Execution cancelled -- Finishing pending tasks before exit
WARN: Input tuple does not match input set cardinality declared by process separate_mitochondrion:PRINT_READS -- offending value: [file, /path/file.bam]
Error executing process > 'separate_mitochondrion:PRINT_READS (1)'

Caused by:
Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

Hello there again, I am trying this pipeline again this time with fastq files and I am getting errors.
See attached txt file.
Thank you.

error0928.txt

Thank you for your previous assistance. I am getting the following when running against HG19.

nextflow run lmtani/wf-human-mito -r main --alignments "/20220803_BAM/*.ba{i,m}" --restore_hardclips false --outdir "/DATA/JSTUDY/" --reference "/DATA/HG19/hg19.fa" -profile docker
N E X T F L O W ~ version 22.04.5
Launching https://github.com/lmtani/wf-human-mito [evil_lavoisier] DSL2 - revision: a12bad4 [main]
executor > local (1)
[- ] process > separate_mitochondrion:GATK4_FASTQTOSAM -
[- ] process > separate_mitochondrion:ALIGN_RAW_READS -
[- ] process > separate_mitochondrion:SORT_SAM -
[cc/711d83] process > separate_mitochondrion:PRINT_READS (1) [ 0%] 0 of 1
[- ] process > separate_mitochondrion:SELECT_MITO_READS -
[- ] process > variant_call:CALL_DEFAULT:ALIGN_MITO -
[- ] process > variant_call:CALL_DEFAULT:MARK_DUPLICATES -
[- ] process > variant_call:CALL_DEFAULT:SORT_SAM -
[- ] process > variant_call:CALL_DEFAULT:COLLECT_ALIGNMENT_METRICS -
[- ] process > variant_call:CALL_DEFAULT:COLLECT_WGS_METRICS -
[- ] process > variant_call:CALL_DEFAULT:CALL_MUTECT -
[- ] process > variant_call:CALL_SHIFTED:ALIGN_MITO -
[- ] process > variant_call:CALL_SHIFTED:MARK_DUPLICATES -
[- ] process > variant_call:CALL_SHIFTED:SORT_SAM -
executor > local (1)
[- ] process > separate_mitochondrion:GATK4_FASTQTOSAM -
[- ] process > separate_mitochondrion:ALIGN_RAW_READS -
[- ] process > separate_mitochondrion:SORT_SAM -
[cc/711d83] process > separate_mitochondrion:PRINT_READS (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > separate_mitochondrion:SELECT_MITO_READS -
[- ] process > variant_call:CALL_DEFAULT:ALIGN_MITO -
[- ] process > variant_call:CALL_DEFAULT:MARK_DUPLICATES -
[- ] process > variant_call:CALL_DEFAULT:SORT_SAM -
[- ] process > variant_call:CALL_DEFAULT:COLLECT_ALIGNMENT_METRICS -
[- ] process > variant_call:CALL_DEFAULT:COLLECT_WGS_METRICS -
[- ] process > variant_call:CALL_DEFAULT:CALL_MUTECT -
[- ] process > variant_call:CALL_SHIFTED:ALIGN_MITO -
[- ] process > variant_call:CALL_SHIFTED:MARK_DUPLICATES -
[- ] process > variant_call:CALL_SHIFTED:SORT_SAM -
[- ] process > variant_call:CALL_SHIFTED:COLLECT_ALIGNMENT_METRICS -
executor > local (1)
[- ] process > separate_mitochondrion:GATK4_FASTQTOSAM -
[- ] process > separate_mitochondrion:ALIGN_RAW_READS -
[- ] process > separate_mitochondrion:SORT_SAM -
[cc/711d83] process > separate_mitochondrion:PRINT_READS (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > separate_mitochondrion:SELECT_MITO_READS -
[- ] process > variant_call:CALL_DEFAULT:ALIGN_MITO -
[- ] process > variant_call:CALL_DEFAULT:MARK_DUPLICATES -
[- ] process > variant_call:CALL_DEFAULT:SORT_SAM -
[- ] process > variant_call:CALL_DEFAULT:COLLECT_ALIGNMENT_METRICS -
[- ] process > variant_call:CALL_DEFAULT:COLLECT_WGS_METRICS -
[- ] process > variant_call:CALL_DEFAULT:CALL_MUTECT -
[- ] process > variant_call:CALL_SHIFTED:ALIGN_MITO -
[- ] process > variant_call:CALL_SHIFTED:MARK_DUPLICATES -
[- ] process > variant_call:CALL_SHIFTED:SORT_SAM -
[- ] process > variant_call:CALL_SHIFTED:COLLECT_ALIGNMENT_METRICS -
[- ] process > variant_call:CALL_SHIFTED:COLLECT_WGS_METRICS -
[- ] process > variant_call:CALL_SHIFTED:CALL_MUTECT -
[- ] process > variant_call:LIFTOVER_VCF -
[- ] process > variant_call:MERGE_VCFS -
[- ] process > variant_call:MERGE_STATS -
[- ] process > variant_call:FILTER_MUTECT_CALLS -
[- ] process > variant_call:LEFT_ALIGN_AND_TRIM_VARIANTS -
[- ] process > variant_call:SELECT_VARIANTS -
[- ] process > variant_call:HAPLOCHECK -
[- ] process > make_report:CREATE_JSON -
[- ] process > make_report:AGGREGATE_SAMPLES_IN_CSV -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'separate_mitochondrion:PRINT_READS (1)'

Caused by:
Process separate_mitochondrion:PRINT_READS (1) terminated with an error exit status (2)

Command executed:

BAM=find -L ./ -name "*.bam" -or -name "*.cram" # point to BAM, not BAI, in the gatk

Uses the ref.dict to infer if the mitochondrial genome is named MT or chrMT

CHROM_NAME=grep -q "MT" hg19.dict && echo "MT" || echo "chrM"

gatk PrintReads -R hg19.fa -L "$CHROM_NAME" --read-filter MateOnSameContigOrNoMappedMateReadFilter --read-filter MateUnmappedAndUnmappedReadFilter -I $BAM -O mito.bam

Command exit status:
2

Command output:
(empty)

Command error:
Using GATK jar /usr/local/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-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 -jar /usr/local/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar PrintReads -R hg19.fa -L chrM --read-filter MateOnSameContigOrNoMappedMateReadFilter --read-filter MateUnmappedAndUnmappedReadFilter -I ./CPM00022730_BS_DNA_J101B_12m_20220803-dragen.bam -O mito.bam
22:18:46.608 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.2.5.0-0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Aug 15, 2022 10:18:46 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
22:18:46.770 INFO PrintReads - ------------------------------------------------------------
22:18:46.771 INFO PrintReads - The Genome Analysis Toolkit (GATK) v4.2.5.0
22:18:46.771 INFO PrintReads - For support and documentation go to https://software.broadinstitute.org/gatk/
22:18:46.771 INFO PrintReads - Executing as ec2-user@37d4a3087459 on Linux v5.10.126-117.518.amzn2.x86_64 amd64
22:18:46.771 INFO PrintReads - Java runtime: OpenJDK 64-Bit Server VM v11.0.9.1-internal+0-adhoc..src
22:18:46.771 INFO PrintReads - Start Date/Time: August 15, 2022 at 10:18:46 PM GMT
22:18:46.771 INFO PrintReads - ------------------------------------------------------------
22:18:46.772 INFO PrintReads - ------------------------------------------------------------
22:18:46.773 INFO PrintReads - HTSJDK Version: 2.24.1
22:18:46.773 INFO PrintReads - Picard Version: 2.25.4
22:18:46.773 INFO PrintReads - Built for Spark Version: 2.4.5
22:18:46.773 INFO PrintReads - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:18:46.773 INFO PrintReads - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:18:46.773 INFO PrintReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:18:46.774 INFO PrintReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:18:46.774 INFO PrintReads - Deflater: IntelDeflater
22:18:46.774 INFO PrintReads - Inflater: IntelInflater
22:18:46.774 INFO PrintReads - GCS max retries/reopens: 20
22:18:46.774 INFO PrintReads - Requester pays: disabled
22:18:46.774 INFO PrintReads - Initializing engine
22:18:46.826 INFO PrintReads - Shutting down engine
[August 15, 2022 at 10:18:46 PM GMT] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=121634816

---

A USER ERROR has occurred: Couldn't read file file://hg19.fa. Error was: Sequence dictionary and index contain different numbers of contigs

---

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Work dir:
/home/MITO_NF/work/cc/711d8397e91beda477218a34435894

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