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Error about blastn #24

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Songq-20 opened this issue Feb 21, 2024 · 1 comment
Open

Error about blastn #24

Songq-20 opened this issue Feb 21, 2024 · 1 comment

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@Songq-20
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Hi Dr Chen:
I try to run COBRA today with

source activate cobra
cobra-meta -f Megahit_out/611PES1/611PES1_megahit.contigs.fa -q checkv_in/611RW.fa -o COBRA/611_RW_MV_COBRA -c coverage/611RW_coverage.txt -m mapping/611RW-MV.sam -a megahit -mink 21 -maxk 141
conda deactivate

and it works at beginning.
But it stop at cobra.py, line 1531:r = open('blastdb_2.vs.blastdb_1', 'r')
The error is

makeblastdb: error while loading shared libraries: libzstd.so.1: cannot open shared object file: No such file or directory
blastn: error while loading shared libraries: libzstd.so.1: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/data01nfs/user/songq/anaconda3/envs/cobra/bin/cobra-meta", line 10, in <module>
    sys.exit(main())
  File "/data01nfs/user/songq/anaconda3/envs/cobra/lib/python3.8/site-packages/cobra.py", line 1531, in main
    r = open('blastdb_2.vs.blastdb_1', 'r')
FileNotFoundError: [Errno 2] No such file or directory: 'blastdb_2.vs.blastdb_1'

blastdb_1.fa and blastdb_2.fa are written and not empty, and I also install BLAST in cobra env, so I guess The error was not caused by BLAST.
Please help me solve this problem, I am willing to provide you with any other information you need.
Thanks

@linxingchen
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Hi, thanks for reporting this issue.

Did you have the same issue while running other samples?

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