How does athena calling other programmes ?

[Zhong17]

without installing virtualenv, I have installed all the required software and add in my environment path (add the /path/to/software/bin to ~/.bashrc), and the athena were installed in ~/miniconda2/bin/athena-meta, when I run athena, the output showed that could not find bwa command: $ athena-meta config.json ============================== bin_reads ============================== 1 chunks to run. Starting... 2018-11-19 21:11:04 - --starting logging BinMetaReadsStep -- 2018-11-19 21:11:04 - get seed contigs from input assembly 2018-11-19 21:11:04 - computing seed coverages (required pass thru *bam) 2018-11-19 21:11:04 - 3 total inputs seeds covering 809 bases 2018-11-19 21:11:04 - 1 input seed contigs >= 400bp and >= 10.0x coverage covering 400 bases 2018-11-19 21:11:04 - created 2 bins from seeds 2018-11-19 21:11:04 - -> finished running step; time elapsed: 0:00:00.030149 2018-11-19 21:11:04 - --stopping logging-- --> bin_reads completed.

============================== index_reads ============================== 1 chunks to run. Starting... 2018-11-19 21:11:04 - --starting logging IndexReadsStep_tianchen -- 2018-11-19 21:11:04 - index fastq /home/tianchen/10x/barcoded.fastq 2018-11-19 21:11:04 - done 2018-11-19 21:11:04 - -> finished running step; time elapsed: 0:00:00.004956 2018-11-19 21:11:04 - --stopping logging-- --> index_reads completed.

============================== assemble_bins ============================== 2 chunks to run. Starting... 2018-11-19 21:11:05 - --starting logging AssembleMetaBinnedStep.bin.0 -- 2018-11-19 21:11:05 - performing local assembly for 1 seeds 2018-11-19 21:11:05 - --starting logging AssembleMetaBinnedStep.bin.1 -- 2018-11-19 21:11:05 - targeting 100x short-read subassembly coverage 2018-11-19 21:11:05 - using barcodes mapped within 10000bp from seed end-points for seed subassembly 2018-11-19 21:11:05 - performing local assembly for 0 seeds 2018-11-19 21:11:05 - targeting 100x short-read subassembly coverage 2018-11-19 21:11:05 - using barcodes mapped within 10000bp from seed end-points for seed subassembly 2018-11-19 21:11:05 - assembling barcoded reads for seed k99_25 2018-11-19 21:11:05 - merging all outputs 2018-11-19 21:11:05 - done 2018-11-19 21:11:05 - removing bin directory ./working/bin.1 2018-11-19 21:11:05 - -> finished running step; time elapsed: 0:00:00.000714 2018-11-19 21:11:05 - --stopping logging-- 2018-11-19 21:11:05 - determing local assemblies 2018-11-19 21:11:05 - 0 initial link candidates to check 2018-11-19 21:11:05 - - 0 pass reciprocal filtering 2018-11-19 21:11:05 - root-ctg:k99_25;numreads:136;checks:0;trunc-checks:False;asms:0;trunc-asms:False 2018-11-19 21:11:05 - - found 1 candidates 2018-11-19 21:11:05 - performing local assemblies 2018-11-19 21:11:05 - assembling with neighbor None 2018-11-19 21:11:05 - - 92 orig barcodes 2018-11-19 21:11:05 - - 92 downsampled barcodes 2018-11-19 21:11:05 - - 43.18x estimated local coverage 2018-11-19 21:11:05 - - 2 min_support required number of threads 2 reads 184 long reads 10 seed contigs 1 extra reads 0 read_length 150 kmer 20 kmers 4233 4243 merge bubble 0 contigs: 3 n50: 293 max: 293 mean: 125 total length: 375 n80: 62 aligned 8 reads confirmed bases: 79 correct reads: 0 bases: 0 distance mean 86 sd 0 seed contigs 1 local contigs 6 kmer 40 kmers 931 926 merge bubble 0 contigs: 1 n50: 293 max: 293 mean: 293 total length: 293 n80: 293 aligned 8 reads confirmed bases: 79 correct reads: 0 bases: 0 distance mean 86 sd 0 seed contigs 1 local contigs 2 kmer 60 kmers 354 354 merge bubble 0 contigs: 1 n50: 293 max: 293 mean: 293 total length: 293 n80: 293 aligned 8 reads confirmed bases: 79 correct reads: 0 bases: 0 distance mean 86 sd 0 seed contigs 1 local contigs 2 kmer 80 kmers 330 328 merge bubble 0 contigs: 1 n50: 293 max: 293 mean: 293 total length: 293 n80: 293 aligned 8 reads confirmed bases: 79 correct reads: 0 bases: 0 distance mean 86 sd 0 seed contigs 1 local contigs 2 kmer 100 kmers 194 193 merge bubble 0 contigs: 1 n50: 0 max: 0 mean: 0 total length: 0 n80: 0 aligning seed contigs

• 0 aligned hit 0 connected components
• retained 0 of 0 contigs reads 184 aligned 0 reads distance mean -nan sd -nan invalid insert distance :::: -11 2018-11-19 21:11:05 - something funky happened while running idba_ud (got error code -11) but there's not much we can do so continuing 2018-11-19 21:11:05 - failed to produce correctly formatted contigs in ./working/bin.0/asm/k99_25/local-asm.0/contig.fa 2018-11-19 21:11:05 - - finished 1 2018-11-19 21:11:05 - merge long output contigs from local assemblies 2018-11-19 21:11:05 - contig path for local asm k99_25_None.0 not generated 2018-11-19 21:11:05 - - 0 contigs covering 0 bases 2018-11-19 21:11:05 - merging all outputs 2018-11-19 21:11:05 - done 2018-11-19 21:11:05 - removing bin directory ./working/bin.0 2018-11-19 21:11:05 - -> finished running step; time elapsed: 0:00:00.428354 2018-11-19 21:11:05 - --stopping logging-- --> assemble_bins completed.

============================== assembleolc ============================== 1 chunks to run. Starting... 2018-11-19 21:11:05 - --starting logging AssembleOLCStep -- 2018-11-19 21:11:05 - jointly overlap-assemble 2018-11-19 21:11:05 - merge input contigs cmd bwa mem -t 4 /home/tianchen/10x/final.contigs.fa ./results/olc/pre-flye-input-contigs.fa | samtools view -bS - | samtools sort -o ./results/olc/align-inputs.bam - **/bin/sh: bwa: command not found_** cmd samtools index ./results/olc/align-inputs.bam 2018-11-19 21:11:05 - filter short subassembled contigs and merge with seeds 2018-11-19 21:11:05 - ========== Exception ========== 2018-11-19 21:11:05 - Traceback (most recent call last): 2018-11-19 21:11:05 - File "/home/tianchen/miniconda2/lib/python2.7/site-packages/athena/pipeline.py", line 50, in _run_chunk 2018-11-19 21:11:05 - chunk.run() 2018-11-19 21:11:05 - File "/home/tianchen/miniconda2/lib/python2.7/site-packages/athena/stages/assemble_olc.py", line 96, in run 2018-11-19 21:11:05 - premergedfiltfa_path, 2018-11-19 21:11:05 - File "/home/tianchen/miniconda2/lib/python2.7/site-packages/athena/stages/assemble_olc.py", line 160, in filter_inputs 2018-11-19 21:11:05 - ctg_size_map = util.get_fasta_sizes(mergedfa_path) 2018-11-19 21:11:05 - File "/home/tianchen/miniconda2/lib/python2.7/site-packages/athena/mlib/util.py", line 151, in get_fasta_sizes 2018-11-19 21:11:05 - fasta = pysam.FastaFile(fa_path) 2018-11-19 21:11:05 - File "pysam/libcfaidx.pyx", line 123, in pysam.libcfaidx.FastaFile.cinit 2018-11-19 21:11:05 - File "pysam/libcfaidx.pyx", line 183, in pysam.libcfaidx.FastaFile._open 2018-11-19 21:11:05 - IOError: error when opening file ./results/olc/pre-flye-input-contigs.fa 2018-11-19 21:11:05 - 2018-11-19 21:11:05 - error when opening file ./results/olc/pre-flye-input-contigs.fa Traceback (most recent call last): File "/home/tianchen/miniconda2/bin/athena-meta", line 11, in sys.exit(main()) File "/home/tianchen/miniconda2/lib/python2.7/site-packages/main.py", line 104, in main run(options) File "/home/tianchen/miniconda2/lib/python2.7/site-packages/main.py", line 36, in run runner.run_stage(stage, stage_name) File "/home/tianchen/miniconda2/lib/python2.7/site-packages/athena/pipeline.py", line 33, in run_stage cluster.map(_run_chunk, to_run) File "/home/tianchen/miniconda2/lib/python2.7/site-packages/athena/cluster.py", line 43, in map return pool.map_async(fn, args).get(9999999) File "/home/tianchen/miniconda2/lib/python2.7/multiprocessing/pool.py", line 572, in get raise self._value IOError: error when opening file ./results/olc/pre-flye-input-contigs.fa

and also, the error showed that fail to open the ./results/olc/pre-flye-input-contigs.fa. I think I need help,thanks!

[abishara]

If it's easier for setup, please see #13. Athena can now be installed using conda.