Assembly failed because all gap consensus failed

Dear @alekseyzimin,

I always get this error while running hybrid Masurca assembly on an ubuntu wokstaion with 1 TB RAM. Although, the warning suggests that the assembly can proceed normnally, it doesn't. The assembly failed at this stage.

Best, Julien

 ./do_consensus.sh: line 5: 142249 Done                    /disk2/nguinkal/Zander_Project/pipelines/masurca/MaSuRCA-3.3.3/bin/../CA8/Linux-amd64/bin/blasr to_blasr.$1.fa ref.$1.fa -minMatch 15 -nproc 16 -bestn 10 -m 5 2> blasr.err
     142250 Broken pipe             | sort -k6 -S2%
     142251 Segmentation fault      | /disk2/nguinkal/Zander_Project/pipelines/masurca/MaSuRCA-3.3.3/bin/../CA8/Linux-amd64/bin/pbdagcon -j 8 -t 0 -c 1 /dev/stdin 2> pbdagcon.err
     142252                       | tee join_consensus.$1.fasta
     142253                       | /disk2/nguinkal/Zander_Project/pipelines/masurca/MaSuRCA-3.3.3/bin/nucmer --delta /dev/stdout --maxmatch -l 17 -c 51 -L 200 -t 16 to_join.$1.fa /dev/stdin
     142254                       | /disk2/nguinkal/Zander_Project/pipelines/masurca/MaSuRCA-3.3.3/bin/filter_delta_file_for_qrys.pl qrys.txt
     142255                       | /disk2/nguinkal/Zander_Project/pipelines/masurca/MaSuRCA-3.3.3/bin/show-coords -lcHq -I 88 /dev/stdin > coords.$1
cat: 'merges.[0-9]*.txt': No such file or directory
[Wed 26 Jun 2019 05:34:13 PM CEST] Warning! Some or all gap consensus jobs failed, see files in mr.41.15.17.0.029.join_consensus.tmp, however this is fine and assembly can proceed normally
[Wed 26 Jun 2019 05:35:53 PM CEST] Running assembly with Flye
[Wed 26 Jun 2019 05:36:23 PM CEST] Assembly with flye failed, see files under flye/

alekseyzimin / masurca

Assembly failed because all gap consensus failed #118