RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, <STDIN> line 2004.

[caixu0518]

Hello MaSuRCA team,

I used MaSuRCA (3.2.7) to hybrid assemble Brassica genome, and i meet the following two errors:

**./assemble.sh: line 158: work2.1/readPlacementsInSuperReads.final.read.superRead.offset.ori.txt: No such file or directory

RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004.**

[Sat Jun 30 13:09:06 CST 2018] Processing pe library reads [Sat Jun 30 13:27:49 CST 2018] Processing sj library reads [Sat Jun 30 13:49:18 CST 2018] Average PE read length 150 [Sat Jun 30 13:49:19 CST 2018] Using kmer size of 99 for the graph [Sat Jun 30 13:49:20 CST 2018] MIN_Q_CHAR: 33 [Sat Jun 30 13:49:20 CST 2018] Creating mer database for Quorum [Sat Jun 30 14:22:21 CST 2018] Error correct PE. [Sat Jun 30 15:30:09 CST 2018] Error correct JUMP. [Sat Jun 30 16:10:38 CST 2018] Estimating genome size. [Sat Jun 30 19:26:30 CST 2018] Estimated genome size: 423828686 [Sat Jun 30 19:26:30 CST 2018] Creating k-unitigs with k=99 [Sat Jun 30 21:51:17 CST 2018] Creating k-unitigs with k=31 [Sat Jun 30 23:51:16 CST 2018] Filtering mate pairs Assuming outtie orientation ./assemble.sh: line 158: work2.1/readPlacementsInSuperReads.final.read.superRead.offset.ori.txt: No such file or directory Chimeric/Redundant jump reads: 80879566 chimeric_sj.txt 385590798 redundant_sj.txt 466470364 total [Sun Jul 1 11:00:32 CST 2018] Creating FRG files [Sun Jul 1 11:09:06 CST 2018] Computing super reads from PE Using CABOG from is /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../CA8/Linux-amd64/bin Running mega-reads correction/assembly Using mer size 15 for mapping, B=17, d=0.029 Estimated Genome Size 423828686 Estimated Ploidy 1 Using 30 threads Output prefix mr.41.15.17.0.029 Pacbio coverage <30x, using the longest subreads Reducing super-read k-mer size Mega-reads pass 1 Running locally in 1 batch compute_psa 4268399 1643220171 Processed 500000 super reads, irreducible 370521, processing 682 super reads per second Processed 1000000 super reads, irreducible 797782, processing 841 super reads per second Processed 1500000 super reads, irreducible 1258713, processing 1392 super reads per second Processed 2000000 super reads, irreducible 1715565, processing 1655 super reads per second Processed 2500000 super reads, irreducible 2141569, processing 2118 super reads per second Mega-reads pass 2 Running locally in 1 batch compute_psa 2237976 6053800446 Refining alignments RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2002. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /data/mg1/caix/src/AssemblySoftware/MaSuRCA-3.2.7/bin/../lib/perl/mummer.pm line 262, line 2004.

[arbarhm]

Hi, Did you manage to find the reason or overcome this problem. I am also having similar issues and couldn't yet resolve it. Any help is appreciated. This is what I am getting: ..... Mega-reads pass 1 Running locally in 1 batch compute_psa 12540457 2138040560 Processed 500000 super reads, irreducible 475701, processing 4950 super reads per second Processed 1000000 super reads, irreducible 909290, processing 14705 super reads per second Processed 1500000 super reads, irreducible 1307868, processing 16666 super reads per second Processed 2000000 super reads, irreducible 1681665, processing 13157 super reads per second Processed 2500000 super reads, irreducible 2032475, processing 25000 super reads per second Mega-reads pass 2 Running locally in 1 batch compute_psa 2083036 2031184020 Refining alignments RuntimeError Usage: new_Options(); at /home/program_bins/MaSuRCA-3.2.6/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /home/program_bins/MaSuRCA-3.2.6/bin/../lib/perl/mummer.pm line 262, line 2002. RuntimeError Usage: new_Options(); at /home/program_bins/MaSuRCA-3.2.6/bin/../lib/perl/mummer.pm line 262, line 2004. RuntimeError Usage: new_Options(); at /home/program_bins/MaSuRCA-3.2.6/bin/../lib/perl/mummer.pm line 262, line 8607. RuntimeError Usage: new_Options(); at /home/program_bins/MaSuRCA-3.2.6/bin/../lib/perl/mummer.pm line 262, line 8513. RuntimeError Usage: new_Options(); at /home/program_bins/MaSuRCA-3.2.6/bin/../lib/perl/mummer.pm line 262, line 8337. RuntimeError Usage: new_Options(); at /home/program_bins/MaSuRCA-3.2.6/bin/../lib/perl/mummer.pm line 262, line 8800. RuntimeError Usage: new_Options(); at /home/program_bins/MaSuRCA-3.2.6/bin/../lib/perl/mummer.pm line 262, line 8316.

[daniazi]

Hi,

Similar problem here using 3.3.7 and 3..38.

RuntimeError Usage: new_Options(); at /export/home/adnan/bin/MaSuRCA-3.3.8/bin/../lib/perl/mummer.pm line 262, line 129. read sequence for not found [Wed 11 Mar 23:50:47 CET 2020] Gap consensus failed

It seems to occur during Refine_alignment step. I re-installed several times but did not solve it.

Did anyone find the answer?

[Jin-Sun-OUC]

Hi, I also got the similar error using version 3.4.1 [Fri Jul 3 23:53:27 HKT 2020] Processing pe library reads [Fri Jul 3 23:53:27 HKT 2020] Average PE read length 150 [Fri Jul 3 23:53:27 HKT 2020] Using kmer size of 49 for the graph [Fri Jul 3 23:53:28 HKT 2020] MIN_Q_CHAR: 33 [Fri Jul 3 23:53:28 HKT 2020] Creating mer database for Quorum [Sat Jul 4 00:06:26 HKT 2020] Error correct PE [Sat Jul 4 00:56:41 HKT 2020] Estimating genome size [Sat Jul 4 01:05:42 HKT 2020] Estimated genome size: 544751901 [Sat Jul 4 01:05:42 HKT 2020] Creating k-unitigs with k=49 [Sat Jul 4 01:49:14 HKT 2020] Computing super reads from PE [Sat Jul 4 03:52:07 HKT 2020] Using CABOG from /home/qiulab/App/MaSuRCA-3.4.1/bin/../CA8/Linux-amd64/bin [Sat Jul 4 03:52:07 HKT 2020] Running mega-reads correction/assembly [Sat Jul 4 03:52:07 HKT 2020] Using mer size 15 for mapping, B=15, d=0.02 [Sat Jul 4 03:52:07 HKT 2020] Estimated Genome Size 544751901 [Sat Jul 4 03:52:07 HKT 2020] Estimated Ploidy 2 [Sat Jul 4 03:52:07 HKT 2020] Using 32 threads [Sat Jul 4 03:52:07 HKT 2020] Output prefix mr.41.15.15.0.02 [Sat Jul 4 03:52:07 HKT 2020] Using 35x of the longest ONT reads [Sat Jul 4 03:55:12 HKT 2020] Reducing super-read k-mer size [Sat Jul 4 04:18:59 HKT 2020] Mega-reads pass 1 [Sat Jul 4 04:18:59 HKT 2020] Running locally in 1 batch Processed 500000 super reads, irreducible 416936, processing 5319 super reads per second Processed 1000000 super reads, irreducible 793174, processing 5102 super reads per second Processed 1500000 super reads, irreducible 1152791, processing 7812 super reads per second Processed 2000000 super reads, irreducible 1490720, processing 9615 super reads per second Processed 2500000 super reads, irreducible 1811144, processing 9803 super reads per second Processed 3000000 super reads, irreducible 2111338, processing 10204 super reads per second Processed 3500000 super reads, irreducible 2408114, processing 8064 super reads per second Processed 4000000 super reads, irreducible 2713163, processing 6410 super reads per second Processed 4500000 super reads, irreducible 3033558, processing 5376 super reads per second Processed 5000000 super reads, irreducible 3380140, processing 4587 super reads per second Processed 5500000 super reads, irreducible 3754625, processing 5000 super reads per second Processed 6000000 super reads, irreducible 4168551, processing 4807 super reads per second Processed 6500000 super reads, irreducible 4595491, processing 4901 super reads per second Processed 7000000 super reads, irreducible 4997878, processing 5319 super reads per second Processed 7500000 super reads, irreducible 5350160, processing 5747 super reads per second Processed 8000000 super reads, irreducible 5567237, processing 7246 super reads per second [Wed Jul 8 14:12:33 HKT 2020] Mega-reads pass 2 [Wed Jul 8 14:12:33 HKT 2020] Running locally in 1 batch [Fri Jul 10 22:27:48 HKT 2020] Refining alignments RuntimeError Usage: new_Options(); at /home/qiulab/App/MaSuRCA-3.4.1/bin/../lib/perl/mummer.pm line 262, line 5610. RuntimeError Usage: new_Options(); at /home/qiulab/App/MaSuRCA-3.4.1/bin/../lib/perl/mummer.pm line 262, line 5820. RuntimeError Usage: new_Options(); at /home/qiulab/App/MaSuRCA-3.4.1/bin/../lib/perl/mummer.pm line 262, line 5820. RuntimeError Usage: new_Options(); at /home/qiulab/App/MaSuRCA-3.4.1/bin/../lib/perl/mummer.pm line 262, line 5820. RuntimeError Usage: new_Options(); at /home/qiulab/App/MaSuRCA-3.4.1/bin/../lib/perl/mummer.pm line 262, line 5820. RuntimeError Usage: new_Options(); at /home/qiulab/App/MaSuRCA-3.4.1/bin/../lib/perl/mummer.pm line 262, line 5820. RuntimeError Usage: new_Options(); at /home/qiulab/App/MaSuRCA-3.4.1/bin/../lib/perl/mummer.pm line 262, line 5818. RuntimeError Usage: new_Options(); at /home/qiulab/App/MaSuRCA-3.4.1/bin/../lib/perl/mummer.pm line 262, line 5820. RuntimeError Usage: new_Options(); at /home/qiulab/App/MaSuRCA-3.4.1/bin/../lib/perl/mummer.pm line 262, line 5820.

I am wondering anyone knows what is going on?