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A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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MetAMOS Warning: soapdenovo2 assembler did not run successfully! #215

Open TakashiKoyama opened 9 years ago

TakashiKoyama commented 9 years ago

Hello.

Sorry for give you questions several times. I got an error in soapdenovo2 assembly step. The soapdenovo2 ran out of memory in last post but at this time I did not see such message. Could you tell me reasons? Below is the part of ASSEMBLE.log where soapdenovo2 seems to be involved.

********************
Pregraph
********************

Parameters: pregraph -p 40 -K 89 -R -s /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/soap2config.txt -o /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/soapdenovo2.89.asm 

In /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/soap2config.txt, 7 lib(s), maximum read length 100, maximum name length 256.

40 thread(s) initialized.
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib6.fastq
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib7.fastq
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib4.1.fastq
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib4.2.fastq
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib3.1.fastq
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib3.2.fastq
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib2.1.fastq
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib2.2.fastq
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib5.1.fastq
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib5.2.fastq
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib1.1.fastq
Import reads from file:
 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib1.2.fastq
Time spent on hashing reads: 1s, 522658 read(s) processed.
LIB(s) information:
 [LIB] 0, avg_ins 0, reverse 0.
 [LIB] 1, avg_ins 0, reverse 0.
 [LIB] 2, avg_ins 340, reverse 0.
 [LIB] 3, avg_ins 348, reverse 0.
 [LIB] 4, avg_ins 360, reverse 0.
 [LIB] 5, avg_ins 361, reverse 0.
 [LIB] 6, avg_ins 398, reverse 0.
617057 node(s) allocated, 6065226 kmer(s) in reads, 6065226 kmer(s) processed.

Version 2.04: released on July 13th, 2012
Compile Jul  9 2013 11:57:30

********************
Contig
********************

Parameters: contig -g /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/soapdenovo2.89.asm -R -M 3 

Cannot open /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/soapdenovo2.89.asm.preGraphBasic. Now exit to system...

Version 2.04: released on July 13th, 2012
Compile Jul  9 2013 11:57:30

********************
Map
********************

Parameters: map -g /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/soapdenovo2.89.asm -p 40 -s /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/soap2config.txt 

Kmer size: 23.
Contig length cutoff: 25.
Cannot open /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/soapdenovo2.89.asm.contig. Now exit to system...

Version 2.04: released on July 13th, 2012
Compile Jul  9 2013 11:57:30

********************
Scaff
********************

Parameters: scaff -g /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/soapdenovo2.89.asm -p 40 

/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/soapdenovo2.89.asm.Arc: no such file or empty file!

Can not open file /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/soapdenovo2.89.asm.peGrads.
Cannot open /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/soapdenovo2.89.asm.preGraphBasic. Now exit to system...
Command line: /home/samba/public/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/spades/bin/spades.py -o spades.89/ -m 61 -t 40 --pe1-1 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib1.1.fastq --pe1-2 /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib1.2.fastq -k 21,33,89 --careful --phred-offset 33

System information:
  SPAdes version: 3.0.0
  Python version: 2.7.8
  OS: Linux-2.6.32-504.el6.x86_64-x86_64-with-centos-6.6-Final

Output dir: /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/spades.89
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib1.1.fastq']
      right reads: ['/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Preprocess/out/lib1.2.fastq']
      interlaced reads: not specified
      single reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset: 33
  Corrected reads will be compressed (with gzip)
Assembly parameters:
  k: [21, 33, 89]
  MismatchCorrector will be used
  Repeat resolution is enabled
Other parameters:
  Dir for temp files: /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/spades.89/tmp
  Threads: 40
  Memory limit (in Gb): 61
skoren commented 9 years ago

It looks like there was a failure early on in SOAPdenovo2:

Cannot open /home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/045p01/assembly1/Assemble/out/soapdenovo2.89.asm.preGraphBasic. Now exit to system...

As for the reason, I can't say why. You can try running the SOAPdenovo2 commands manually to see if they run or contact the SOAPdenovo2 developers. You can also just use one of the other assemblies generated by metAMOS. metAMOS can continue as long as one of the assemblers selected runs sucessfully.