Open marcDabad opened 1 year ago
Hi, I have the same issue when I am running nanoseq 3.1.0
encountered the issue as well. "bash: line 1: minimap2: command not found"
ERROR ~ Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:JAFFAL (6)'
Caused by:
Process NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:JAFFAL (6)
terminated with an error exit status (1)
Command executed:
bpipe run -p refBase=for_jaffal for_jaffal/JAFFAL.groovy PVYP334523_pass_barcode03.fastq.gz
cat <<-END_VERSIONS > versions.yml "NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:JAFFAL": jaffa: $( echo 'jaffa 2.0' ) END_VERSIONS
Command exit status: 1
Command output: | Starting Pipeline at 2024-07-09 02:23 | ╘══════════════════════════════════════════════════════════════════════════════════════════════════╛
========================================= Stage run_check ========================================== Running JAFFA version 2.1 Checking for required data files... for_jaffal/hg38_genCode22.fa for_jaffal/hg38_genCode22.tab for_jaffal/known_fusions.txt for_jaffal/hg38.fa for_jaffal/Masked_hg38.1.bt2 for_jaffal/hg38_genCode22.1.bt2 All looking good
=========================== Stage get_fasta (PVYP334523_pass_barcode03) ============================ java -ea -Xms300m -cp /usr/local/opt/bbmap-38.96-1/current/ jgi.ReformatReads threads=16 ignorebadquality=t in=PVYP334523_pass_barcode03.fastq.gz out=PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.fasta Executing jgi.ReformatReads [threads=16, ignorebadquality=t, in=PVYP334523_pass_barcode03.fastq.gz, out=PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.fasta]
Set threads to 16 Input is being processed as unpaired Changed from ASCII-33 to ASCII-64 on input Z: 90 -> 59 Input: 5132931 reads 7327093108 bases Output: 5132931 reads (100.00%) 7327093108 bases (100.00%)
Time: 234.195 seconds. Reads Processed: 5132k 21.92k reads/sec Bases Processed: 7327m 31.29m bases/sec
===================== Stage minimap2_transcriptome (PVYP334523_pass_barcode03) ===================== bash: line 1: minimap2: command not found Cleaned up file PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.paf to .bpipe/trash/PVYP334523_pass_barcode03.fastq.paf ERROR: stage minimap2_transcriptome failed: Command in stage minimap2_transcriptome failed with exit status = 127 :
minimap2 -t 16 -x map-ont -c for_jaffal/hg38_genCode22.fa PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.fasta > PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.paf ;
========================================= Pipeline Failed ==========================================
In stage Unknown: One or more parallel stages aborted. The following messages were reported:
------------------- minimap2_transcriptome ( PVYP334523_pass_barcode03.fastq ) -------------------
Command in stage minimap2_transcriptome failed with exit status = 127 :
minimap2 -t 16 -x map-ont -c for_jaffal/hg38_genCode22.fa PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.fasta > PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.paf ;
Use 'bpipe errors' to see output from failed commands.
Command error: INFO: Converting SIF file to temporary sandbox... mkdir: cannot create directory ‘/home/xzhong/.bpipedb’: Read-only file system ln: failed to create symbolic link '/home/xzhong/.bpipedb/jobs/91': No such file or directory INFO: Cleaning up image...
Work dir: /scratch/ms002/xzhong/06_nanopore/work/6b/e74e2b04ed202b4efc4dc195abe96d
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
-- Check '.nextflow.log' file for details Execution cancelled -- Finishing pending tasks before exit
@Xiao-Zhong, maybe you post this in a new post/issue. I am encountered the same issue as you at this moment
@Xiao-Zhong, maybe you post this in a new post/issue. I am encountered the same issue as you at this moment
I don't think the tool is being under active development or well-maintained. We have to skip the problematic step(s) at the moment, otherwise will waste too much time.
For JAFFAL, install and run it directly following the homepage: https://github.com/Oshlack/JAFFA
The NF pipeline might have a nice final report including JAFFAL output, but I don't know and gave up after the bambu step.
I am expanding a nextflow pipeline for my internship. I tried to implement JAFFA from the modules they used for nanoseq. I alreaday tested JAFFA separately via command line )JAFFA direct), that worked fine. My question at this moment: how to implement JAFFA in a nextflow pipeline without having these errors?
Description of the bug
JAFFAL pipeline crashes when singularity is used because singularity container has not minimap2 (at least)
Command used and terminal output
Relevant files
No response
System information