Comments (9)
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.
Related Issues (20)
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- Metagenome HOT 1
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- Meanings of both '--keep-halotypes' and '--no-alt-contigs'. HOT 7
- free(): invalid next size (fast) at "Simplifying the graph" HOT 4
- Assembly of complex genomes with high rate of genome rearrangements HOT 2
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- What parameter for R10.4.1 FAST mode data HOT 1
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from flye.