AdjList: command not found

[spencer411]

Please report

• [x] version of ABySS with abyss-pe version abyss-pe (ABySS) 2.2.3
• [x] distribution of Linux with lsb_release -d Oracle Linux Server release 7.7 using openmpi/3.1.4

Assembly error

• [x] complete abyss-pe command line abyss-pe k=50 name=bowfin lib='pea peb' mp='mpc mpd mpe mpf mpg mph mpi mpj mpk' \ pea='bowfin.trimmed.deduped.noMito.corrected_1.fq bowfin.trimmed.deduped.noMito.corrected_2.fq' \ peb='bowfin_F.trimmed-pe-500_1.fq bowfin_F.trimmed-pe-500_2.fq' \ se='bowfin.extendedFrags.deduped.noMito.corrected.fq'\ mpc='bowfin_F.trimmed-mp-1000_1.fq bowfin_F.trimmed-mp-1000_2.fq' \ mpd='bowfin_F.trimmed-mp-1500_1.fq bowfin_F.trimmed-mp-1500_2.fq' \ mpe='bowfin_F.trimmed-mp-2000_1.fq bowfin_F.trimmed-mp-2000_2.fq' \ mpf='bowfin_F.trimmed-mp-5000_1.fq bowfin_F.trimmed-mp-5000_2.fq' \ mpg='bowfin_F.trimmed-mp-10000_1.fq bowfin_F.trimmed-mp-10000_2.fq' \ mph='bowfin_F.trimmed-mp-20000_1.fq bowfin_F.trimmed-mp-20000_2.fq' \ mpi='bowfin_F.trimmed-mp-50000_1.fq bowfin_F.trimmed-mp-50000_2.fq' \ mpj='bowfin_F.trimmed-mp-100000_1.fq bowfin_F.trimmed-mp-100000_2.fq' \ mpk='bowfin_F.trimmed-mp-200000_1.fq bowfin_F.trimmed-mp-200000_2.fq' done
• [x] last 20 lines of the output of abyss-pe 10: Assembled 12560659 k-mer in 78906 contigs. 16: Assembled 13378421 k-mer in 81927 contigs. 5: Assembled 13147159 k-mer in 77436 contigs. 6: Assembled 13273717 k-mer in 78524 contigs. 13: Assembled 13083574 k-mer in 77066 contigs. 8: Assembled 13540861 k-mer in 83938 contigs. 17: Assembled 13453296 k-mer in 78324 contigs. 12: Assembled 13802190 k-mer in 82345 contigs. Assembled 783839157 k-mer in 4794531 contigs. Concatenating fasta files to bowfin-1.fa Concatenating fasta files to bowfin-bubbles.fa Done. [rhea-05.rit.albany.edu:23226] PMIX ERROR: NO-PERMISSIONS in file dstore_base.c at line 234 AdjList -k50 -m0 --dot bowfin-1.fa >bowfin-1.dot bash: AdjList: command not found make: [bowfin-1.dot] Error 127 make: Deleting file bowfin-1.dot' /tmp/slurmd/job680957/slurm_script: line 32: syntax error near unexpected tokendone' /tmp/slurmd/job680957/slurm_script: line 32: `done'
• [ ] number of sequenced bases unknown
• [x] estimated genome size and ploidy diploid, the organisms is ~945 Mb in size, although we arent expecting to have a full assembly (our assembly likely only partially covers the whole genome)
• [ ] estimated sequencing depth of coverage unknwon

[jwcodee]

can you show me your slurm script? and ls the path where you installed ABySS?

[spencer411]

see below, and script attached here.

-bash-4.2$ cd /network/rit/misc/software/abyss-2.2.3/ -bash-4.2$ ls ABYSS CITATION.md DataLayer Konnector ParseAligns aclocal.m4 Common depcomp Layout PathOverlap AdjList config.guess dialign LICENSE PopBubbles Align config.h DistanceEst LogKmerCount README.md Assembly config.h.in doc m4 Scaffold autogen.sh config.log Dockerfile Makefile Sealer autom4te.cache config.status doxygen.conf Makefile.am SimpleGraph azure-pipelines.yml config.sub FilterGraph Makefile.in stamp-h1 bin configure FMIndex Map test-driver Bloom configure.ac GapFiller MergePaths Unittest BloomDBG _config.yml Graph Misc vendor boost_1_56_0 Consensus install-sh missing boost_1_56_0.tar.bz2 COPYRIGHT IntegrationTest Overlap ChangeLog DAssembler KAligner PairedDBG CITATION.bib DataBase kmerprint Parallel

abyss-parallel_2.txt

[jwcodee]

I meant the binary directory where you installed the abyss binaries.

[spencer411]

-bash-4.2$ cd bin -bash-4.2$ ls ABYSS abyss-joindist abyss-adjtodot.pl abyss-kaligner abyss-bloom-dist.mk abyss-nompi abyss-bowtie ABYSS-P abyss-bowtie2 abyss-pe abyss-bwa abyss-samtoafg abyss-bwamem abyss-stack-size abyss-bwasw abyss-tabtomd abyss-cstont Makefile abyss-dida Makefile.am abyss-fac.pl Makefile.in abyss-fatoagp -bash-4.2$

[jwcodee]

Just to be clear, did you do this?

./configure
make
sudo make install

or

./configure --prefix=/opt/abyss
make
sudo make install

[spencer411]

It was a problem with the make, I went through and linked every command that for some reason didn't seem to be connected originally. Sorry about the delayed response, but I wanted to get everything squared away and run a full assembly before updating. Nevertheless, I am having a new problem, see error below related to my 8th pair of mp reads:

abyss-map -j60 -l40 bowfin_F.trimmed-mp-100000_1.fq bowfin_F.trimmed-mp-100000_2.fq bowfin-6.fa \ |abyss-fixmate -l40 -h mpj-6.hist \ |sort -snk3 -k4 \ |DistanceEst --dot --median -j60 -k50 -l40 -s1000 -n10 -o mpj-6.dist.dot mpj-6.hist Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 43 0.227% Singleton 669 3.53% FR 0 RF 0 FF 0 Different 18244 96.2% Total 18956 error: the histogram mpj-6.hist' is empty make: *** [mpj-6.dist.dot] Error 1 make: *** Deleting filempj-6.dist.dot' /tmp/slurmd/job735697/slurm_script: line 32: syntax error near unexpected token done' /tmp/slurmd/job735697/slurm_script: line 32:done'

Note that the mp reads referenced above are rather small (around 4.6MB a piece), so maybe there is just no usable information in those files? The seven pairs before them seemed to work fine. Just a guess, I dunno, any inference would be appreciated...

[lcoombe]

Hi @spencer411,

This looks to be related to a couple previous issues: #104, #208 - it is a known issue that ABySS fails when a library has no pairs of reads that map to the same contig.

Of the different mate-pair libraries you are using, do they each have a different estimated fragment size? If not, I'd suggest merging this very small one with a library with a similar/same fragment size to get past this error.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[sjackman]

Please consider installing ABySS using Homebrew on Linux. See

https://brew.sh for instructions to install Homebrew then run brew install abyss Bioconda is an alternative to Homebrew.