[shovill] Assembly failed - spades.fasta has zero contigs!

[firstpachar]

Hello I ran Shovill previously. it is totally fine. However, I just got this problem this month. it looks like there is some problem with Spades. could you help me figure it our what I have done wrong

Thank you so much
Pacharapong

[spades] == Error == system call for: "['/usr/local/Cellar/spades/3.15.3/bin/spades-core', '/Users/pacharapongkhrongsee/Desktop/phage_project/MiGS_sequencing/Bp82_newyear/proline/spades/K31/configs/config.info', '/Users/pacharapongkhrongsee/Desktop/phage_project/MiGS_sequencing/Bp82_newyear/proline/spades/K31/configs/isolate_mode.info']" finished abnormally, OS return value: 22
[spades] None
[spades]
[spades] In case you have troubles running SPAdes, you can write to [email protected]
[spades] or report an issue on our GitHub re
(https://github.com/tseemann/shovill/files/7907386/shovill.log)
pository github.com/ablab/spades
[spades] Please provide us with params.txt and spades.log files from the output directory.
[spades]
[spades] SPAdes log can be found here: /Users/pacharapongkhrongsee/Desktop/phage_project/MiGS_sequencing/Bp82_newyear/proline/spades/spades.log
[spades]
[spades] Thank you for using SPAdes!
[shovill] Assembly failed - spades.fasta has zero contigs! [shovill.log
spades.log
shovill.log
]

[arptier]

I also got this error and attempted the following (none of which solved the problem):

1. Re-downloaded the fastq files
2. Changed the assembler to SKESA (also had zero contigs)
3. Ran spades alone (failed)

It seems the problem is with the reads, because the error also includes that there are an unequal number of reads between the two fastq files (see printout below from spades--full file name redacted). This was one of 100 assemblies I was able to do successfully with shovill, so I don't think it's a problem with shovill, and the fact that SKESA gave the same result suggests it's not an issue with spades either.

 0:00:03.769    21M / 293M  ERROR   General                 (paired_readers.cpp        :  37)   The number of right read-pairs is larger than the number of left read-pairs
 0:00:03.769    21M / 293M  ERROR   General                 (paired_readers.cpp        :  41)   Unequal number of read-pairs detected in the following files: /fastq/SRR10123349_1.fastq  /fastq/SRR10123349_2.fastq