Question: PASA: Error during sample run
0
gravatar for Chirag Parsania
3.3 years ago by
Chirag Parsania1.4k
University of Macau
Chirag Parsania1.4k wrote:

Dear All

I running PASA on sample data with following command. But unfortunately I encountered an error. Please help.

Command :

Command 1 : ../scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS gmap,blat --CPU 2

ERROR:1

Unable to retrieve queryseq for request

Error, cmd: gmap -D . -d genome_sample.fasta.gmap all_transcripts.fasta.clean -f 3 -n 0 -x 50 -t 2 -B 5  --intronlength=500000  died with ret (2304) at /usr/local/bin/PASA/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl line 108.

Thread 1 terminated abnormally: Error, cmd:

/usr/local/bin/PASA/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl --genome genome_sample.fasta  --transcripts all_transcripts.fasta.clean --CPU 2 -N 1  -I 500000  > gmap.spliced_alignments.gff3

 died with ret (512) at /usr/local/bin/PASA/scripts/../PerlLib/Process_cmd.pm line 18 thread 1.

Process_cmd::process_cmd("/usr/local/bin/PASA/scripts/process_GMAP_alignments_gff3_chim"...) called at /usr/local/bin/PASA/scripts/..//scripts/run_spliced_aligners.pl line 109 thread 1

main::run_gmap() called at /usr/local/bin/PASA/scripts/..//scripts/run_spliced_aligners.pl line 70 thread 1

eval {...} called at /usr/local/bin/PASA/scripts/..//scripts/run_spliced_aligners.pl line 70 thread 1

ERROR, thread 1 exited with error Error, cmd:

/usr/local/bin/PASA/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl --genome genome_sample.fasta  --transcripts all_transcripts.fasta.clean --CPU 2 -N 1  -I 500000  > gmap.spliced_alignments.gff3

 died with ret (512) at /usr/local/bin/PASA/scripts/../PerlLib/Process_cmd.pm line 18 thread 1.

Process_cmd::process_cmd("/usr/local/bin/PASA/scripts/process_GMAP_alignments_gff3_chim"...) called at /usr/local/bin/PASA/scripts/..//scripts/run_spliced_aligners.pl line 109 thread 1

main::run_gmap() called at /usr/local/bin/PASA/scripts/..//scripts/run_spliced_aligners.pl line 70 thread 1

eval {...} called at /usr/local/bin/PASA/scripts/..//scripts/run_spliced_aligners.pl line 70 thread 1


Thread(1) ERROR CMD: unknown Time to complete: 43 seconds

Thread(2) SUCCESS CMD: unknown Time to complete: 43 seconds

Error, 1 threads failed.

ERROR: The following command died with exit code (65280):

/usr/local/bin/PASA/scripts/..//scripts/run_spliced_aligners.pl --aligners gmap,blat --genome genome_sample.fasta --transcripts all_transcripts.fasta.clean -I 500000 -N 1 --CPU 2

Must re-run pipeline starting at index [2] via running Launch_PASA_pipeline with parameter '-s 2' (exclude param '-C' since db already created)

 

Command 2 : To get rid of this I have tried running PASA again but this time only with blat aligner.  Again I encountered new error as  shown below. Please help.

 

Error : 2

 

## Processing CMD: 15/25

16:49:36 CMD: /usr/local/bin/PASA/scripts/..//scripts/assemble_clusters.dbi -G genome_sample.fasta  -M sample_mydb_pasa  -T 2  > sample_mydb_pasa.pasa_alignment_assembly_building.ascii_illustrations.out

pasa(61207,0x7fff7688e000) malloc: *** mach_vm_map(size=7020674649187815424) failed (error code=3)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

libc++abi.dylib: terminating with uncaught exception of type std::bad_alloc: std::bad_alloc

sh: line 1: 61207 Abort trap: 6           /usr/local/bin/PASA/scripts/../bin/pasa /var/folders/cd/psplt0nn2j5918wr6sv4r1x80000gn/T//pasa.1455612576-0.296695261568861.+.in > /var/folders/cd/psplt0nn2j5918wr6sv4r1x80000gn/T//pasa.1455612576-0.296695261568861.+.out

PASA died on input file.  See pasa_killer.inputThread 1 terminated abnormally: Died at /usr/local/bin/PASA/scripts/..//PerlLib/CDNA/PASA_alignment_assembler.pm line 262.

ERROR, thread 1 exited with error Died at /usr/local/bin/PASA/scripts/..//PerlLib/CDNA/PASA_alignment_assembler.pm line 262.

Thanks

Chirag

blat myposts pasa gmap • 2.0k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Chirag Parsania1.4k
0
gravatar for Chirag Parsania
3.3 years ago by
Chirag Parsania1.4k
University of Macau
Chirag Parsania1.4k wrote:

Hi,

Do follow link below.

https://groups.google.com/forum/#!topic/pasapipeline-users/RGDWemVS-LI

Thanks 

Chirag

 

ADD COMMENTlink written 3.3 years ago by Chirag Parsania1.4k
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