zorro fails on opening amos bank/ missing file zorro.REPASSEMBLY.bnk/RED.ifo

[Juliane]

Dear Zorro team,

I am trying to use zorro for merging two de novo mira assemblies of an invertebrate transcriptome (using contigs, not scaffolds).

Unfortunately no merged contigs or singletons are returned (files are created but are empty).

As far as I can see it, the problem seems to be that the amos bank gets locked (maybe a program accessing the bank crashed and thereby locked it?).
Another problem (maybe related) seems to be that zorro.REPASSEMBLY.bnk/RED.ifo is empty. I am using amos version 3.1.0.

(I am posting the log from the zorro run at the end of this post, because attaching files doesn't work at the moment)

Do you have any idea what might be going on?

Thanks a lot for your help!

Best regards,
Juliane

Zorro log:

$ zorro.pl -1 assembly1 -2 assembly2 -r reads.subsample -p zorro
Loading assembly1...DONE
Loading assembly2...DONE

==> ENFORCING CONSISTENCY BETWEEN ASSEMBLY1 AND ASSEMBLY2
Running nucmer (alignAssembliesBRK)...DONE
Running delta-filter (alignAssembliesBRK)...DONE
Running show-coords (alignAssembliesBRK)...DONE
Generating new fasta files for assembly1...DONE
Generating new fasta file for assembly2...DONE
FIXED ASSEMBLY1: zorro.assembly1.BRK
FIXED ASSEMBLY2: zorro.assembly2.BRK

==> REPEAT MASKING
Counting 22-mers in reads.subsample...DONE
Generating kmer-cov-plot for zorro.reads.22mers...DONE
Generating kmer frequency histogram for zorro.assembly1.22mers_covplot...DONE
Generating masking file zorro.reads.22mers.cutoff4...DONE
Generating masking file zorro.reads.22mers.cutoff6...DONE
Running bowtie-build (zorro.assembly1.BRK,zorro.reads.22mers.cutoff4)...Running bowtie (zorro.assembly1.BRK,zorro.reads.22mers.cutoff4)...DONE
Merging neighbouring masked regions for zorro.assembly1.BRK...DONE
Running bowtie-build (zorro.assembly2.BRK,zorro.reads.22mers.cutoff4)...Running bowtie (zorro.assembly2.BRK,zorro.reads.22mers.cutoff4)...DONE
Merging neighbouring masked regions for zorro.assembly2.BRK...DONE

===> CORE ASSEMBLY
Creating AMOS BANK...Max ID: 594717
DONE
Mapping old contig ids to new AMOS BANK ids...DONE
Running nucmer with masked sequences...DONE
Parsing pairs of aligned sequences...DONE
Running nucmer with unmasked sequences...DONE
Filtering confident overlaps...DONE
Converting confident overlaps to AMOS format...DONE
Loading overlaps to AMOS BANK...DONE
Making hybrid contigs layout...DONE
Calling hybrid contigs consensus...DONE
Retrieving hybrid contigs from AMOS BANK...Failed to open contig account in bank zorro.ALL.bnk:
WHAT: Could not open bank for reading, locked by 'w 2338 jwippler'
LINE: 1164
FILE: Bank_AMOS.cc

DONE
Retrieving singlets from AMOS BANK...DONE

===> TRIM REPETITIVE CONTIG ENDS (up to 100 bp)  COVERED BY ONLY 1 ASSEMBLY
Running bowtie-build (zorro.hybrid.fasta,zorro.reads.22mers.cutoff6)...Running bowtie (zorro.hybrid.fasta,zorro.reads.22mers.cutoff6)...DONE
Merging neighbouring masked regions for zorro.hybrid.fasta...DONE
Retrieving consensus positions covered by a single source assembly...DONE
Retrieving repetitive consensus positions and marking positions to be trimmed...DONE
Trimming repetitive contig ends covered by only one source assembly...DONE

===> FORCING SINGLETS ASSEMBLY
Loading sequences into a new AMOS BANK...DONE
Mapping old contig ids to new AMOS BANK ids...DONE
Finding rep overlaps...Starting on Tue Nov 20 14:10:36 2012

Read bank is zorro.REPASSEMBLY.bnk
Alignment error rate is 0.06
Minimum overlap bases is 40
** AMOS Exception **
WHAT: Could not open bank file, zorro.REPASSEMBLY.bnk/RED.ifo, No such file or directory
LINE: 1264
FILE: Bank_AMOS.cc

DONE
Layout... AMOS Read Bank zorro.REPASSEMBLY.bnk does not exist
 AMOS Overlap Bank zorro.REPASSEMBLY.bnk does not exist
 total contained reads hidden 0
 number of contigs 0
 total contained reads unhidden 0
 Writing layouts to bank zorro.REPASSEMBLY.bnk
DONE
Calling rep contigs consensus...Starting on Tue Nov 20 14:10:36 2012

Read bank is zorro.REPASSEMBLY.bnk
Alignment error rate is 0.06
Minimum overlap bases is 5
Output will be written to the bank
Input is being read from the bank
** AMOS Exception **
WHAT: Could not open bank file, zorro.REPASSEMBLY.bnk/RED.ifo, No such file or directory
LINE: 1264
FILE: Bank_AMOS.cc

DONE
Retrieving hybrid contigs from AMOS BANK...Failed to open contig account in bank zorro.REPASSEMBLY.bnk:
WHAT: Could not open bank for reading, locked by 'w 2338 jwippler'
LINE: 1164
FILE: Bank_AMOS.cc

DONE
Retrieving singlets from AMOS BANK...DONE

===> FINISHING ZORRO ASSEMBLY
Renaming final contigs...DONE
DONE

[Erik Lysøe]

Hi

I have exactly the same problem, could not open bank for reading.

Anybody?

Cheers
Erik