Permission denied

[TKsh6]

When I ran the test data, I met this problem, command line: nohup ./argoap_pipeline_stageone_version2.3 -i example/inputfqs -o testoutdir -m example/meta-data.txt -n 8 error:

testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 4: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/diamondv0.9.24: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 5: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/diamondv0.9.24: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 6: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/bbmap/repair.sh: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 7: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/minimap2: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 8: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/extract_usearch_reads.pl: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 9: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/extract_usearch_reads.pl: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 12: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/diamond: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 13: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/diamond: Permission denied
cat: testoutdir/STAS.uscmg_1.dmd: No such file or directory
cat: testoutdir/STAS.uscmg_2.dmd: No such file or directory
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 18: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/diamondv0.9.24: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 19: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/diamondv0.9.24: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 20: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/bbmap/repair.sh: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 21: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/minimap2: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 22: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/extract_usearch_reads.pl: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 23: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/extract_usearch_reads.pl: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 26: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/diamond: Permission denied
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 27: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/diamond: Permission denied
cat: testoutdir/SWHAS104.uscmg_1.dmd: No such file or directory
cat: testoutdir/SWHAS104.uscmg_2.dmd: No such file or directory
testoutdir/ublastx_bash_Thu-Mar-9-15:49:48-2023.sh: line 30: /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/merge_extracted_fa_update_metadate.v2.3.pl: Permission denied
diamond
/bin/bash: line 7: diamond: command not found

So how can I do to solve this?

yours tk,

[TKsh6]

so I changed the mode, it worked. But I had another problem

Set INTERLEAVED to false
Started output stream.

Input:                          200000 reads            20000000 bases.
Result:                         200000 reads (100.00%)  20000000 bases (100.00%)
Pairs:                          200000 reads (100.00%)  20000000 bases (100.00%)
Singletons:                     0 reads (0.00%)         0 bases (0.00%)

Time:                           1.112 seconds.
Reads Processed:        200k    179.80k reads/sec
Bases Processed:      20000k    17.98m bases/sec
/beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/minimap2: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/minimap2)

[biofuture]

It may from your fastq file, the file somehow have problem. You can have a check at the integrety of your data.

TKsh6 @.***> 于 2023年3月9日周四 19:16写道：

so I changed the mode, it worked. But I had another problem

Set INTERLEAVED to false Started output stream.

Input: 200000 reads 20000000 bases. Result: 200000 reads (100.00%) 20000000 bases (100.00%) Pairs: 200000 reads (100.00%) 20000000 bases (100.00%) Singletons: 0 reads (0.00%) 0 bases (0.00%)

Time: 1.112 seconds. Reads Processed: 200k 179.80k reads/sec Bases Processed: 20000k 17.98m bases/sec /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/minimap2: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by /beegfs/home/syl/database_db/arg/Ublastx_stageone2.3/bin/minimap2)

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[TKsh6]

ok, thanks,. I have solved it.