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How to overcome OS return value: 4 with SPAdes

I have some reads from a phage/virus that I would like to assemble with SPAdes. I ran the following:

spades.py -1 phiM/Trimmed/phiM_1_TrmDed.fq.gz -2 phiM/Trimmed/phiM_2_TrmDed.fq.gz -o phiM/Assemble --isolate

but I got the error:

spades.py -1 phiM/Trimmed/phiM_1_TrmDed.fq.gz -2 phiM/Trimmed/phiM_2_TrmDed.fq.gz -o phiM/Assemble --isolate 
Command line: ***SPAdes/bin/spades.py   -1  ***phiM/Trimmed/phiM_1_TrmDed.fq.gz -2  ***phiM/Trimmed/phiM_2_TrmDed.fq.gz -o  ***phiM/Assemble    --isolate   

System information:
  SPAdes version: 4.2.0
  Python version: 3.13.7
  OS: Linux-6.15.10-200.fc42.x86_64-x86_64-with-glibc2.41

Output dir: ***phiM/Assemble
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
  Isolate mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['***phiM/Trimmed/phiM_1_TrmDed.fq.gz']
      right reads: ['***phiM_2_TrmDed.fq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: automatic selection based on read length
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
  Assembly graph output will use GFA v1.2 format
Other parameters:
  Dir for temp files: ***phiM/Assemble/tmp
  Threads: 16
  Memory limit (in Gb): 62


======= SPAdes pipeline started. Log can be found here: ***phiM/Assemble/spades.log

***phiM/Trimmed/phiM_1_TrmDed.fq.gz: max reads length: 150
***phiM/Trimmed/phiM_2_TrmDed.fq.gz: max reads length: 150

Reads length: 150

Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (150) is equal to or greater than 150

===== Before start started. 


===== Assembling started. 


===== K21 started. 


== Running: ***phiM/Assemble/K21/configs/config.info ***phiM/Assemble/K21/configs/isolate_mode.info

Exception caught conversion of data to type "std::filesystem::__cxx11::path" failed


== Error ==  system call for: "['***SPAdes/bin/spades-core', phiM/Assemble/K21/configs/config.info', '***phiM/Assemble/K21/configs/isolate_mode.info']" finished abnormally, 
**OS return value: 4**
None
...

Where do these config.info files come from?

I also tried with the --careful option instead of --isolate but I got the same error.

Also, what wold be the best option to assemble viral reads?

Thank you

spades de novo genome assemble
• 5,103 views • link
written by marongiu.luigi marongiu.luigi

1 answer

I am going to hazard a guess that the spaces and email address in file path (you may want to redact your email from post above) is causing this: /home/gigiux/Insync/xxxxx@gmail.com/Google Drive/_shareDir_/BactDir/Vibrio Spain/PHAGES/phiM/Assemble/K21/configs/config.info

Try running everything off local storage instead of google drive mount(?).

• 0 views • link
written by GenoMax GenoMax

Yep, that was it. I was using a G:-sync folder... Thank you.

• 0 views • link
written by marongiu.luigi marongiu.luigi

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