PASA: Error during sample run

Question

[Chirag Parsania]

Dear All

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

Commands:

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

Answer 1

[Chirag Parsania]

Hi,

Do follow link below.

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

Thanks
Chirag