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arzwa / wgd

Python package and CLI for whole-genome duplication related analyses. This package is deprecated in favor of https://github.com/heche-psb/wgd.
http://wgd.readthedocs.io/en/latest/
GNU General Public License v3.0
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WARNING:root:No codeml results #88

Closed abcbot123 closed 9 months ago

abcbot123 commented 9 months ago

Hi, I uesd WGD with the command : python3 wgd-1.1.2/wgd_cli.py ksd -o ./ -n 8 ./newCDS.fa.blast.tsv.mcl newCDS.fa

2024-01-04 00:37:01: INFO codeml stdout: AAML in paml version 4.9j, October 2019 2024-01-04 00:37:01: INFO codeml stderr: Error: file name empty.. 2024-01-04 00:37:01: INFO codeml found 2024-01-04 00:37:01: INFO mafft stdout: 2024-01-04 00:37:01: INFO mafft stderr: v7.453 (2019/Nov/8) 2024-01-04 00:37:01: INFO FastTree stdout: 2024-01-04 00:37:01: INFO FastTree stderr: Unknown or incorrect use of option --version

What are these stderr? Are those effect to the output?

I got these errors as well. How can I fix it?

2024-01-04 00:37:18: WARNING There were 0 warnings during translation 2024-01-04 00:37:18: INFO Started whole paranome Ks analysis 2024-01-04 00:37:18: WARNING Filtered out the 1 largest gene families because n*(n-1)/2 > max_pairwise 2024-01-04 00:37:18: WARNING If you want to analyse these large families anyhow, please raise the max_pairwise parameter. 2024-01-04 00:37:18: INFO Started analysis in parallel (n_threads = 8) ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000008.codeml WARNING:root:No codeml results for GF_000008! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000007.codeml WARNING:root:No codeml results for GF_000007! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000010.codeml WARNING:root:No codeml results for GF_000010! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000004.codeml WARNING:root:No codeml results for GF_000004! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000013.codeml WARNING:root:No codeml results for GF_000013! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000014.codeml WARNING:root:No codeml results for GF_000014! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000012.codeml WARNING:root:No codeml results for GF_000012! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000016.codeml WARNING:root:No codeml results for GF_000016! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000018.codeml WARNING:root:No codeml results for GF_000018! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000019.codeml WARNING:root:No codeml results for GF_000019! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000020.codeml WARNING:root:No codeml results for GF_000020! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000022.codeml WARNING:root:No codeml results for GF_000022! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000023.codeml WARNING:root:No codeml results for GF_000023! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000024.codeml WARNING:root:No codeml results for GF_000024! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000025.codeml WARNING:root:No codeml results for GF_000025! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000026.codeml WARNING:root:No codeml results for GF_000026! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000028.codeml WARNING:root:No codeml results for GF_000028! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000029.codeml WARNING:root:No codeml results for GF_000029! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000031.codeml WARNING:root:No codeml results for GF_000031! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000032.codeml WARNING:root:No codeml results for GF_000032! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000034.codeml WARNING:root:No codeml results for GF_000034! ERROR:root:Not all gene pairs present in /var/lib/condor/execute/slot1/dir_2232/ks_tmp.3c8cc74cc935be/GF_000036.codeml WARNING:root:No codeml results for GF_000036!

arzwa commented 9 months ago

Please consider using the latest version of wgd available here. If you would still have issues, you can raise them there.