Process map_reads (1) terminated with an error exit status (127) Command error: .command.sh: line 2: clockwork: command not found

[ybdong919]

../tools/Varpipeline -q JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz -r ../tools/ref2.fa -n JTT20001087-FL-M04613-200220_S40 -q2 JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz -a -v

---[ nextflow remove contamination ]---
Command:
/blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/tools/clockwork-0.11.3/results/nextflow run /blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/tools/clockwork-0.11.3/nextflow/remove_contam.nf --ref_fasta /blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/tools/clockwork-0.11.3/OUT/ref.fa --ref_metadata_tsv /blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/tools/clockwork-0.11.3/OUT/remove_contam_metadata.tsv --reads_in1 JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz --reads_in2 JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz --outprefix Output_01_31_2023/JTT20001087-FL-M04613-200220_S40/clockwork/JTT20001087-FL-M04613-200220_S40 --mapping_threads 12

Standard Output:
N E X T F L O W ~ version 20.07.1
Launching /blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/tools/clockwork-0.11.3/nextflow/remove_contam.nf [trusting_engelbart] - revision: b2f84f8ad4
[- ] process > make_jobs_tsv -
[- ] process > map_reads -
[- ] process > sam_to_fastq_files -

executor > local (1)
[8c/453495] process > make_jobs_tsv [ 0%] 0 of 1
[- ] process > map_reads -
[- ] process > sam_to_fastq_files -

executor > local (2)
[8c/453495] process > make_jobs_tsv [100%] 1 of 1 ✔
[10/85594a] process > map_reads (1) [ 0%] 0 of 1
[- ] process > sam_to_fastq_files -
Error executing process > 'map_reads (1)'

Caused by:
Process map_reads (1) terminated with an error exit status (127)

Command executed:

clockwork map_reads --threads 12 --unsorted_sam sample_name /blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/tools/clockwork-0.11.3/OUT/ref.fa contam_sam /blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz

Command exit status:
127

Command output:
(empty)

Command error:
.command.sh: line 2: clockwork: command not found

Work dir:
/blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/data/work/10/85594a9b2d5231d548e3b1fbc61d51

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

executor > local (2)
[8c/453495] process > make_jobs_tsv [100%] 1 of 1 ✔
[10/85594a] process > map_reads (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > sam_to_fastq_files -
Error executing process > 'map_reads (1)'

Caused by:
Process map_reads (1) terminated with an error exit status (127)

Command executed:

clockwork map_reads --threads 12 --unsorted_sam sample_name /blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/tools/clockwork-0.11.3/OUT/ref.fa contam_sam /blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/data/JTT20001087-FL-M04613-200220_S40_R1_001.fastq.gz /blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/data/JTT20001087-FL-M04613-200220_S40_R2_001.fastq.gz

Command exit status:
127

Command output:
(empty)

Command error:
.command.sh: line 2: clockwork: command not found

Work dir:
/blue/bphl-florida/share/cdc_tb_pipeline/NCHHSTP-DTBE-Varpipe-WGS/data/work/10/85594a9b2d5231d548e3b1fbc61d51

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run