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------------------------------- get-nf workflow ----------------------------
I L L U M I N A - N F P I P E L I N E
V1.2.4
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NextFlow Run Name : nauseous_shockley
Project : DUALITY
Run : Duality-pool2
###############################################
## GeT-nextflow-NGL-Bi/wf-Illumina-nf execution completed unsuccessfully! ## ###############################################
The exit status of the task that caused the workflow execution to fail was: 137.
The full error message was:
Error executing process > 'QC_ANALYSIS:ILLUMINA_QC:RNA_QC:SORTMERNA (13_S13_L002)'
Caused by:
Process `QC_ANALYSIS:ILLUMINA_QC:RNA_QC:SORTMERNA (13_S13_L002)` terminated with an error exit status (137)
Command executed:
sortmerna \
--ref silva-euk-18s-id95.fasta --ref silva-euk-28s-id98.fasta --ref silva-bac-16s-id90.fasta --ref silva-bac-23s-id98.fasta --ref silva-arc-16s-id95.fasta --ref silva-arc-23s-id98.fasta \
--reads 13_S13_L002_R2_001_subset1000000.fastq \
--reads 13_S13_L002_R1_001_subset1000000.fastq \
--threads 3 \
--workdir . \
--aligned rRNA_reads \
--fastx \
--other non_rRNA_reads \
--paired_in \
--out2 \
mv rRNA_reads.log 13_S13_L002.sortmerna.log
mv non_rRNA_reads_fwd.f* 13_S13_L002_R1.non_rRNA.fastq
mv non_rRNA_reads_rev.f* 13_S13_L002_R2.non_rRNA.fastq
cat <<-END_VERSIONS > versions.yml
"QC_ANALYSIS:ILLUMINA_QC:RNA_QC:SORTMERNA":
sortmerna: $(echo $(sortmerna --version 2>&1 | grep 'SortMeRNA version' | sed 's/^SortMeRNA version//g'))
END_VERSIONS
Command exit status:
137
Command output:
done.
[build_index:2108] ==== Done index building in 180.355 sec ====
[init:108] Readfeed init started
[define_format:885] file: "13_S13_L002_R2_001_subset1000000.fastq" is FASTQ flat ASCII
[define_format:885] file: "13_S13_L002_R1_001_subset1000000.fastq" is FASTQ flat ASCII
[count_reads:919] started count ...
[next:311] EOF FWD reached. Total reads: 1000000
[next:311] EOF REV reached. Total reads: 1000000
[count_reads:949] done count. Elapsed time: 3.77176 sec. Total reads: 2000000
[init_split_files:971] added file: ./readb/fwd_0.fq
[init_split_files:971] added file: ./readb/rev_0.fq
[init_split_files:971] added file: ./readb/fwd_1.fq
[init_split_files:971] added file: ./readb/rev_1.fq
[init_split_files:971] added file: ./readb/fwd_2.fq
[init_split_files:971] added file: ./readb/rev_2.fq
[split:583] start splitting. Using number of splits equals number of processing threads: 3
[next:311] EOF FWD reached. Total reads: 1000000
[next:311] EOF REV reached. Total reads: 1000000
[split:694] Done splitting. Reads count: 2000000 Runtime sec: 7.1325
[init:135] Readfeed init done in sec [10.9084]
[store_to_db:292] Stored Reads statistics to DB:
all_reads_count= 2000000 all_reads_len= 300000000 min_read_len= 150 max_read_len= 150 total_aligned= 0 total_aligned_id= 0 total_aligned_cov= 0 total_aligned_id_cov= 0 total_denovo= 0 num_short= 0 reads_matched_per_db= TODO is_stats_calc= 0 is_total_reads_mapped_cov= 0
[align:143] ==== Starting alignment ====
[align:146] Number of cores: 64
[align:163] Using number of Processor threads: 3
[Refstats:60] Index Statistics calculation starts ... done in: 4.75387 sec
[align:185] Loading index: 0 part: 1/1 Memory KB: 53 ...
[align:190] done in [1.2399] sec Memory KB: 373
[align:193] Loading references ...
[align:197] done in [0.0347975] sec. Memory KB: 387
[align2:70] Processor 1 thread 139848086152960 started
[align2:70] Processor 2 thread 139848589485824 started
[align2:70] Processor 0 thread 139848077760256 started
[next:433] EOF FWD reached. Total reads: 333333
[next:433] EOF REV reached. Total reads: 333333
[align2:133] Processor 1 thread 139848086152960 done. Processed 666666 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 262893 Runtime sec: 749.411
[next:433] EOF FWD reached. Total reads: 333334
[next:433] EOF REV reached. Total reads: 333334
[align2:133] Processor 0 thread 139848077760256 done. Processed 666668 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 263136 Runtime sec: 750.894
[next:433] EOF FWD reached. Total reads: 333333
[next:433] EOF REV reached. Total reads: 333333
[align2:133] Processor 2 thread 139848589485824 done. Processed 666666 reads. Skipped already processed: 0 reads Aligned reads (passing E-value): 263395 Runtime sec: 751.894
[align:220] done index: 0 part: 1 in 751.894 sec Memory KB: 694
[align:227] Index and References unloaded in 0.217265 sec. Memory KB: 694
[align:185] Loading index: 1 part: 1/1 Memory KB: 694 ...
[align:190] done in [1.20084] sec M
Command error:
.command.sh: line 13: 5911 Killed sortmerna --ref silva-euk-18s-id95.fasta --ref silva-euk-28s-id98.fasta --ref silva-bac-16s-id90.fasta --ref silva-bac-23s-id98.fasta --ref silva-arc-16s-id95.fasta --ref silva-arc-23s-id98.fasta --reads 13_S13_L002_R2_001_subset1000000.fastq --reads 13_S13_L002_R1_001_subset1000000.fastq --threads 3 --workdir . --aligned rRNA_reads --fastx --other non_rRNA_reads --paired_in --out2
Work dir:
/work/sbsuser/Nextflow/wf-illumina-nf/results/230424_A00318_0407_AH7T55DSX5_Lane2_1682497836/work/d6/e25b92723d04c14ae51b180553dea0
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
The workflow was completed at 26/04/2023 15:05:00 (duration: 2h 15m 20s)
The command used to launch the workflow was as follows:
nextflow run /save/sbsuser/scripts-ngs/wf-Illumina-nf_Current/main.nf -ansi-log false -profile prod -params-file /work/sbsuser/data/NovaSeq/230424_A00318_0407_AH7T55DSX5_Lane2_1682497836/DUALITY_params.yml
Pipeline Configuration:
-----------------------
- Nextflow Run Name: nauseous_shockley
- Analysis Run Name: Duality-pool2
- Begin Date: 26/04/2023 12:49:42
- Sequencing Type: Multiplex
- Reference: /save/ng6/TODO/HiSeqIndexedGenomes/new_struct/Medicago_truncatula//genome/GCF_003473485.1_MtrunA17r5.0/star/GCF_003473485_normalized.fa
- Input dir: /work/sbsuser/data/NovaSeq/230424_A00318_0407_AH7T55DSX5_Lane2_1682497836
- Launch dir: /work/sbsuser/Nextflow/wf-illumina-nf/results/230424_A00318_0407_AH7T55DSX5_Lane2_1682497836
- Working dir: /work/sbsuser/Nextflow/wf-illumina-nf/results/230424_A00318_0407_AH7T55DSX5_Lane2_1682497836/work
- Output dir: /work/sbsuser/data/NovaSeq/230424_A00318_0407_AH7T55DSX5_Lane2_1682497836/nextflow/DUALITY_Duality-pool2_20230426124938
- Script dir: /save/sbsuser/scripts-ngs/wf-Illumina-nf_Current
- User: sbsuser
- Config Profile: prod
- E-mail Address: matilda.zaffuto@inrae.fr
- E-mail on failure: jules.sabban@inrae.fr
- Date Completed: 2023-04-26T15:05:00.471470+02:00
- Pipeline script file path: /save/sbsuser/scripts-ngs/wf-Illumina-nf_Current/main.nf
- Pipeline script hash ID: a83f5003f09a727575364188c639d734
- Docker image: /save/sbsuser/scripts-ngs/wf-Illumina-nf_Current/template-nf.sif
- Nextflow Version: 22.12.0-edge
- Nextflow Build: 5830
- Nextflow Compile Timestamp: 13-12-2022 21:22 UTC
---
GeT-nextflow-NGL-Bi/wf-illumina-nf
https://forgemia.inra.fr/get-nextflow-ngl-bi/wf-illumina-nf