NFCORE_RNAVAR:RNAVAR:SPLITNCIGAR:GATK4_SPLITNCIGARREADS error

[gianfilippo]

Description of the bug

Hi,

I am getting the following error. Can you please help ?

Thanks

-[nf-core/rnavar] Pipeline completed with errors- Error executing process > 'NFCORE_RNAVAR:RNAVAR:SPLITNCIGAR:GATK4_SPLITNCIGARREADS (CCA002MV_17scattered)'

Caused by: Process NFCORE_RNAVAR:RNAVAR:SPLITNCIGAR:GATK4_SPLITNCIGARREADS (CCA002MV_17scattered) terminated with an error exit status (247)

Command executed:

gatk --java-options "-Xmx36g" SplitNCigarReads
--input CCA002MV.markdup.sorted.bam
--output CCA002MV_17scattered.bam
--reference GRCh38.p13.genome.fa
--intervals 17scattered.interval_list
--tmp-dir .
--create-output-bam-index false

cat <<-END_VERSIONS > versions.yml "NFCORE_RNAVAR:RNAVAR:SPLITNCIGAR:GATK4_SPLITNCIGARREADS": gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.(GATK) v//; s/ .$//') END_VERSIONS

Command exit status: 247

Command output: (empty)

Command error: 06:48:10.811 INFO ProgressMeter - chr14:49862713 180.9 69860000 386247.7 06:48:20.830 INFO ProgressMeter - chr14:49862713 181.0 69912000 386178.7 06:48:30.984 INFO ProgressMeter - chr14:49862713 181.2 69974000 386160.2 06:48:41.142 INFO ProgressMeter - chr14:49862713 181.4 70017000 386036.8 06:48:51.269 INFO ProgressMeter - chr14:49862713 181.5 70081000 386030.4 06:49:01.274 INFO ProgressMeter - chr14:49862713 181.7 70121000 385896.3 06:49:11.396 INFO ProgressMeter - chr14:49862713 181.9 70183000 385879.3 06:49:21.524 INFO ProgressMeter - chr14:49862713 182.0 70227000 385763.2 06:49:31.565 INFO ProgressMeter - chr14:49862713 182.2 70292000 385765.6 06:49:41.762 INFO ProgressMeter - chr14:49862713 182.4 70337000 385652.9 06:49:51.861 INFO ProgressMeter - chr14:49862713 182.6 70403000 385658.8 06:50:02.020 INFO ProgressMeter - chr14:49862713 182.7 70453000 385575.1 06:50:12.111 INFO ProgressMeter - chr14:49862713 182.9 70513000 385548.6 06:50:22.141 INFO ProgressMeter - chr14:49862713 183.1 70564000 385475.1 06:50:32.222 INFO ProgressMeter - chr14:49862713 183.2 70625000 385454.6 06:50:42.231 INFO ProgressMeter - chr14:49862713 183.4 70676000 385382.0 06:50:52.287 INFO ProgressMeter - chr14:49862713 183.6 70746000 385411.5 06:51:02.391 INFO ProgressMeter - chr14:49862713 183.7 70801000 385357.6 06:51:12.589 INFO ProgressMeter - chr14:49862713 183.9 70862000 385333.2 06:51:22.603 INFO ProgressMeter - chr14:49862713 184.1 70923000 385315.1 06:51:32.788 INFO ProgressMeter - chr14:49862713 184.2 70976000 385247.8 06:51:42.866 INFO ProgressMeter - chr14:49862714 184.4 71032000 385200.6 06:51:52.973 INFO ProgressMeter - chr14:49862714 184.6 71076000 385087.4 06:52:03.087 INFO ProgressMeter - chr14:49862714 184.7 71128000 385017.5 06:52:13.107 INFO ProgressMeter - chr14:49862714 184.9 71182000 384961.9 06:52:23.107 INFO ProgressMeter - chr14:49862714 185.1 71227000 384858.3 06:52:33.666 INFO ProgressMeter - chr14:49862714 185.2 71278000 384768.0 06:52:43.743 INFO ProgressMeter - chr14:49862714 185.4 71335000 384726.9 06:52:53.789 INFO ProgressMeter - chr14:49862714 185.6 71390000 384676.1 06:53:03.815 INFO ProgressMeter - chr14:49862714 185.8 71453000 384669.3 06:53:13.905 INFO ProgressMeter - chr14:49862714 185.9 71501000 384579.5 06:53:23.955 INFO ProgressMeter - chr14:49862714 186.1 71550000 384496.6 06:53:34.029 INFO ProgressMeter - chr14:49862714 186.3 71610000 384472.2 06:53:44.156 INFO ProgressMeter - chr14:49862714 186.4 71651000 384344.0 06:53:54.211 INFO ProgressMeter - chr14:49862714 186.6 71717000 384352.5 06:54:04.377 INFO ProgressMeter - chr14:49862714 186.8 71773000 384303.7 06:54:14.437 INFO ProgressMeter - chr14:49862714 186.9 71822000 384221.1 06:54:24.594 INFO ProgressMeter - chr14:49862714 187.1 71880000 384183.5 06:54:34.698 INFO ProgressMeter - chr14:49862715 187.3 71926000 384083.6 06:54:44.769 INFO ProgressMeter - chr14:49862715 187.4 71971000 383979.8 06:54:54.827 INFO ProgressMeter - chr14:49862715 187.6 72017000 383881.9 06:55:05.008 INFO ProgressMeter - chr14:49862717 187.8 72069000 383811.9 06:55:15.058 INFO ProgressMeter - chr14:49862721 187.9 72112000 383698.6 06:55:25.066 INFO ProgressMeter - chr14:49862725 188.1 72158000 383602.9 06:55:35.077 INFO ProgressMeter - chr14:49862732 188.3 72200000 383486.1 06:55:45.258 INFO ProgressMeter - chr14:49862750 188.4 72267000 383496.3 06:55:53.430 INFO SplitNCigarReads - 0 read(s) filtered by: AllowAllReadsReadFilter

06:55:53.696 INFO OverhangFixingManager - Overhang Fixing Manager saved 1338690 reads in the first pass 06:55:53.698 INFO SplitNCigarReads - Starting traversal pass 2

Command used and terminal output

I am running then following
nextflow run nf-core/rnavar \
    -r 1.0.0 \
    -c "$inDIR/yale.config" \
    -profile singularity \
    -work-dir $workDIR \
    --input $inDIR/samplesheet.csv \
    --outdir $inDIR/RNAvar \
    --fasta $FASTA_PATH \
    --gtf $GTF_PATH \
    --star_index $STAR_INDEX \
    --aligner star \
    --star_twopass true \
    --read_length 101 \
    --save_reference \
    --dbsnp $DBSNP \
    --dbsnp_tbi $DBSNPTBI \
    --known_indels $INDELS \
    --known_indels_tbi $INDELSTBI \
    --gatk_hc_call_conf 20 \
    --gatk_vf_cluster_size 3 \
    --gatk_vf_window_size 35 \
    --gatk_vf_fs_filter 30.0 \
    --gatk_vf_qd_filter 2.0

Relevant files

No response

System information

No response