name fabulous_pike Duration 2h 56m 53s Status ✅ Success Tasks Completed: 64, Failed: 5 Nov 2, 2026 at 4:09 PM
  • m
    nf core scroll nf-core/createpanelrefs 1.1.0 (Abisko 🇸🇪 ❄️) is out! https://github.com/nf-core/createpanelrefs/releases/tag/1.1.0 What's new: • CNVkit: 
    --cnvkit_method
    (
    hybrid
    , 
    amplicon
    or 
    wgs
    , default 
    wgs
    ) for exome, panel and amplicon panels of normals, and 
    --cnvkit_annotate
    to label target regions with gene names (both need 
    --cnvkit_targets
    for targeted methods) • GENS: 
    --gens_mosdepth_fast_mode
    to turn mosdepth 
    --fast-mode
    on or off for long-read (
    lrs
    ) panels of normals • Tools used are now AUTOMATICALLY cited in the MultiQC methods description, built from the modules' metadata • Updated tools: CNVkit 0.9.14, GATK4 4.7.0.0, samtools 1.24 • nf-core template 4.2.1, nf-core-utils 0.7.0, plus a metro map of the pipeline in the README Thanks to @Matthias De Smet, @mashehu, @Nicolas Vannieuwkerke, @Evangelos Karatzas, @Daniel Lundin, @Famke Bäuerle and @Rike Hanssen for all comments, discussions and reviews 🙏
    👌 2
    🙌 2
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    ✅ createpanelrefs/test_full completed successfully! 🎉 Run Name trusting_wiles Duration 2h 45m 3s Status ✅ Success Tasks Completed: 64, Failed: 3 Nov 3, 2026 at 1:18 PM
    🎉 1
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    ✅ createpanelrefs/test_full completed successfully! 🎉 Run Name nostalgic_kowalevski Duration 2h 44m 36s Status ✅ Success Tasks Completed: 64, Failed: 4 Nov 3, 2026 at 3:37 PM