Trouble resuming from completed iteration

[ppericard]

Hi,
I've been having some difficulties for a while resuming Emirge runs from a completed iteration.
All my last attempts resulted in the same errors. See below:

If you use EMIRGE in your work, please cite these manuscripts, as appropriate.

Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF (2011)
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data.
Genome biology 12: R44. doi:10.1186/gb-2011-12-5-r44.

Miller CS, Handley KM, Wrighton KC, Frischkorn KR, Thomas BC, Banfield JF (2013)
Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments.
PloS one 8: e56018. doi:10.1371/journal.pone.0056018.

imported _emirge C functions from: /home/pierre.pericard/anaconda3/envs/py27/lib/python2.7/site-packages/_emirge.so
Command:
/home/pierre.pericard/anaconda3/envs/py27/bin/emirge.py emirge_outdir -1 /workdir/pierre.pericard/paper/16S_rRNA/human_microbiome_project/SRS049896/SRS049896.denovo_duplicates_marked.trimmed.1.fastq -2 /workdir/pierre.pericard/paper/16S_rRNA/human_microbiome_project/SRS049896/SRS049896.denovo_duplicates_marked.trimmed.2.fastq -f /workdir/pierre.pericard/paper/16S_rRNA/ref_db/emirge_default_db/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.fasta -b /workdir/pierre.pericard/paper/16S_rRNA/ref_db/emirge_default_db/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -l 101 -i 150 -s 50 -j 1 -p 0.001 -n 100 -r 9 -a 16 --phred33

EMIRGE started at Fri Jan 13 11:31:25 2017
Resuming EMIRGE from iteration 09 at Fri Jan 13 11:31:25 2017 ...
Starting from information in directory:
/workdir/pierre.pericard/paper/16S_rRNA/human_microbiome_project/SRS049896/emirge/raw_default_db_j1_p0.001/emirge_outdir/iter.09
DONE with resume initialization at Fri Jan 13 11:31:25 2017...
Starting iteration 9 at Fri Jan 13 11:31:25 2017...
Reading bam file /workdir/pierre.pericard/paper/16S_rRNA/human_microbiome_project/SRS049896/emirge/raw_default_db_j1_p0.001/emirge_outdir/iter.08/bowtie.iter.08.PE.bam at Fri Jan 13 11:31:25 2017...
DONE Reading bam file /workdir/pierre.pericard/paper/16S_rRNA/human_microbiome_project/SRS049896/emirge/raw_default_db_j1_p0.001/emirge_outdir/iter.08/bowtie.iter.08.PE.bam at Fri Jan 13 11:32:32 2017 [0:01:07.117363]...
Calculating likelihood (13671, 378106) for iteration 9 at Fri Jan 13 11:32:35 2017...
Calculating Pr(N=n) for iteration 9 at Fri Jan 13 11:32:35 2017...
Loading probN for resume case from /workdir/pierre.pericard/paper/16S_rRNA/human_microbiome_project/SRS049896/emirge/raw_default_db_j1_p0.001/emirge_outdir/iter.09/probN.pkl
DONE calculating Pr(N=n) for iteration 9 at Fri Jan 13 11:32:37 2017 [0:00:02.734468]...
DONE Calculating likelihood for iteration 9 at Fri Jan 13 11:34:30 2017 [0:01:55.514443]...
Calculating posteriors for iteration 9 at Fri Jan 13 11:34:30 2017...
/home/pierre.pericard/anaconda3/envs/py27/bin/emirge.py:1180: RuntimeWarning: invalid value encountered in divide
self.posteriors[-1].data = self.posteriors[-1].data / denom[(self.posteriors[-1].col,)] # index out denom with column indices from coo format.
DONE Calculating posteriors for iteration 9 at Fri Jan 13 11:34:34 2017 [3.878 seconds]...
Writing consensus for iteration 9 at Fri Jan 13 11:34:34 2017...
snp_minor_prob_thresh = 0.100
snp_percentage_thresh = 0.001
Traceback (most recent call last):
File "/home/pierre.pericard/anaconda3/envs/py27/bin/emirge.py", line 1697, in
main()
File "/home/pierre.pericard/anaconda3/envs/py27/bin/emirge.py", line 1688, in main
do_iterations(em, max_iter = options.iterations, save_every = options.save_every)
File "/home/pierre.pericard/anaconda3/envs/py27/bin/emirge.py", line 1444, in do_iterations
os.path.join(subdir, "iter.%02d.cons.fasta"%(em.iteration_i)))
File "/home/pierre.pericard/anaconda3/envs/py27/bin/emirge.py", line 499, in do_iteration
self.write_consensus(consensus_filename) # culls and splits
File "/home/pierre.pericard/anaconda3/envs/py27/bin/emirge.py", line 590, in write_consensus
if self.min_depth is not None and self.coverage[seq_i] < self.min_depth: # could also do this only after self.iteration_i > 5 or something
IndexError: list index out of range
Command exited with non-zero status 1
Command being timed: "emirge.py emirge_outdir -1 /workdir/pierre.pericard/paper/16S_rRNA/human_microbiome_project/SRS049896/SRS049896.denovo_duplicates_marked.trimmed.1.fastq -2 /workdir/pierre.pericard/paper/16S_rRNA/human_microbiome_project/SRS049896/SRS049896.denovo_duplicates_marked.trimmed.2.fastq -f /workdir/pierre.pericard/paper/16S_rRNA/ref_db/emirge_default_db/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.fasta -b /workdir/pierre.pericard/paper/16S_rRNA/ref_db/emirge_default_db/SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -l 101 -i 150 -s 50 -j 1 -p 0.001 -n 100 -r 9 -a 16 --phred33"
User time (seconds): 185.75
System time (seconds): 6.40
Percent of CPU this job got: 99%
Elapsed (wall clock) time (h:mm:ss or m:ss): 3:13.40
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 8311924
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 62
Minor (reclaiming a frame) page faults: 5182494
Voluntary context switches: 9793
Involuntary context switches: 765
Swaps: 0
File system inputs: 798784
File system outputs: 140032
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 1