Hi, I tried to test the test_full profile, and my command is like

nextflow run nf-core/circrna -profile test,full,singularity -r dev -bg

And there is an error:

Empty hisat2 bam generated

.How did that happen?? ERROR ~ Error executing process > 'NFCORE_CIRCRNACIRCRNACIRCRNA_DISCOVERYCIRIQUANTMAIN (fust1_2)' Caused by: Process

NFCORE_CIRCRNA:CIRCRNA:CIRCRNA_DISCOVERY:CIRIQUANT:MAIN (fust1_2)

terminated with an error exit status (1) Command executed: BWA=

which bwa

HISAT2=

which hisat2

STRINGTIE=

which stringtie

SAMTOOLS=

which samtools

BWA_FILE=

ls bwa/*.bwt

BWA_PREFIX=

basename $BWA_FILE .bwt

HISAT2_FILE=

ls hisat2/*.1.ht2

HISAT2_PREFIX=

basename $HISAT2_FILE .1.ht2

printf "name: ciriquant\ntools:\n bwa: $BWA\n hisat2: $HISAT2\n stringtie: $STRINGTIE\n samtools: $SAMTOOLS\n\nreference:\n fasta: chrI.fa\n gtf: chrI.gtf\n bwa_index: bwa/$BWA_PREFIX\n hisat_index: hisat2/$HISAT2_PREFIX" > config.yml CIRIquant \ -t 2 \ -1 fust1_2_1_val_1.fq.gz \ -2 fust1_2_2_val_2.fq.gz \ --config config.yml \ --no-gene \ -o fust1_2 \ -p fust1_2 \ \ cat <<-END_VERSIONS > versions.yml "NFCORE_CIRCRNACIRCRNACIRCRNA_DISCOVERYCIRIQUANTMAIN": bwa: $(echo $(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*$//') ciriquant: $(echo $(CIRIquant --version 2>&1) | sed 's/CIRIquant //g' ) samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//') stringtie: $(stringtie --version 2>&1) hisat2: 2.1.0 END_VERSIONS Command exit status: 1 Command output: (empty) Command error: WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_NXF_TASK_WORKDIR as environment variable will not be supported in the future, use APPTAINERENV_NXF_TASK_WORKDIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_NXF_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_NXF_DEBUG instead INFO: fuse: warning: library too old, some operations may not work [Tue 2024-06-25 195040] [INFO ] Input reads: fust1_2_1_val_1.fq.gz,fust1_2_2_val_2.fq.gz [Tue 2024-06-25 195040] [INFO ] Library type: unstranded [Tue 2024-06-25 195040] [INFO ] Output directory: fust1_2, Output prefix: fust1_2 [Tue 2024-06-25 195040] [INFO ] Config: ciriquant Loaded [Tue 2024-06-25 195040] [INFO ] 64 CPU cores availble, using 2 [Tue 2024-06-25 195040] [INFO ] Align RNA-seq reads to reference genome .. Traceback (most recent call last): File "/usr/local/bin/CIRIquant", line 10, in <module> sys.exit(main()) File "/usr/local/lib/python2.7/site-packages/CIRIquant/main.py", line 155, in main hisat_bam = pipeline.align_genome(log_file, thread, reads, outdir, prefix) File "/usr/local/lib/python2.7/site-packages/CIRIquant/pipeline.py", line 52, in align_genome raise utils.PipelineError('Empty hisat2 bam generated, please re-run CIRIquant with -v and check the fastq and hisat2-index.') CIRIquant.utils.PipelineError: Empty hisat2 bam generated, please re-run CIRIquant with -v and check the fastq and hisat2-index.

Have seen this several times been never really been able to trace it back - but I tested the

test_full

configuration several times successfully

I just ran into the same error recently. Looking forward to the updates.