Cd-hit-est problem

[anagaga27]

Hello, I'm trying to run panaroo but this problem came out:

subprocess.CalledProcessError: Command 'cd-hit-est -T 10 -i /home/agargam/TFM/Archivos gff/Archivos_GFF/CV_Schmerer_Salmeron_Carlos_Green/output_moderate_Carlos_2/tmp8kkiizc9/tmphnvod1mo -o /home/agargam/TFM/Archivos gff/Archivos_GFF/CV_Schmerer_Salmeron_Carlos_Green/output_moderate_Carlos_2/tmp8kkiizc9/tmpmyti8td1 -c 0.99 -s 0.0 -aL 0.0 -AL 99999999 -aS 99999999 -AS 99999999 -r 1 -M 0 -d 999 -mask NX -n 7 > /dev/null' returned non-zero exit status 1.

The first time I ran panaroo I had no problem, and I'm using the same parameters as then. Do you know why this error happens?

Thank you.

[nzmacalasdair]

Hello, I think this is almost definitely the same issue as #284. We've seen similar issues in the past (eg #247 and #253), and been unable to reproduce the error. It seems very likely to be a problem with the installation -- could you let me know how you installed panaroo, and also try running the cd-hit-est command on the file separately?

cd-hit-est -T 10 -i /home/agargam/TFM/Archivos gff/Archivos_GFF/CV_Schmerer_Salmeron_Carlos_Green/output_moderate_Carlos_2/tmp8kkiizc9/tmphnvod1mo -o /home/agargam/TFM/Archivos gff/Archivos_GFF/CV_Schmerer_Salmeron_Carlos_Green/output_moderate_Carlos_2/tmp8kkiizc9/tmpmyti8td1 -c 0.99 -s 0.0 -aL 0.0 -AL 99999999 -aS 99999999 -AS 99999999 -r 1 -M 0 -d 999 -mask NX -n 7

[anagaga27]

I've tried running the cd-hit-est command on the file separately, but I just get cd-hit options. I've reinstall panaroo in another new environmet, but the same error came out.

I install panaroo with mamba, as is specified in docs/gettingstarted/installation.md:

conda install mamba -c conda-forge mamba install -c conda-forge -c bioconda -c defaults 'panaroo>=1.3'

[nzmacalasdair]

Sorry, is there no error message when you try and run the cd-hit command outside of panaroo? If you could upload the message you see here when trying to run the command that would be great. It's also worth double checking that you're running it with the conda environment in which panaroo is installed active.

[anagaga27]

The environment is active, as panaroo creates these files: combined_DNA_CDS.fasta, combined_protein_cdhit_out.txt gene_data.csv, tmpl_2byl3b, combined_protein_CDS.fasta combined_protein_cdhit_out.txt.clstr, pre_filt_graph.gml but it stops with cd-hit.

If I run cd-hit outside I get usage ooptions, but no error message:

================================================================ Program: CD-HIT, V4.8.1 (+OpenMP), Apr 11 2024, 11:47:57 Command: cd-hit-est -T 10 -i /home/agargam/TFM/Archivos gff/Archivos_GFF/CV_Schmerer_Salmeron_Carlos_Green/output_moderate_Carlos_2/tmp8kkiizc9/tmphnvod1mo -o /home/agargam/TFM/Archivos gff/Archivos_GFF/CV_Schmerer_Salmeron_Carlos_Green/output_moderate_Carlos_2/tmp8kkiizc9/tmpmyti8td1 -c 0.99 -s 0.0 -aL 0.0 -AL 99999999 -aS 99999999 -AS 99999999 -r 1 -M 0 -d 999 -mask NX -n 7

Started: Thu Apr 18 07:47:25 2024

                        Output                              

---

    ====== CD-HIT version 4.8.1 (built on Apr 11 2024) ======

Usage: cd-hit [Options]

Options

-i input filename in fasta format, required, can be in .gz format -o output filename, required -c sequence identity threshold, default 0.9 this is the default cd-hit's "global sequence identity" calculated as: number of identical amino acids or bases in alignment divided by the full length of the shorter sequence -G use global sequence identity, default 1 if set to 0, then use local sequence identity, calculated as : number of identical amino acids or bases in alignment divided by the length of the alignment NOTE!!! don't use -G 0 unless you use alignment coverage controls see options -aL, -AL, -aS, -AS -b band_width of alignment, default 20 -M memory limit (in MB) for the program, default 800; 0 for unlimitted; -T number of threads, default 1; with 0, all CPUs will be used -n word_length, default 5, see user's guide for choosing it -l length of throw_away_sequences, default 10 -t tolerance for redundance, default 2 -d length of description in .clstr file, default 20 if set to 0, it takes the fasta defline and stops at first space -s length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to be at least 90% length of the representative of the cluster -S length difference cutoff in amino acid, default 999999 if set to 60, the length difference between the shorter sequences and the representative of the cluster can not be bigger than 60 -aL alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence -AL alignment coverage control for the longer sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the alignment must be >= 340 (400-60) residues -aS alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence -AS alignment coverage control for the shorter sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the alignment must be >= 340 (400-60) residues -A minimal alignment coverage control for the both sequences, default 0 alignment must cover >= this value for both sequences -uL maximum unmatched percentage for the longer sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tailing gaps) must not be more than 10% of the sequence -uS maximum unmatched percentage for the shorter sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tailing gaps) must not be more than 10% of the sequence -U maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be more than 10 bases -B 1 or 0, default 0, by default, sequences are stored in RAM if set to 1, sequence are stored on hard drive !! No longer supported !! -p 1 or 0, default 0 if set to 1, print alignment overlap in .clstr file -g 1 or 0, default 0 by cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast cluster). If set to 1, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode) but either 1 or 0 won't change the representatives of final clusters -sc sort clusters by size (number of sequences), default 0, output clusters by decreasing length if set to 1, output clusters by decreasing size -sf sort fasta/fastq by cluster size (number of sequences), default 0, no sorting if set to 1, output sequences by decreasing cluster size this can be very slow if the input is in .gz format -bak write backup cluster file (1 or 0, default 0) -h print this help

Questions, bugs, contact Weizhong Li at liwz@sdsc.edu For updated versions and information, please visit: http://cd-hit.org or https://github.com/weizhongli/cdhit

cd-hit web server is also available from http://cd-hit.org

If you find cd-hit useful, please kindly cite:

"CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences", Weizhong Li & Adam Godzik. Bioinformatics, (2006) 22:1658-1659 "CD-HIT: accelerated for clustering the next generation sequencing data", Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu & Weizhong Li. Bioinformatics, (2012) 28:3150-3152

[nzmacalasdair]

Hi,

Thanks for your patience. I did some additional testing today and was unable to reproduce this error using the same version (v4.8.1) of cd-hit, which makes me wonder if this is actually a problem with the generation of the input files during this step of panaroo.

Can I ask what platform (particularly which OS) you are using to run panaroo? Also, if you would also be willing to share a small dataset which can reproduce the error, that would allow me to investigate further.

Finally, to double check that this is not an install error, you could try running the cd-hit command on another file, for instance:

cd-hit-est -T 10 -i combined_DNA_CDS.fasta -o test1.cdhit -c 0.99 -s 0.0 -aL 0.0 -AL 99999999 -aS 99999999 -AS 99999999 -r 1 -M 0 -d 999 -mask NX -n 7