Open lizzymomo opened 3 years ago
It's highly likely that there are sequences with the same name in your input contig file. Can you double check?
It's highly likely that there are sequences with the same name in your input contig file. Can you double check?
Indeed. Now it can run successfully after I remove duplicated sequence names. Thank you for your reply!
Dear jiarong, I'm using virsoter 2.2.1 and stucked in an error when running virsorter. The error occur after Step 2 - extract-feature finished. The linux command is:
main()
File "/lustre1/hqzhu_pkuhpc/mli/6_proj/comparison/vs2/VirSorter2/virsorter/./scripts/add-extra-to-table.py", line 64, in main
if max_score_group_ser.loc[i] != df_info.loc[i, 'max_score_group']:
File "/lustre1/hqzhu_pkuhpc/mli/6_proj/comparison/vs2/VirSorter2/db/conda_envs/e6a1828d/lib/python3.8/site-packages/pandas/core/generic.py", line 1478, in nonzero
raise ValueError(
ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().
[Wed Apr 14 15:53:51 2021]
Error in rule finalize:
jobid: 7
output: final-viral-score.tsv, final-viral-combined.fa, final-viral-boundary.tsv
conda-env: /lustre1/hqzhu_pkuhpc/mli/6_proj/comparison/vs2/VirSorter2/db/conda_envs/e6a1828d
shell:
virsorter run -w vs2_out -i contigs.fa --min-score 0.5 -j 20 all
Here is the error message: [2021-04-14 12:25 INFO] # of seqs < 0 bp and removed: 0 [2021-04-14 12:25 INFO] # of circular seqs: 82 [2021-04-14 12:25 INFO] # of linear seqs : 199918 [2021-04-14 12:25 INFO] Finish spliting circular contig file with common rbs [2021-04-14 12:25 INFO] Finish spliting linear contig file with common rbs [2021-04-14 12:28 INFO] Step 1 - preprocess finished. [2021-04-14 15:18 INFO] Step 2 - extract-feature finished. Traceback (most recent call last): File "/lustre1/hqzhu_pkuhpc/mli/6_proj/comparison/vs2/VirSorter2/virsorter/./scripts/add-extra-to-table.py", line 72, inExiting because a job execution failed. Look above for error message
What might be the problem? Thank you for your help!