tail: +: invalid number of bytes with run-asm-pipeline.sh in haploid mode
Neo-xbx-00 opened this issue · 4 comments
Hello ! I hope for some solutions for my questions. My Bash version is: GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu), and my 3d-dna version is version 180114. When running run-asm-pipeline.sh in haploid mode, I got a wrong FINAL fasta with full of N's. And when I set -s finalize to rerun run-asm-pipeline.sh, I got a run.log with content like this:
/home/line/local/app/3d-dna/run-asm-pipeline.sh -r 2 -s finalize /mnt/5E100E34100E1425/CYM/01_Genome/output/02_polish/next_polish/02_rundir/genome.nextpolish.fasta /mnt/5E100E34100E1425/CYM/01_Genome/output/04_hic/juicer/aligned/merged_nodups.txt
version: 180922
-r|--rounds flag was triggered, will run 2 round(s) of misjoin correction.
-s|--stage flag was triggered, fast-forwarding to "finalize" pipeline section.
###############
Finilizing output:
... -s flag was triggered, treating all contigs/scaffolds shorter than 15000 as unattempted.
... -l flag was triggered. Output will appear with headers of the form genome.nextpolish_hic_scaffold_#.
... -g flag was triggered, making gap size between scaffolded draft sequences to be equal to 500.
Analyzing the merged assembly
...trimming N overhangs
...adding gaps
tail: +: invalid number of bytes
tail: +: invalid number of bytes
tail: +: invalid number of bytes
tail: +: invalid number of bytes
tail: +: invalid number of bytes
tail: +: invalid number of bytes
tail: +: invalid number of bytes
tail: +: invalid number of bytes
tail: +: invalid number of bytes
tail: +: invalid number of bytes
How can I solve it?
And my first run with run-asm-pipeline.sh get the error.log with many like these:
nohup: ignoring input
:| Warning: no explicit bundle size was listed. Will use the same one as listed for false positive size threshold: this is the most typical scenario.
:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"
:| Warning: No input for label2 was provided. Default for label2 is ":::debris"
:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"
:| Warning: No input for label2 was provided. Default for label2 is ":::debris"
:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"
:| Warning: No input for label2 was provided. Default for label2 is ":::debris"
...
Is this the problems?
I check my the lengthes in mismatch_narrow.at.step.0.bed, with awk '{print $3-$2}' mismatch_narrow.at.step.0.bed | sort -k1,1nr | head, my results are:
143000
126000
113000
101000
98000
92000
89000
87000
81000
81000
If there anyone can help me? For I have sent questions in 3d-dna groups, but I have not approved.
try to check the assembly file, may be there are same comtigs with wrong length