ERROR: CMD ended with status code 1

[vini8cs]

Hi! I'm encountering an issue with Trans-Abyss that appears to be a problem in the code. When executing the abyss-filtergraph command, it seems that too many arguments are being passed to the function abyss-filtergraph:

CMD: bash -euo pipefail -c 'abyss-filtergraph --shim --assemble --kmer=25 --island=0 --remove=/home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.braid.cids --graph=/home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.filtered.adj1 /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-1.adj /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-1.fa > /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.path'
abyss-filtergraph: too many arguments
Try abyss-filtergraph --help for more information.
ERROR: CMD ended with status code 1

I attempted to address this issue by removing the last argument, achieved by deleting this line, but the problem persists:

remove_rref_cmd_params1.append(last_good_fasta)

While attempting to merge the contigs, another issue arises:

CMD: bash -euo pipefail -c 'abyss-filtergraph --shim --assemble --kmer=25 --island=0 --remove=/home/apis/Gabriela_data_metagenomics/SRR1370499 2/25_assembly_trans_abyss-unitigs.r1.braid.cids --graph=/home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.f iltered.adj1 /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-1.adj > /home/apis/Gabriela_data_metagenomics/SRR137049 92/25_assembly_trans_abyss-unitigs.r1.path'
Elapsed time: 0 h 0 m 17 s
CMD: bash -euo pipefail -c 'MergeContigs --kmer=25 --out=/home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1. filtered.fa --adj --graph=/home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.filtered.adj /home/apis/Gabriel a_data_metagenomics/SRR13704992/25_assembly_trans_abyss-1.fa /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs .r1.filtered.adj1 /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.path'
error: unexpected ID: 113'
Aborted (core dumped)
Elapsed time: 0 h 0 m 47 s
ERROR: CMD ended with status code 134

What should I do?

[kmnip]

Please confirm whether you have the correct version of ABySS installed.
As mentioned in our README, Trans-ABySS only works with ABySS version 2.0.x, e.g. https://github.com/bcgsc/abyss/releases/tag/2.0.3
If you installed Trans-ABySS and its dependencies with conda, you shouldn't have any issues.

[vini8cs]

However, for some reason, I am unable to download the 2.0.3 version using conda, even when I specify the version. The installation only proceeds with the 1.5.2 version. I will attempt to install it from the source instead.

[vlad0x00]

That often happens if there are conflicting versions with other installed packages. You can try installing abyss and transabyss in a fresh conda environment.

[kmnip]

Yes, I agree with @vlad0x00. Please install Trans-ABySS into a dedicated conda environment, e.g.

conda create -n transabyss -c bioconda transabyss

Activate this environment and try your assembly again:

conda activate transabyss
transabyss ...