I am using my university's HPC cluster to de novo assemble paired-end HiSeq 400 reads I've used Trimmomatic for adapter trimming and quality-based trimming I used BBmap's kmercountexact.sh to determine my preferred k-mer value for assembly Now I want to use ABySS for my de novo asssembly - the HPC uses SLURM scheduler
module load openmpi Module openmpi/2.0.1 loaded module load abyss Module abyss/1.9.0 loaded srun --partition=high --mem=24000 --time=12:00:00 --nodes=1 abyss-pe np=8 name=EthFoc-11_trimmomatic7_corr k=41 in='EthFoc-11_S285_L007_trimmomatic7_1P.00.0_0.cor.fastq EthFoc-11_S285_L007_trimmomatic7_2P.00.0_0.cor.fastq'
There is a lot of text in STDOUT - available at http://txt.do/d61vl Briefly, in STDOUT the last lines that indicate the the run was still working read as follows:
Assembling... 0: Assembled 51879929 k-mer in 81891 contigs. Assembled 51879929 k-mer in 81891 contigs. Concatenating fasta files to EthFoc-11_trimmomatic7_corr-1.fa Concatenating fasta files to EthFoc-11_trimmomatic7_corr-bubbles.fa Done.
But soon after this in the STDOUT, the run terminates with the following error message:
Concatenating fasta files to EthFoc-11_trimmomatic7_corr-1.fa error: `contigs-0.fa': No such file or directory make: *** [EthFoc-11_trimmomatic7_corr-1.fa] Error 1 srun: error: c11-96: task 0: Exited with exit code 2
I went through several biostars posts on ABySS run errors, but I don't think I have a direct solution to my problem... A: abyss mpirun non zero code, abyss-pe without openmpi, Error running Abyss with openMPI, Abyss-pe de-novo assembler error
Could it be a share access mis-configuration on the HPCC? - ABySS fails to write out coverage.hist file and stops
The files generated from this run are listed below:
-rw-rw-r-- 1 aksrao aksrao 42 Aug 18 00:01 EthFoc-11_trimmomatic7_corr-1.dot
-rw-rw-r-- 1 aksrao aksrao 0 Aug 17 23:16 EthFoc-11_trimmomatic7_corr-1.fa
-rw-rw-r-- 1 aksrao aksrao 1.3M Aug 17 23:15 EthFoc-11_trimmomatic7_corr-bubbles.fa
I wanted to test whether removing MPI from the equation will allow the run to completion, I tried
srun --partition=high --mem=24000 --time=12:00:00 --nodes=1 abyss-pe name=EthFoc-11_trimmomatic7_corr k=41 in='EthFoc-11_S285_L007_trimmomatic7_1P.00.0_0.cor.fastq EthFoc-11_S285_L007_trimmomatic7_2P.00.0_0.cor.fastq' srun: job 13800791 queued and waiting for resources srun: job 13800791 has been allocated resources
And the error I see happens almost right away, with the STDOUT looking as follows:
abyss-filtergraph --dot -k41 -g EthFoc-11_trimmomatic7_corr-2.dot1 EthFoc-11_trimmomatic7_corr-1.dot EthFoc-11_trimmomatic7_corr-1.fa >EthFoc-11_trimmomatic7_corr-1.path abyss-filtergraph: ../Graph/DotIO.h:302: std::istream& read_dot(std::istream&, Graph&, BetterEP) [with Graph = DirectedGraph<ContigProperties, Distance>; BetterEP = DisallowParallelEdges; std::istream = std::basic_istream<char>]: Assertion `num_vertices(g) > 0' failed. /bin/bash: line 1: 27510 Aborted abyss-filtergraph --dot -k41 -g EthFoc-11_trimmomatic7_corr-2.dot1 EthFoc-11_trimmomatic7_corr-1.dot EthFoc-11_trimmomatic7_corr-1.fa > EthFoc-11_trimmomatic7_corr-1.path make: *** [EthFoc-11_trimmomatic7_corr-1.path] Error 134 make: *** Deleting file `EthFoc-11_trimmomatic7_corr-1.path' srun: error: c11-91: task 0: Exited with exit code 2
What am I doing wrong? And how can I fix it? Since I am only a couple of days new to genome assembly and an hour into ABySS use, the more detailed your reply, the more useful it might be for me. Thanks!