Lastal error

[Anna Tigano]

Hi,

I've been trying to run Redundans but it keeps failing. It actually starts and produces some files

lrwxrwxrwx 1 at829 nt246_0001        83 Jun 12 15:07 contigs.fa.fai -> /local/workdir/Menidia_Genome/newassembly_at/menidia_q30_scaffolds_spades.fasta.fai

lrwxrwxrwx 1 at829 nt246_0001        79 Jun 12 15:07 contigs.fa -> /local/workdir/Menidia_Genome/newassembly_at/menidia_q30_scaffolds_spades.fasta

-rw-rw-r-- 1 at829 nt246_0001         0 Jun 12 15:07 contigs.reduced.fa

-rw-rw-r-- 1 at829 nt246_0001   8924236 Jun 12 15:07 contigs.fa.ssp

-rw-rw-r-- 1 at829 nt246_0001 997687574 Jun 12 15:07 contigs.fa.tis

-rw-rw-r-- 1 at829 nt246_0001   8924236 Jun 12 15:08 contigs.fa.sds

-rw-rw-r-- 1 at829 nt246_0001  76241113 Jun 12 15:08 contigs.fa.des

-rw-rw-r-- 1 at829 nt246_0001 750466164 Jun 12 15:10 contigs.fa.suf

-rw-rw-r-- 1 at829 nt246_0001       504 Jun 12 15:10 contigs.fa.prj

-rw-rw-r-- 1 at829 nt246_0001 125230004 Jun 12 15:10 contigs.fa.bck

This is the code I'm using

redundans.py -i menidia_trimmed_q20_R* -f menidia_q30_scaffolds_spades.fasta -o redundans0.95_spades -t 12 --identity 0.95 --nogapclosing --noscaffolding

and the error I get

Traceback (most recent call last):

  File "/workdir/anna/programs/redundans/redundans.py", line 517, in <module>

    main()

  File "/workdir/anna/programs/redundans/redundans.py", line 512, in main

    o.norearrangements, o.verbose, o.log)

  File "/workdir/anna/programs/redundans/redundans.py", line 302, in redundans

    info = fasta2homozygous(out, open(fastas[-1]), identity, overlap, minLength, threads, verbose=0, log=log)

  File "/workdir/anna/programs/redundans/bin/fasta2homozygous.py", line 206, in fasta2homozygous

    contig2skip = fasta2skip(out, fasta, faidx, threads, identity, overlap, minLength, verbose)

  File "/workdir/anna/programs/redundans/bin/fasta2homozygous.py", line 129, in fasta2skip

    if not contig2skip[q] or score > contig2skip[q][0]:

KeyError: 'NODE_15321_length_4291_cov_21.3723'

lastal: write error

I used Redundans a few weeks ago on a different cluster and with a different dataset and everything went smoothly. Any insight would be much appreciated. 

Thanks in advance

Anna

[l.p.p...@gmail.com]

Dear Anna, 

This is really unexpected error and I don't really see why it appeared! In principle it should never occur, as the contig names in fasta and lastal output should be equivalent... 

Could you please share with me the contigs so I can evaluate it in details? 

Nevertheless, I've added solution, so the error should be gone now. Just update using

  git pull origin master

Bests, 

L.

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[Anna Tigano]

Hi Leszek,

Thank you very much for fixing this! It worked perfectly! How do you want me to send you the contig file?

Also, I keep getting this warning with both of the 2 datasets I've been working on (see below). What does it mean?

[WARNING] Poor quality: Major orientation (FR) represent 81.13% of pairs in menidia_trimmed_q20_R1.fq - menidia_trimmed_q20_R2.fq: [2, 8113, 1880, 5]

--

Anna Tigano, Ph.D.

Postdoctoral Associate

Therkildsen Lab

Department of Natural Resources

Cornell University

www.annatigano.weebly.com

[l.p.p...@gmail.com]

Thank you very much for fixing this! It worked perfectly! How do you want me to send you the contig file?

Is the assembly very big? FTP or some file sharing website will be ok. 

for me having just menidia_q30_scaffolds_spades.fasta will be enough. Gzip it before (it'll decrease the file size 3-4x). 

 

Also, I keep getting this warning with both of the 2 datasets I've been working on (see below). What does it mean?

[WARNING] Poor quality: Major orientation (FR) represent 81.13% of pairs in menidia_trimmed_q20_R1.fq - menidia_trimmed_q20_R2.fq: [2, 8113, 1880, 5]

Is is mate-pair data? This warning means that 81% of paired reads is FR, but there are quite some (18%) RF pairs. It could be due to several reasons:

• mate-pair library (typically RF) contaminated with paired-end reads (FR). if that's the case, your MP is really poor
• but it can be also due to mis-assemblies to some extent or alignment difficulties

Bests, 

L.