wrapper_run_trinity Issue #102
Description
Hii,
I am trying to run FunGAP for my fungus genome. I have successfully installed the tool and was facing error mentioned in issue #91 , resolved it as by making changes in the check_input.py script. It is now throwing a new error:
[04-29 18:28] START: wrapper_run_trinity
[Wrapper] /home/user/FunGAP/run_trinity.py --bam_files /home/user/FunGAP/s_hep_self/hisat2_out/SRR29464655.bam --output_dir /home/user/FunGAP/s_hep_self/trinity_out --log_dir /home/user/FunGAP/s_hep_self/logs --num_cores 28 --max_intron 2000 --jaccard_clip
[04-29 18:28] START: Trinity for SRR29464655
[Run] /home/user/anaconda3/envs/fungap/bin/Trinity --jaccard_clip --genome_guided_bam /home/user/FunGAP/s_hep_self/hisat2_out/SRR29464655.bam --genome_guided_max_intron 2000 --max_memory 10G --CPU 28 --output /home/user/FunGAP/s_hep_self/trinity_out/trinity_SRR29464655 > /home/user/FunGAP/s_hep_self/logs/trinity_SRR29464655.log 2>&1
Traceback (most recent call last):
File "/home/user/FunGAP/run_trinity.py", line 160, in
main()
File "/home/user/FunGAP/run_trinity.py", line 99, in main
jaccard_clip_flag, logger
File "/home/user/FunGAP/run_trinity.py", line 149, in run_trinity
os.rename(trinity_output, new_output)
FileNotFoundError: [Errno 2] No such file or directory: '/home/user/FunGAP/s_hep_self/trinity_out/trinity_SRR29464655/Trinity-GG.fasta' -> '/home/user/FunGAP/s_hep_self/trinity_out/trinity_SRR29464655/Trinity_SRR29464655.fasta'
Traceback (most recent call last):
File "/home/user/FunGAP/fungap.py", line 839, in
main()
File "/home/user/FunGAP/fungap.py", line 190, in main
logger
File "/home/user/FunGAP/fungap.py", line 393, in run_trinity
check_call(command_args)
File "/home/user/anaconda3/envs/fungap/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/user/FunGAP/run_trinity.py', '--bam_files', '/home/user/FunGAP/s_hep_self/hisat2_out/SRR29464655.bam', '--output_dir', '/home/user/FunGAP/s_hep_self/trinity_out', '--log_dir', '/home/user/FunGAP/s_hep_self/logs', '--num_cores', '28', '--max_intron', '2000', '--jaccard_clip']' returned non-zero exit status 1.
Upon checking the logs, the file trinity_SRR29464655.log , encountered the error: Trinity version: Trinity-v2.12.0
Tuesday, April 29, 2025: 18:28:52 CMD: /home/user/anaconda3/envs/fungap/opt/trinity-2.12.0/util/support_scripts/ensure_coord_sorted_sam.pl /home/user/FunGAP/s_hep_self/hisat2_out/SRR29464655.bam
** NOTE: Latest version of Trinity is Trinity-v2.15.2, and can be obtained at:
https://github.com/trinityrnaseq/trinityrnaseq/releases
-appears to be a coordinate sorted bam file. ok.
samtools view: writing to standard output failed: Broken pipe
samtools view: error reading file "/home/user/FunGAP/s_hep_self/hisat2_out/SRR29464655.bam": Broken pipe
samtools view: error closing standard output: -1
Error, cannot determine salmon version installed from (salmon: error while loading shared libraries: libboost_iostreams.so.1.85.0: cannot open shared object file: No such file or directory
) at /home/user/anaconda3/envs/fungap/bin/Trinity line 4051.
I also tried installing it in a fresh system but still the same.
I also tried installing the singularity docker image but the busco dataset error isn't getting resolved.
I also tried installing using docker , however,
there is some issue with the genemark filenames. "docker build -t fungap .
[+] Building 649.1s (9/10) docker:default
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 546B 0.0s
=> [internal] load metadata for docker.io/taniguti/fungap-base:v1.1.1 0.8s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [1/6] FROM docker.io/taniguti/fungap-base:v1.1.1@sha256:b84460e6c8b3b2feda78014a8e4e6a9e224599163fdc70e4c09ba58303312cd7 644.7s
=> => resolve docker.io/taniguti/fungap-base:v1.1.1@sha256:b84460e6c8b3b2feda78014a8e4e6a9e224599163fdc70e4c09ba58303312cd7 0.0s
=> => sha256:b84460e6c8b3b2feda78014a8e4e6a9e224599163fdc70e4c09ba58303312cd7 2.01kB / 2.01kB 0.0s
=> => sha256:a6236801494d5ca9acfae6569427398c2942c031375b96cac887cafe1de5a09b 80.38MB / 80.38MB 31.4s
=> => sha256:39e1693c4b6235a3ab419d341fda2bacebf9f009ecf03ab041e25cdd18685a8a 6.41kB / 6.41kB 0.0s
=> => sha256:852e50cd189dfeb54d97680d9fa6bed21a6d7d18cfb56d6abfe2de9d7f173795 27.11MB / 27.11MB 6.4s
=> => sha256:679c171d6942954a759f2d3a1dff911321940f23b0cdbe1d186f36bef0025124 52.98MB / 52.98MB 11.1s
=> => extracting sha256:852e50cd189dfeb54d97680d9fa6bed21a6d7d18cfb56d6abfe2de9d7f173795 0.8s
=> => sha256:ef30dbf9acca902eabdf15cfe0ade653b9d04f8721743e2d2bb1daccc89b4e79 3.18GB / 3.18GB 545.9s
=> => sha256:4353ee556454fc2a4574644b017b211847c1d1b4dcbf05a6c8e5d4d975326008 1.39GB / 1.39GB 382.9s
=> => extracting sha256:a6236801494d5ca9acfae6569427398c2942c031375b96cac887cafe1de5a09b 2.0s
=> => sha256:d716013be0eff2d579f891aaf887d7660e447bd14d36868416c8d53bedfb74d4 148B / 148B 34.8s
=> => extracting sha256:679c171d6942954a759f2d3a1dff911321940f23b0cdbe1d186f36bef0025124 1.9s
=> => sha256:21c64686b6516ea51c9782ec239198a3c3b1fe37753e7596186475bb7417c41d 1.18GB / 1.18GB 333.5s
=> => sha256:cdddf06f2e175e76fb3b8073ee94d876be5336ce59c112fc3944bf79fc27bcf3 15.25MB / 15.25MB 339.1s
=> => extracting sha256:ef30dbf9acca902eabdf15cfe0ade653b9d04f8721743e2d2bb1daccc89b4e79 50.0s
=> => extracting sha256:4353ee556454fc2a4574644b017b211847c1d1b4dcbf05a6c8e5d4d975326008 32.5s
=> => extracting sha256:d716013be0eff2d579f891aaf887d7660e447bd14d36868416c8d53bedfb74d4 0.0s
=> => extracting sha256:21c64686b6516ea51c9782ec239198a3c3b1fe37753e7596186475bb7417c41d 14.4s
=> => extracting sha256:cdddf06f2e175e76fb3b8073ee94d876be5336ce59c112fc3944bf79fc27bcf3 0.2s
=> [internal] load build context 0.1s
=> => transferring context: 18.28MB 0.1s
=> [2/6] COPY gmes_linux_64.tar.gz /workspace/FunGAP/external/ 2.9s
=> [3/6] COPY gm_key_64.gz /workspace/FunGAP/external/ 0.0s
=> [4/6] WORKDIR /workspace/FunGAP/external/ 0.0s
=> ERROR [5/6] RUN tar -zxvf gmes_linux_64_4.tar.gz && gunzip gm_key_64.gz && cp gm_key_64 ~/.gm_key && cd /workspace/FunGAP/external/gmes_linux_64_4/ && cp other/reformat_fasta.pl 0.5s
[5/6] RUN tar -zxvf gmes_linux_64_4.tar.gz && gunzip gm_key_64.gz && cp gm_key_64 ~/.gm_key && cd /workspace/FunGAP/external/gmes_linux_64_4/ && cp other/reformat_fasta.pl . && perl change_path_in_perl_scripts.pl "/usr/bin/env perl":
0.495 tar (child): gmes_linux_64_4.tar.gz: Cannot open: No such file or directory
0.495 tar (child): Error is not recoverable: exiting now
0.495 tar: Child returned status 2
0.495 tar: Error is not recoverable: exiting now
Dockerfile:11
10 | WORKDIR /workspace/FunGAP/external/
11 | >>> RUN tar -zxvf gmes_linux_64_4.tar.gz
12 | >>> && gunzip gm_key_64.gz
13 | >>> && cp gm_key_64 ~/.gm_key
14 | >>> && cd $FUNGAP_DIR/external/gmes_linux_64_4/
15 | >>> && cp other/reformat_fasta.pl .
16 | >>> && perl change_path_in_perl_scripts.pl "/usr/bin/env perl"
17 |
ERROR: failed to solve: process "/bin/sh -c tar -zxvf gmes_linux_64_4.tar.gz && gunzip gm_key_64.gz && cp gm_key_64 ~/.gm_key && cd $FUNGAP_DIR/external/gmes_linux_64_4/ && cp other/reformat_fasta.pl . && perl change_path_in_perl_scripts.pl "/usr/bin/env perl"" did not complete successfully: exit code: 2"
Any help is welcome.
Thanks and Regards
Jatin