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PASA software
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Thread 4 terminated abnormally: Can't open file /tmp/pasa.1642948049-0.114172514136047 #235

Open Aannaw opened 2 years ago

Aannaw commented 2 years ago

Hello,everyone I installed PASA with a conda environment. My command is :/data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/Launch_PASA_pipeline.pl -c align.conf -C -R -g Split-1.fa -t 1.Ma6.cdhit.trinity.fasta.clean -T -u 1.Ma6.cdhit.trinity.fasta --ALIGNERS blat --CPU 30. But I got the error:

* [Sun Jan 23 22:26:08 2022] Running CMD: /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/assemble_clusters.dbi -G Split-1.fa  -M '/data/01/user157/fenshu/fenshu.annotation/EST/pasa/Ma6/03.pasa/02.run.pasa/all/1/all.sqlite'  -T 30  > all.sqlite.pasa_alignment_assembly_building.ascii_illustration
s.out
Thread 4 terminated abnormally: Can't open file /tmp/pasa.1642948049-0.114172514136047.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 2.Thread 6 terminated abnormally: Can't open file /tmp/pasa.1642948049-0.23185840326278.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlL
ib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 2.
Thread 5 terminated abnormally: Can't open file /tmp/pasa.1642948049-0.821591424829425.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/Perl
Lib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 2.Thread 7 terminated abnormally: Can't open file /tmp/pasa.1642948049-0.0335138766831768.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/Per
lLib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 1.
Thread 1 terminated abnormally: Can't open file /tmp/pasa.1642948050-0.628015166455047.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 2.
ERROR, thread 1 exited with error Can't open file /tmp/pasa.1642948050-0.628015166455047.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 2.

I checked and found all the files "data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm" are present and are executable. Anyone got the error? could you give any suggestions? Best wishes!

brianjohnhaas commented 2 years ago

hi,

Sorry, there's nothing obvious here as to why it failed. If you rerun the original Launch PASA command, it should pick up where it left off and retry any failures. You might need to discard the -C parameter since the database is already created, though.

Also, for future pasa runs, if you upgrade to the latest release, it has better support for multithreading with pblat and the other aligners.

best,

~b

On Mon, Feb 14, 2022 at 8:43 PM Aannaw @.***> wrote:

Hello,everyone I installed PASA with a conda environment. My command is :/data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/Launch_PASA_pipeline.pl -c align.conf -C -R -g Split-1.fa -t 1.Ma6.cdhit.trinity.fasta.clean -T -u 1.Ma6.cdhit.trinity.fasta --ALIGNERS blat --CPU 30. But I got the error:

  • [Sun Jan 23 22:26:08 2022] Running CMD: /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/assemble_clusters.dbi -G Split-1.fa -M '/data/01/user157/fenshu/fenshu.annotation/EST/pasa/Ma6/03.pasa/02.run.pasa/all/1/all.sqlite' -T 30 > all.sqlite.pasa_alignment_assembly_building.ascii_illustration s.out Thread 4 terminated abnormally: Can't open file /tmp/pasa.1642948049-0.114172514136047.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 2.Thread 6 terminated abnormally: Can't open file /tmp/pasa.1642948049-0.23185840326278.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlL ib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 2. Thread 5 terminated abnormally: Can't open file /tmp/pasa.1642948049-0.821591424829425.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/Perl Lib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 2.Thread 7 terminated abnormally: Can't open file /tmp/pasa.1642948049-0.0335138766831768.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/Per lLib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 1. Thread 1 terminated abnormally: Can't open file /tmp/pasa.1642948050-0.628015166455047.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 2. ERROR, thread 1 exited with error Can't open file /tmp/pasa.1642948050-0.628015166455047.+.in at /data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 232, <$fh> line 2.

I checked and found all the files "data/00/user/user157/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm" are present and are executable. Anyone got the error? could you give any suggestions? Best wishes!

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Aannaw commented 2 years ago

Hi I installed the latest version v2.5.2 following the guide https://github.com/PASApipeline/PASApipeline/wiki/Pasa_installation_instructions and https://github.com/PASApipeline/PASApipeline/blob/master/Docker/Dockerfile. Then I run the command /data/01/user157/software/PASApipeline/Launch_PASA_pipeline.pl -c align.conf -C -R -g Split-1.fa -t 1.Ma6.cdhit.trinity.fasta.clean -T -u 1.Ma6.cdhit.trinity.fasta --ALIGNERS blat --CPU 30 &&/data/01/user157/software/PASApipeline/scripts/pasa_asmbls_to_training_set.dbi --pasa_transcripts_fasta all.sqlite.assemblies.fasta --pasa_transcripts_gff3 all.sqlite.pasa_assemblies.gff3 > 02.pasa_asmbls_to_training_set.log. But I go tan error: Can't exec "cdbfasta": No such file or directory at /data/01/user157/software/PASApipeline/PerlLib/CdbTools.pm line 58.. It seems that I need to install cbdasta but I do not find the pre-requirements is needed in the above installing guide. Could give me any suggestions? Best wishes! 01.pasa.err.log 01.pasa.out.log

Aannaw commented 2 years ago

Hello When I check, it seems that my pasapipeline installation is incorrect. I found in the PASApipeline , there is no bin directory. So I then run the make command and the bin directory generates. Then I again run the command above.

brianjohnhaas commented 2 years ago

Is it working ok now?

On Wed, Feb 16, 2022 at 9:46 PM Aannaw @.***> wrote:

Hello When I check, it seems that my pasapipeline installation is incorrect. I found in the PASApipeline , there is no bin directory. So I then run the make command and the bin directory generates. Then I again run the command above.

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Aannaw commented 2 years ago

Hello,professor It seems that works and finish and the log file is no error infomation. But the output directory has many empty tmp file. And the results is weird. When I check the fileMa6.sqlite.assemblies.fasta.transdecoder.genome.gff3, which I plan to run EVMas input file. When I use "awk '{if($3=="gene")print $5-$4}' Ma6.sqlite.assemblies.fasta.transdecoder.genome.gff3 | wc -l " to calculate gene number, the gene number is 100299, which is impossible. And "awk '{if($3=="gene")print $5-$4}' Ma6.sqlite.assemblies.fasta.transdecoder.genome.gff3 | awk '{sum+=$1} END {print "Average = ", sum/NR}‘" to calculated the gene length , the gene average length is 29023.2.
Could you give me any suggestions about so large number of gene numbers. Or I need to do some pre-deal with the Ma6.sqlite.assemblies.fasta.transdecoder.genome.gff3 and then use as the input as EVM? 01.pasa.err.txt 01.pasa.out.txt pasa

brianjohnhaas commented 2 years ago

The best thing to do is to look at the results in IGV or some genome viewer and see if they make sense.

If you need to define a gene count and want to avoid including minimally supported gene annotations, you could leverage the expression data like so:

https://github.com/trinityrnaseq/trinityrnaseq/wiki/There-are-too-many-transcripts!-What-do-I-do%3F

(which is targeted to Trinity assemblies, but would work here more generally too)

~b

On Fri, Feb 18, 2022 at 2:06 AM Aannaw @.***> wrote:

Hello,professor It seems that works and finish and the log file is no error infomation. But the output directory has many empty tmp file. And the results is weird. When I check the file Ma6.sqlite.assemblies.fasta.transdecoder.genome.gff3, which I plan to run EVM as input file. When I use "awk '{if($3=="gene")print $5-$4}' Ma6.sqlite.assemblies.fasta.transdecoder.genome.gff3 | wc -l " to calculate gene number, the gene number is 100299, which is impossible. And " awk '{if($3=="gene")print $5-$4}' Ma6.sqlite.assemblies.fasta.transdecoder.genome.gff3 | awk '{sum+=$1} END {print "Average = ", sum/NR}‘" to calculated the gene length , the gene average length is 29023.2. Could you give me any suggestions about so large number of gene numbers. Or I need to do some pre-deal with the Ma6.sqlite.assemblies.fasta.transdecoder.genome.gff3 and then use as the input as EVM? 01.pasa.err.txt https://github.com/PASApipeline/PASApipeline/files/8094812/01.pasa.err.txt 01.pasa.out.txt https://github.com/PASApipeline/PASApipeline/files/8094813/01.pasa.out.txt [image: pasa] https://user-images.githubusercontent.com/82857778/154633925-1280892b-408c-4f0b-b40a-66360e577580.png

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