Comments (4)
iankorf
commented on August 21, 2024
Possibly a permissions issue or a stale file handle?
… On Jun 22, 2022, at 5:59 AM, Christina Pavloudi ***@***.***> wrote:
Hello!
I know that CEGMA is no longer being supported but I thought of asking, just in case.
I am trying to run this command
cegma --genome genome.masked.fa -threads 40
but I get this output
Loading CEGMA/v2
Loading requirement: ncbi-blast/2.12.0+ hmmer/3.3 geneid/1.4.4
** MAPPING PROTEINS TO GENOME (TBLASTN) **
Negative repeat count does nothing at /mnt/big/bioSW/CEGMA/v2/bin/cegma line 339.
Negative repeat count does nothing at /mnt/big/bioSW/CEGMA/v2/bin/cegma line 339.
RUNNING: genome_map -n genome -p 6 -o 5000 -c 2000 -t 40 path/data/kogs.fa genome.masked.fa 2>output.cegma.errors
FATAL ERROR when running genome_map 32512: ""
readdir() attempted on invalid dirhandle DIR at /mnt/big/bioSW/CEGMA/v2/bin/cegma line 320.
closedir() attempted on invalid dirhandle DIR at /mnt/big/bioSW/CEGMA/v2/bin/cegma line 321.
Ending CEGMA
and this error
sh: 1: path/bin/genome_map: not found
Do you have any idea what might be going on?
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cpavloud
commented on August 21, 2024
This is what the folder looks like
drwxr-x--- 2 root users 242 Jun 3 2020 .
drwxr-x--- 16 root users 4096 Jun 3 2020 ..
-rwxr-x--- 1 root users 27792 Jun 3 2020 cegma
-rwxr-x--- 1 root users 28420 Jun 3 2020 cegma.mod.pl
-rwxr-x--- 1 root users 11478 Jun 3 2020 completeness
-rwxr-x--- 1 root users 11874 Jun 3 2020 completeness.mod.pl
-rwxr-x--- 1 root users 3761 Jun 3 2020 geneid-train
-rwxr-x--- 1 root users 15582 Jun 3 2020 genome_map
-rwxr-x--- 1 root users 5940 Jun 3 2020 hmm_select
-rwxr-x--- 1 root users 8684 Jun 3 2020 local_map
-rwxr-x--- 1 root users 4176 Jun 3 2020 make_paramfile
-rwxr-x--- 1 root users 6151 Jun 3 2020 parsewise
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maolulu1
commented on August 21, 2024
"Have you solved it?"
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maolulu1
commented on August 21, 2024
这是文件夹的样子
drwxr-x--- 2 root 用户 242 3 6月 2020 . drwxr-x--- 16 root 用户 4096 3 6月 2020 .. -rwxr-x--- 1 个 root 用户 27792 3 6月 2020 cegma -rwxr-x--- 1 root users 28420 3 6月 2020 cegma.mod.pl -rwxr-x--- 1 root users 11478 3 6月 2020 completeness -rwxr-x--- 1 root users 11874 3 6月 2020 completeness.mod.pl -rwxr-x--- 1 root users 3761 3 6月 2020 geneid-train -rwxr-x--- 1 root users 15582 3 6月 2020 genome_map -rwxr-x--- 1 root users 5940 3 6月 2020 hmm_select-rwxr-x--- 1 个 root 用户 8684 3 6月 2020 local_map -rwxr-x--- 1 root users 4176 3 6月 2020 make_paramfile -rwxr-x--- 1 root users 6151 3 6月 2020 parsewise
我也出现了这种情况，请问您现在解决了吗
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