ERROR: parse error in 1-consensus/consensus.fasta on line 1: empty sequence about flye HOT 9 CLOSED

Hi,

Seems very strange. Looks like the contigs were assembled, but consensus failed. Can you send me the full log, and also run 'ls -l 1-consensus' in the output directory? Is it possible that you ran out of disk space?

from flye.

Thank you for your quick reply!

Here is the full logs: flye.log

And the 1-consensus directory:

$ ls -sh 1-consensus/
total 149G
   0 consensus.fasta  149G minimap.sam

There's more than 100TB left on the hard drive. And I confirmed to our administrator that I have enough quota. So I think it's maybe not relevant to the disk space.

from flye.

Looks strange, I don't see anything suspicious in the log.

Could you also do 'tail 1-consensus/minimap.sam' and post the output somewhere?

from flye.

Hi, this is the last 10 line of 1-consensus/minimap.sam: tail_minimap_sam.txt.

from flye.

Ok, it seems that the problem is that your read IDs start from @ symbol, which is also marks the beginning of header lines in sam file format. These headers are ignored by Flye - so as a result no alignments were actually read.

This is unusual naming for PacBio reads - most likely is an artifact of fastq -> fasta conversion. I will try to come up with more sophisticated header filtering, but if you don't want to wait you can simply remove '@' from your reads fastq and rerun Flye with '--resume' option.

from flye.

Thank you very much! Yes, I got this fasta from a fastq file.

Should I remove '@' from the minimap.sam or remove '@' from raw fasta then use --resume?

from flye.

Let's take the second option to be safe.

from flye.

It cannot be resumed.

[2018-05-20 14:22:52] INFO: Running Flye 2.3.3-g47cdd0b
[2018-05-20 14:22:52] INFO: Resuming previous run
[2018-05-20 14:22:52] INFO: Performing repeat analysis
[2018-05-20 14:22:52] INFO: Reading sequences
[2018-05-20 14:22:52] ERROR: parse error in /parastor300/niuyw/Project/Goqi_genome_180207/flye/run1.1/1-consensus/consensus.fasta on line 1: empty sequence
[2018-05-20 14:22:52] ERROR: Command '['flye-repeat', '-l', '/parastor300/niuyw/Project/Goqi_genome_180207/flye/run1.1/flye.log', '-t', '40', '-g', '/parastor300/niuyw/Project/Goqi_genome_180207/flye/run1.1/1-consensus/consensus.fasta', '/home/zhangll/Tasks/Gouqi/data/Pacbio/[email protected]', '/parastor300/niuyw/Project/Goqi_genome_180207/flye/run1.1/2-repeat', '2147483648', '/home/niuyw/software/Flye-2.3.3/flye/resource/asm_raw_reads.cfg']' returned non-zero exit status 1

I'll just re-run from the start. Thank you!

from flye.

My mistake - please do '--resume-from consensus' instead.

from flye.