HELP! Error- [a5] Error building contigs with IDBA

Question

[ccelispuga]

When trying to run a genome assembly with the a5 pipeline I receive an error [a5] error buildings contigs with IDB. I have tried running it over 10 times and no luck

this is the code

Last login: Mon Jan  6 13:50:28 on ttys012

The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit https://support.apple.com/kb/HT208050.
(base) Christinas-MacBook-Air-2:~ christinacelispuga$ cd Desktop/
(base) Christinas-MacBook-Air-2:Desktop christinacelispuga$ mkdir a5lastdemo
(base) Christinas-MacBook-Air-2:Desktop christinacelispuga$ cd a5lastdemo/
(base) Christinas-MacBook-Air-2:a5lastdemo christinacelispuga$ /Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin/a5_pipeline.pl /Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/example/phiX_p1.fastq /Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/example/phiX_p2.fastq a5demotest
[a5] Found the following libraries:
     raw1:
      id=raw1
      p1=/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/example/phiX_p1.fastq
      p2=/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/example/phiX_p2.fastq
[a5] Found 1 libraries
[a5] Starting pipeline at step 1
[a5] Cleaning reads with SGA
[a5] Cleaning reads with SGA
cleaning each PE lib

p1 is /Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/example/phiX_p1.fastq
Cleaning reads

[a5] java -Xmx512m -jar '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/trimmomatic.jar SE -threads 4 -phred64  a5demotest.s1/phiX_p1.fastq.both.fastq a5demotest.s1/phiX_p1.fastq.trim.fastq ILLUMINACLIP:/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin/../adapter.fasta:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
TrimmomaticSE: Started with arguments: -threads 4 -phred64 a5demotest.s1/phiX_p1.fastq.both.fastq a5demotest.s1/phiX_p1.fastq.trim.fastq ILLUMINACLIP:/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin/../adapter.fasta:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'TCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'
Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GCCTTGCCAGCCCGCTCAGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGA'
Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCTGATGGCGCGAGGGAGGC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCTGAGCGGGCTGGCAAGGC'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
Using Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'
ILLUMINACLIP: Using 3 prefix pairs, 16 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Reads: 6400 Surviving: 6371 (99.55%) Dropped: 29 (0.45%)
TrimmomaticSE: Completed successfully
[a5] '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/sga preprocess -q 25 -f 20 -m 35  --pe-mode=0 --phred64  a5demotest.s1/phiX_p1.fastq.trim.fastq > a5demotest.s1/phiX_p1.fastq.both.pp 2> /dev/null
[a5] sga index -d 2097152 -t 1 a5demotest.s1/a5demotest.pp.fastq > a5demotest.s1/index.out 2> a5demotest.s1/index.err
[a5] '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/sga correct -t 1 -p a5demotest.pp -o a5demotest.s1/phiX_p1.fastq.both.pp.ec.fastq a5demotest.s1/phiX_p1.fastq.both.pp > a5demotest.s1/raw1.correct.out
[timer - sga::correct] wall clock: 1.40s CPU: 1.36s
Running cat a5demotest.s1/phiX_p1.fastq.both.repair.fastq >> a5demotest.s1/a5demotest.ec.fastq
Done merging libraries
[a5_s2] Building contigs from a5demotest.ec.fastq with IDBA
[a5_s2] Building contigs from a5demotest.ec.fastq with IDBA
[a5] a5demotest.s2/a5demotest.ec.fasta has 767171 bytes of FastA sequence data
[a5] '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/idba_ud --num_threads 4 -r a5demotest.s2/a5demotest.ec.fasta  -o a5demotest.s2/a5demotest --mink 35 --maxk 84 --min_pairs 2 
sh: line 1: 11039 Killed: 9               '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/idba_ud --num_threads 4 -r a5demotest.s2/a5demotest.ec.fasta -o a5demotest.s2/a5demotest --mink 35 --maxk 84 --min_pairs 2 > a5demotest.s2/idba.out
[a5] Previous IDBA-UD run failed. Trying again single-threaded.
sh: line 1: 11041 Killed: 9               '/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin'/idba_ud --num_threads 4 -r a5demotest.s2/a5demotest.ec.fasta -o a5demotest.s2/a5demotest --mink 35 --maxk 84 --min_pairs 2 --num_threads 1 > a5demotest.s2/idba.out
[a5] Error building contigs with IDBA
(base) Christinas-MacBook-Air-2:a5lastdemo christinacelispuga$

Please help

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Also, this is a question, not a "blog". I don't understand why the "Blog" option was picked at all.

You should also show us what your perl script does exactly. Right now, you're asking us to help you debug a black box that you have full access to.

Answer 1

[Mensur Dlakic]

I think you need to show some effort here. Other than HELP! in the title, this seems to be a repeat of the same post from a day ago. Have you done any of the things that the error message suggested? Specifically, have you tried running it with a single thread?

It is clear that the error has to do with IDBA. Does the program exist at

/Users/christinacelispuga/Desktop/a5_miseq_macOS_20160825/bin/idba_ud

If so, is it executable? Can you run it by pasting the whole command? If yes, get a processed dataset and run IDBA on it directly - not through A5 - and see if there is an error. When you have done all these things, there should be more clarity.

By the way, most people open up posts because they need help or advice. In that sense, putting HELP! in title is definitely redundant, and it may be off-putting to some people.

Answer 2

[ccelispuga]

Hi! Thank you, I actually figured it out. Totally sorry for re-posting it, might have pushed a wrong bottom.

Thanks for the clarification glad to receive help from an expert like yourself (:

[Ram]

Please edit this answer and add what you figured out. People might make the same mistake you did and what you figured out might help them save time and effort.