problem running with no reduction step

[SN]

Hello,

In my previous run with redundans that included all the three steps: reduction, scaffolding and gapclosure. I found that this assembly didn't include the mate pair libraires because they didn't pass the QC during the scaffolding step. So, as suggested in the manual I modified the "is" file and reran the redundans on the contigs.reduced.fa file with --noreduction and got the following errors, can you please help me troubleshoot it, Thanks! 

python2.7 /redundans-dev/redundans.py -i trim36*.fastq MK-HMTI_*.fastq.int_trimmed -f ./Hmisstrim36_reddev/contigs.reduced.fa -t 20 --log Hmiss_nored-dev.log -o ./HN_noreddev --noreduction

[WARNING] Poor quality: Major orientation (FR) represent 85.11% of pairs in trim36_PE100_500bp_R1.fastq - trim36_PE100_500bp_R2.fastq: [106, 8511, 1294, 89]

[WARNING] Poor quality: Major orientation (FR) represent 86.1% of pairs in trim36_PE100_500bp_R1.fastq - trim36_PE100_500bp_R2.fastq: [96, 8610, 1221, 73]

Traceback (most recent call last):

  File "/redundans-dev/redundans.py", line 517, in <module>

    main()

  File "/redundans-dev/redundans.py", line 512, in main

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

  File "/redundans-dev/redundans.py", line 321, in redundans

    identity, overlap, minLength, resume)

  File "/redundans-dev/redundans.py", line 146, in run_scaffolding

    iters=1, resume=resume, verbose=0, log=log, basename=basename)

  File "/redundans-dev/redundans.py", line 243, in run_gapclosing

    stats     = FastaIndex(pout).stats()

  File "/redundans-dev/bin/FastaIndex.py", line 341, in stats

    longest = max(stats[0] for stats in self.id2stats.itervalues())

ValueError: max() arg is an empty sequence

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

I guess scaffolding step failed. Can you do `ls -lah` on output dir? 

Anyway, I've added function to catch empty FastA files so proper error should be reported now. Just update redundans:  

git pull

Bests, 

L.

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