cannot open input file {sample}.stringtie.gff -- Command fails for one sample but runs for others
Closed this issue · 2 comments
Operating System
Ubuntu 22.04
Other Linux
No response
Workflow Version
Nextflow version version 23.10.1, build 5891
Workflow Execution
Command line
EPI2ME Version
wf-single-cell v1.0.3-g890cab0
CLI command run
nextflow run epi2me-labs/wf-single-cell --fastq /mnt/disk2/Carla_seq/LRONT_samples/CI_1/CI_1.pass.fastq.gz --sample CI_1 --out_dir nextflow_results_CI_1_test --kit_name 3prime --kit_version v3 --ref_genome_dir /mnt/disk2/Carla_seq/reference_genomes/Ensembl/Danio_rerio/GRCz11/v111/v111_10X/ --merge_bam True --matrix_max_mito 60 -profile standard --max_threads 20 --resources_mm2_max_threads 20 --resources_mm2_flags '-I 48G' --mito_prefix mt-
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
I am trying to run the wf-single-cell pipeline. It works for 2 samples but fails for others. It can not find the stringtie.gff input file. I am running the pipeline for zebrafish and the mitochondrial reads are named accordingly (which worked fine for the other samples). I have enough space on my computer and RAM (worked fine for the other samples). What could be going wrong here?
Relevant log output
Mar-11 16:28:11.742 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-11 16:28:11.742 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=pipeline:process_bams:stringtie (8); work-dir=/mnt/disk2/Carla_seq/test/work/5c/f4cf93b0fcc889d0ecd75fb8cbf7f1
error [nextflow.exception.ProcessFailedException]: Process `pipeline:process_bams:stringtie (8)` terminated with an error exit status (1)
Mar-11 16:28:11.742 [Task submitter] INFO nextflow.Session - [c0/66ee2a] Submitted process > pipeline:process_bams:stringtie (28)
Mar-11 16:28:11.751 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'pipeline:process_bams:stringtie (8)'
Caused by:
Process `pipeline:process_bams:stringtie (8)` terminated with an error exit status (1)
Command executed:
# Data from 3prime and multiome kits must be flipped to the transcript strand before building transcriptome.
workflow-glue process_bam_for_stringtie align.bam 16 | tee >(stringtie -L -c 2 -p 5 -G chr.gtf -l "16.stringtie" -o "CI_1.stringtie.gff" - ) | samtools fastq > reads.fastq
# Get transcriptome sequence
gffread -g ref_genome.fa -w "CI_1.transcriptome.fa" "CI_1.stringtie.gff"
Command exit status:
1
Command output:
(empty)
Command error:
[15:27:09 - matplotlib.font_manager] generated new fontManager
/home/epi2melabs/conda/lib/python3.8/site-packages/umap/distances.py:1063: NumbaDeprecationWarning: �[1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.�[0m
@numba.jit()
/home/epi2melabs/conda/lib/python3.8/site-packages/umap/distances.py:1071: NumbaDeprecationWarning: �[1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.�[0m
@numba.jit()
/home/epi2melabs/conda/lib/python3.8/site-packages/umap/distances.py:1086: NumbaDeprecationWarning: �[1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.�[0m
@numba.jit()
/home/epi2melabs/conda/lib/python3.8/site-packages/umap/umap_.py:660: NumbaDeprecationWarning: �[1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.�[0m
@numba.jit()
[15:27:23 - workflow_glue] Starting entrypoint.
GVec error: invalid count: -2083945834
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 2872295 reads
Error: cannot open input file CI_1.stringtie.gff!
Work dir:
/mnt/disk2/Carla_seq/test/work/5c/f4cf93b0fcc889d0ecd75fb8cbf7f1
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`
Mar-11 16:28:11.753 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `pipeline:process_bams:stringtie (8)` terminated with an error exit status (1)
Mar-11 16:28:11.769 [Task monitor] DEBUG nextflow.Session - The following nodes are still active:
[process] pipeline:process_bams:combine_uncorrect_bcsApplication activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
No response
we dug more into this problem and contacted the authors of stringtie. they have released a new version which has possibly resolved this problem. Could you kindly update/provide the dockerfile so that we can remake the docker with the latest version of stringtie? (gpertea/stringtie#320) (https://github.com/gpertea/stringtie/releases/tag/v2.2.2)
Looking forward to your reply!
We have updated the version of stringtie used within our developement version of the code. A new release is pending. We cannot provide a docker file for the released images as the images are built as part of a larger deployment pipeline.