Closed ewels closed 5 years ago
This error seems to be unrelated to the previous problem we had with get_software_versions
. The key line in the log is this:
202 Segmentation fault (core dumped) STAR --version &> v_star.txt
So basically, STAR is failing for some reason (it's not a problem with the configs as discussed in #33).
Ok, I just tested the container and it works fine for me:
$ docker run -it nfcore/rnaseq:1.3 bash -c "STAR --version"
STAR_2.6.1d
@cailiangliang765 - could you try the same command in your terminal please? Also pasting the output from docker image ls
would be helpful:
$ docker image ls
REPOSITORY TAG IMAGE ID CREATED SIZE
nfcore/rnaseq 1.3 e7839e32cee9 4 days ago 3.54GB
this is the same with you.
cailiangliang@clldebian:$ docker image ls
nfcore/rnaseq 1.3 e7839e32cee9 4 days ago 3.54GB
but i can not get the version info like you.
cailiangliang@clldebian:$ docker run -it nfcore/rnaseq:1.3 bash -c "STAR --version"
cailiangliang@clldebian:~$
then i enter the docker container, it shows,
cailiangliang@clldebian:~$ docker run -it nfcore/rnaseq:1.3 bash
(base) root@2a0cbaf0ee30:/# STAR --version
Segmentation fault (core dumped)
(base) root@2a0cbaf0ee30:/#
Bah, this is very strange. I thought the whole point of docker was that stuff should work the same on every system 😞
What system are you running on @cailiangliang765? How is docker installed?
I am on Debian.
cailiangliang@clldebian:$ cat /etc/issue
Debian GNU/Linux buster/sid \n \l
I met this error when i remove the nfcore/rnaseq (e7839e32cee9)
. i do not know why this happened. this error happens to other images too. so i think i need to try reinstall docker.
cailiangliang@clldebian:$ docker rmi e7839e32cee9
Error response from daemon: conflict: unable to delete e7839e32cee9 (must be forced) - image is being used by stopped container dee8ec9a8738
Bah, this is very strange. I thought the whole point of docker was that stuff should work the same on every system 😞
What system are you running on @cailiangliang765? How is docker installed?
@ewels I find the reason for this issue. The docker support the kernel version 4.9.0 not 4.19.0. This issue can be closed now. Many thanks for your help.
Thanks for the info :-)
STARindex (build_star_index)
failed -- Execution is retried (1)"N E X T F L O W ~ version 22.10.0
Launching https://github.com/nf-core/dualrnaseq
[festering_mandelbrot] DSL1 - revision: 3e35f4722e [master] ,--./,-.
___ __ __ __ ___ /,-._.--~'
/ \ |__) |__ } { | \| | \__, \__/ | \ |___ \
-.,--,
.,._,'
nf-core/dualrnaseq v1.0.0[- ] process > get_software_versions -
[- ] process > check_replicates -
[- ] process > uncompress_pathogen_fasta_g... -
[- ] process > uncompress_host_fasta_genome -
[- ] process > uncompress_pathogen_gff -
Pulling Singularity image docker://nfcore/dualrnaseq:1.0.0 [cache /work2/project/gafl/DADI/Peachrnaseq/DualRNAseq/jacques/dualrnaseq/work_test/singularity/nfcore-dualrnaseq-1.0.0.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /work2/project/gafl/DADI/Peachrnaseq/DualRNAseq/jacques/dualrnaseq/work_test/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
executor > local (50)
[ee/36330f] process > get_software_versions [100%] 1 of 1 ✔
[5e/7a8f66] process > check_replicates (check_rep... [100%] 1 of 1 ✔
[4d/41624b] process > uncompress_pathogen_fasta_g... [100%] 1 of 1 ✔
[3f/fb7cfc] process > uncompress_host_fasta_genom... [100%] 1 of 1 ✔
[22/e10439] process > uncompress_pathogen_gff (un... [100%] 1 of 1 ✔
[d9/6cc8d1] process > uncompress_host_gff (uncomp... [100%] 1 of 1 ✔
[67/1c9a5b] process > combine_pathogen_host_fasta... [100%] 1 of 1 ✔
[db/00db48] process > extract_reference_names_hos... [100%] 1 of 1 ✔
[2d/aa53b4] process > extract_reference_names_pat... [100%] 1 of 1 ✔
[ec/a5b1eb] process > fastqc (Bolinha_J15_R1) [100%] 12 of 12 ✔
[54/a657c3] process > bbduk (Bolinha_J15_R1) [100%] 12 of 12 ✔
[82/13b093] process > fastqc_after_trimming (Boli... [100%] 12 of 12 ✔
[e8/a4784b] process > count_total_reads (count_to... [100%] 1 of 1 ✔
[b5/ea9b42] process > count_total_read_pairs (cou... [100%] 1 of 1 ✔
[65/ae84a0] process > STARindex (build_star_index) [ 50%] 1 of 2, failed: 1...
[- ] process > ALIGNMENTstar -
[- ] process > remove_crossmapped_reads -
[- ] process > extract_processed_reads_STAR -
[- ] process > collect_processed_reads_STAR -
[- ] process > unique_mapping_stats_STAR -
[- ] process > collect_stats_STAR_uniquely... -
[- ] process > count_crossmapped_reads -
[- ] process > multi_mapping_stats -
[- ] process > collect_stats_STAR_multi_ma... -
[- ] process > star_mapping_stats -
[- ] process > plot_star_mapping_stats -
[- ] process > multiqc -
[18/5c77fd] process > output_documentation [100%] 1 of 1 ✔
[54/10f034] NOTE: Process STARindex (build_star_index)
failed -- Execution is retried (1)
Many thanks for your help.
Originally posted by @cailiangliang765 in https://github.com/nf-core/rnaseq/issues/33#issuecomment-478321926
I still met the
"ERROR ~ Error executing process > 'get_software_versions'".
: