Stacks not progressing past ustacks

[cav...@gmail.com]

So I am running this code:

id=1

while read file_id; do

    ustacks -f ${file_id}.1.fq.gz -o /scratch/cav3gh/ager_gom/stacks -i $id --name $file_id -M 4 -p 8 --force_diff_len

    id=$((id+1))

done < samples.txt

cstacks -n 6 -P /scratch/cav3gh/ager_gom/stacks/ -M /scratch/cav3gh/ager_gom/popmap_revised.txt.bak2 -p 8

sstacks -P /scratch/cav3gh/ager_gom/stacks/ -M /scratch/cav3gh/ager_gom/popmap_revised.txt.bak2 -p 8

tsv2bam -P /scratch/cav3gh/ager_gom/stacks/ -M /scratch/cav3gh/ager_gom/popmap_revised.txt.bak2 --pe-reads-dir /scratch/cav3gh/ager_gom/Process_radtags -t 8

gstacks -P /scratch/cav3gh/ager_gom/stacks/ -M /scratch/cav3gh/ager_gom/popmap_revised.txt.bak2 -t 8

populations -P /scratch/cav3gh/ager_gom/stacks/ -M /scratch/cav3gh/ager_gom/popmap_revised.txt.bak2 -r 0.65 --vcf --genepop --structure --phylip --fstats --hwe -t 8

The problem is that I am only getting out files that look like this:

BC_B14.alleles.tsv.gz

BC_B14.snps.tsv.gz

BC_B14.tags.tsv.gz

and stacks is not progressing further.

The log output looks like this:

Loading RAD-Tags...

Warning: different sequence lengths detected, this could interfere with Stacks algorithms.

Loaded 42250 reads; formed:

  1221 stacks representing 27108 primary reads (64.2%)

  14145 secondary stacks representing 15142 secondary reads (35.8%)

Stack coverage: mean=22.20; stdev=76.54; max=2010; n_reads=27108(64.2%)

Removing repetitive stacks: cov > 176 (mean+2*stdev)...

  Blacklisted 382 stacks.

Coverage after repeat removal: mean=15.56; stdev=31.24; max=176; n_reads=13059(30.9%)

Assembling stacks (max. dist. M=4)...

ustacks: src/ustacks.cc:1196: int call_consensus(std::map<int, MergedStack*>&, std::map<int, Stack*>&, std::map<int, Rem*>&, bool): Assertion `utag->seq->size() == length' failed.

/var/spool/slurm/slurmd/job2468950/slurm_script: line 24: 197204 Aborted                 (core dumped) ustacks -f ${file_id}.1.fq.gz -o /scratch/cav3gh/ager_gom/stacks -i $id --name $file_id -M 4 -p 8 --force_diff_len

ustacks parameters selected:

  Input file: 'S3_B10.1.fq.gz'

  Sample ID: 635

  Min depth of coverage to create a stack (m): 3

  Repeat removal algorithm: enabled

  Max distance allowed between stacks (M): 4

  Max distance allowed to align secondary reads: 6

  Max number of stacks allowed per de novo locus: 3

  Deleveraging algorithm: disabled

  Gapped assembly: enabled

  Minimum alignment length: 0.8

  Model type: SNP

  Alpha significance level for model: 0.05

  Forcing the allowance of sequences of different length.

Loading RAD-Tags...

Warning: different sequence lengths detected, this could interfere with Stacks algorithms.

Error: Unable to form any primary stacks.

cstacks parameters selected:

  Loci matched based on sequence identity.

  Number of mismatches allowed between stacks: 6

  Gapped alignments: enabled

Constructing catalog from 189 samples.

Initializing new catalog...

 Unable to open '/scratch/cav3gh/ager_gom/stacks/BC-B39.all'

Error: Failed to initialize the catalog.

Aborted.

Searching for matches by sequence identity...

 Unable to open '/scratch/cav3gh/ager_gom/stacks/catalog'

Error: Unable to parse catalog, '/scratch/cav3gh/ager_gom/stacks/catalog'

Aborted.

Error: Unable to find the first paired-end reads file at '/scratch/cav3gh/ager_gom/Process_radtags/BC-B39.all.2.*'

Aborted.

[E::hts_open_format] Failed to open file /scratch/cav3gh/ager_gom/stacks/BC-B39.all.matches.bam

Error: Failed to open BAM file '/scratch/cav3gh/ager_gom/stacks/BC-B39.all.matches.bam'.

Aborted.

Logging to '/scratch/cav3gh/ager_gom/stacks/populations.log'.

Locus/sample distributions will be written to '/scratch/cav3gh/ager_gom/stacks/populations.log.distribs'.

populations parameters selected:

  Percent samples limit per population: 0.65

  Locus Population limit: 1

  Log liklihood filtering: off; threshold: 0

  Minor allele frequency cutoff: 0

  Maximum observed heterozygosity cutoff: 1

  Applying Fst correction: none.

  Pi/Fis kernel smoothing: off

  Fstats kernel smoothing: off

  Bootstrap resampling: off

Parsing population map...

The population map contained 189 samples, 14 population(s), 1 group(s).

Failed to open gzipped file '/scratch/cav3gh/ager_gom/stacks/catalog.fa.gz': No such file or directory.

[Felipe Torquato]

I got the same error!

Could you fixe it?

Best,

Felipe

[Nicolas Rochette]

The error is:

Aborted (core dumped)

With some details above it (in the ustacks output).

When you run the pipeline by hand, make sure you check for failures before moving to the next step. Basically, --force_diff_len works as an option, i.e. ustacks agrees to try to process reads with variable lengths, but then it makes it crash later on.

Best,

Nicolas

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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[Ulavappa Angadi]

How fix this error

The error is:

Aborted (core dumped)

With some details above it (in the ustacks output).

To unsubscribe from this group and stop receiving emails from it, send an email to stacks...@googlegroups.com.

[Tiamiyu Bashir]

Hi, 

I am having same error. How did you fixed this ?

[gary lu]

Hi All, 

I had the same issue by running sstacks 2.68. The output from ustacks are under stacks folder. 

Here is the error message: 

[g...@login1.swan glu]$ sstacks -P stacks/ -M popmaps/popmap -t 32

Searching for matches by sequence identity...

 Unable to open 'stacks/catalog'
Error: Unable to parse catalog, 'stacks/catalog'
Aborted.

I would appreciate it if you could help me to resolve this issue. 

Thanks, 

Gary

[Catchen, Julian]

Hi Gary,

 

This is not the same issue unless you had a core dump running ustacks. In this case, sstacks cannot find the catalog in the location where you specified for it to look. You should have a catalog.tags.tsv.gz (and several other files) in the ‘stacks’ directory that was generated by the cstacks program.

 

Julian