Error 1 when running nanocorrect-overlap.make

[BoMatt]

Hi!
When i run nanocorrect-overlap.make i get this error:

make -f nanocorrect-overlap.make INPUT=~/MinION/sspace_butyricum/all_reads_buty.fasta NAME=cor

nanocorrect-preprocess.pl /home/mattia/MinION/sspace_butyricum/all_reads_buty.fasta > cor.pp.fasta
fasta2DB cor cor.pp.fasta
File cor.pp.fasta, Line 1502272: Warning: Read is longer than 2^16-1. Read truncated.
File cor.pp.fasta, Line 1537720: Warning: Read is longer than 2^16-1. Read truncated.
File cor.pp.fasta, Line 1845517: Warning: Read is longer than 2^16-1. Read truncated.
File cor.pp.fasta, Line 1998480: Warning: Read is longer than 2^16-1. Read truncated.
File cor.pp.fasta, Line 2004327: Warning: Read is longer than 2^16-1. Read truncated.
File cor.pp.fasta, Line 2270391: Warning: Read is longer than 2^16-1. Read truncated.
File cor.pp.fasta, Line 2357344: Warning: Read is longer than 2^16-1. Read truncated.
File cor.pp.fasta, Line 2433997: Warning: Read is longer than 2^16-1. Read truncated.
File cor.pp.fasta, Line 2648752: Warning: Read is longer than 2^16-1. Read truncated.
File cor.pp.fasta, Line 2998765: Warning: Read is longer than 2^16-1. Read truncated.
File cor.pp.fasta, Line 3020306: Warning: Read is longer than 2^16-1. Read truncated.
DBsplit -s50 cor
DBdust cor
HPCdaligner -t5 -mdust cor > HPCcommands.txt
/bin/bash HPCcommands.txt
HPCcommands.txt: line 2: 22420 Segmentation fault (core dumped) daligner -t5 -mdust cor.1 cor.1
HPCcommands.txt: line 3: 22422 Segmentation fault (core dumped) daligner -t5 -mdust cor.2 cor.1 cor.2
daligner: Block cor.3 contains reads < 14bp long ! Run DBsplit.
daligner: Block cor.4 contains reads < 14bp long ! Run DBsplit.
LAsort: Cannot open ./cor.1.cor.1.C0.las for 'r'
LAsort: Cannot open ./cor.1.cor.2.C0.las for 'r'
LAsort: Cannot open ./cor.1.cor.3.C0.las for 'r'
LAsort: Cannot open ./cor.1.cor.4.C0.las for 'r'
LAsort: Cannot open ./cor.2.cor.1.C0.las for 'r'
LAsort: Cannot open ./cor.2.cor.2.C0.las for 'r'
LAsort: Cannot open ./cor.2.cor.3.C0.las for 'r'
LAsort: Cannot open ./cor.2.cor.4.C0.las for 'r'
LAsort: Cannot open ./cor.3.cor.1.C0.las for 'r'
LAsort: Cannot open ./cor.3.cor.2.C0.las for 'r'
LAsort: Cannot open ./cor.3.cor.3.C0.las for 'r'
LAsort: Cannot open ./cor.3.cor.4.C0.las for 'r'
LAsort: Cannot open ./cor.4.cor.1.C0.las for 'r'
LAsort: Cannot open ./cor.4.cor.2.C0.las for 'r'
LAsort: Cannot open ./cor.4.cor.3.C0.las for 'r'
LAsort: Cannot open ./cor.4.cor.4.C0.las for 'r'
LAmerge: Cannot open ./L1.1.1.las for 'r'
LAmerge: Cannot open ./L1.2.1.las for 'r'
LAmerge: Cannot open ./L1.3.1.las for 'r'
LAmerge: Cannot open ./L1.4.1.las for 'r'
nanocorrect-overlap.make:37: recipe for target 'cor.las' failed
make: *** [cor.las] Error 1

All dependencies are updated to the latest version, which can be the problem?

[jts]

The warnings about reads that are too long and too short (<14bp) might indicate the cause. Perhaps you can pre-filter your data to get rid of this and see if it works?

Is your input data 2D nanopore reads?

[BoMatt]

Yes,the input is 2D nanopore reads.
I will try to filter out the short reads and see if it works.

[BoMatt]

In the FASTA there weren't reads shorter than 100bp, I tried to filter out also reads shorter than 500bp with two different tools but I'm getting the same error.

make -f nanocorrect-overlap.make INPUT=~/MinION/sspace_butyricum/all2Dbutyricum_filter_galaxy.fasta NAME=gala

nanocorrect-preprocess.pl /home/mattia/MinION/sspace_butyricum/all2Dbutyricum_filter_galaxy.fasta > gala.pp.fasta
fasta2DB gala gala.pp.fasta
DBsplit -s50 gala
DBdust gala
HPCdaligner -t5 -mdust gala > HPCcommands.txt
/bin/bash HPCcommands.txt
daligner: Block gala.1 contains reads < 14bp long ! Run DBsplit.
LAsort: Cannot open ./gala.1.gala.1.C0.las for 'r'
nanocorrect-overlap.make:37: recipe for target 'gala.las' failed
make: *** [gala.las] Error 1

[jts]

Can you make the input file available to me so I can look into this?

[BoMatt]

I don't know if it works in Google Drive, let me know.
https://drive.google.com/file/d/0BzIk2g1Es23ZMURRdjFWUm9MOVE/view

[jts]

I just tested your file and it worked for me:

>make -f nanocorrect/nanocorrect-overlap.make INPUT=all2Dbutyricum.fasta NAME=test.v1
nanocorrect-preprocess.pl all2Dbutyricum.fasta > test.v1.pp.fasta
fasta2DB test.v1 test.v1.pp.fasta
DBsplit -s50 test.v1
DBdust test.v1
HPCdaligner -t5 -mdust test.v1 > HPCcommands.txt
/bin/bash HPCcommands.txt
LAcat test.v1 > test.v1.las
rm test.v1.*.las

Can you try it again in a completely clean directory? daligner uses hidden files and if these aren't removed it can make subsequent runs crash.

[BoMatt]

I tried it again but always the same error...I don't know how to solve it if I have to be honest, it seems a problem of my PC or of DALIGNER. Also because anytime I run it, then I delete the hidden files.

[jts]

Ok. What OS are you running and what versions of python/daligner?

[BoMatt]

Ubuntu 15.04, Python 2.7.9, daligner I think it's the last version because the git pull says that is already up to date.

[jts]

Can you run the exact command that I pasted above and send me the md5sums of all files?

[BoMatt]

Let me know if you need something else.

3b0c5878414f197d631e176ff90195f9 test.v1.db
6df6413e3fd993c5e89821698a66a16f test.v1.pp.fasta
d54bd5b69d039b84f7420c9495d26ea4 HPCcommands.txt
3cfa46cfb891db70145ae6cbc246ba53 .test.v1.bps
b921d466c5e407f8a5bf5e5ebd14f94c .test.v1.dust.anno
98a015b601fd277736877f622b9c089c .test.v1.dust.data
34fbe33e98d072c4b0cbfce5d09ecfa9 .test.v1.idx

[jts]

They match my files except for .test.v1.dust.anno, .test.v1.dust.data and .test.v1.idx. I don't know why running DBdust on the same file (test.v1.pp.fasta) would give different results.

[joshquick]

I’ve noticed that before whilst running the same input files on two different VM’s

On 18 Aug 2015, at 15:50, Jared Simpson <notifications@github.commailto:notifications@github.com> wrote:

They match my files except for .test.v1.dust.anno, .test.v1.dust.data and .test.v1.idx. I don't know why running DBdust on the same file (test.v1.pp.fasta) would give different results.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/14#issuecomment-132237979.

[BoMatt]

Tried to delete and reinstall DAZZ_DB, now it seems working!

[jts]

Great!