error message with hinge - no alignments

[gabster]

I have come almost to the end with the ecoli demo in hinge but not quite. I do not understand what could be the Problem and would appreciate some help. I have copied the command and the Output below - disappointingly, there was no alignment in the end. Thanks, Gabi

hinge draft --db ecoli --las ecoli --mlas --prefix ecoli --config ../../utils/nominal.ini --out ecoli.draft [2018-08-30 11:10:01.142] [log] [info] draft consensus [2018-08-30 11:10:01.142] [log] [info] name of db: ecoli, name of .las file ecoli [2018-08-30 11:10:01.142] [log] [info] name of fasta: , name of .paf file [2018-08-30 11:10:01.142] [log] [info] filter files prefix: ecoli [2018-08-30 11:10:01.142] [log] [info] output prefix: ecoli.draft [2018-08-30 11:10:01.143] [log] [info] Parameters passed in

[filter] length_threshold = 1000; quality_threshold = 0.23; n_iter = 3; // filter iteration aln_threshold = 1000; min_cov = 5; cut_off = 300; theta = 300; use_qv = true;

[running] n_proc = 12;

[draft] min_cov = 10; trim = 200; edge_safe = 100; tspace = 900; step = 50;

[consensus] min_length = 4000; trim_end = 200; best_n = 1; quality_threshold = 0.23;

[layout] hinge_slack = 1000 min_connected_component_size = 8

ecoli.1.las

Number of files 0 Input string ecoli

[2018-08-30 11:10:01.149] [log] [info] calling glob. [2018-08-30 11:10:01.149] [log] [info] # Reads: 76423 [2018-08-30 11:10:03.058] [log] [info] Total number of active reads: 3222/76423 [2018-08-30 11:10:03.065] [log] [error] No alignments!

[govinda-kamath]

Can you give the output of these commands?

fasta2DB ecoli reads.fasta
DBsplit -x500 -s100 ecoli     
HPC.daligner -t5 ecoli | csh -v

It looks like DAligner did not work here.

[gabster]

I am attaching the log files for the demo run.

Can you give the output of these commands?

fasta2DB ecoli reads.fasta

File reads.fasta, Line 12: Fasta line is too long (> 9998 chars)

hinge correct-head reads.fasta reads.pb.fasta map.txt

DBsplit -x500 -s100 ecoli:

You are about to overwrite the current partition settings. This

will invalidate any tracks, overlaps, and other derivative files.

Are you sure you want to proceed? [Y/N] y

HPC.daligner -t5 ecoli | csh -v

Daligner jobs (6)

daligner ecoli.1 ecoli.1

daligner ecoli.2 ecoli.1 ecoli.2 daligner ecoli.3 ecoli.1 ecoli.2 ecoli.3 daligner ecoli.4 ecoli.1 ecoli.2 ecoli.3 ecoli.4 daligner ecoli.5 ecoli.1 ecoli.2 daligner ecoli.5 ecoli.3 ecoli.4 ecoli.5 . . . LAcheck -vS ecoli ecoli.1 ecoli.1: 2,520,144 all OK LAcheck -vS ecoli ecoli.2 ecoli.2: 2,483,986 all OK LAcheck -vS ecoli ecoli.3 ecoli.3: 2,363,703 all OK LAcheck -vS ecoli ecoli.4 ecoli.4: 2,497,865 all OK LAcheck -vS ecoli ecoli.5 ecoli.5: 734,852 all OK

All that looked okay to me. I am attaching the log files perhaps it can tell you where the error occurred. Thanks for your support, I do appreciate it a lot. Gabi

Gabriele Margos German National Reference Centre for Borrelia Bavarian Health and Food Safety Authority Veterinärstrasse 2 85764 Oberschleißheim Tel. 09131/68085883 email: gmargos1@gmail.commailto:gmargos1@gmail.com gabriele.margos@lgl.bayern.demailto:gabriele.margos@lgl.bayern.de

Von: Govinda Kamath [mailto:notifications@github.com] Gesendet: Donnerstag, 30. August 2018 17:24 An: HingeAssembler/HINGE Cc: Margos, Gabriele, Dr. (LGL); Author Betreff: Re: [HingeAssembler/HINGE] error message with hinge - no alignments (#152)

Can you give the output of these commands?

fasta2DB ecoli reads.fasta

DBsplit -x500 -s100 ecoli

HPC.daligner -t5 ecoli | csh -v

It looks like DAligner did not work here.

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