Como posso fazer o programa EMIRGE ler certos arquivos?
Estou usando o Linux Mint (17.1).
Eu fiz o download de uma chamada de programa EMIRGE , que deve ter arquivos fastq (um formato de arquivo de texto para seqüências biológicas) e execute o algoritmo EMIRGE nessas sequências.
O software está gravando arquivos que não podem ser lidos para as iterações subseqüentes do algoritmo. O programa está gravando esses arquivos para ter -rw-r--r-- de permissões. Independentemente de eu iniciar o programa com o sudo, encontro a seguinte saída:
Working on F3D0_S188_L001_R1_001EMIRGE_output ...
1
If you use EMIRGE in your work, please cite these manuscripts, as appropriate.
Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF (2011)
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data.
Genome biology 12: R44. doi:10.1186/gb-2011-12-5-r44.
Miller CS, Handley KM, Wrighton KC, Frischkorn KR, Thomas BC, Banfield JF (2013)
Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments.
PloS one 8: e56018. doi:10.1371/journal.pone.0056018.
imported _emirge C functions from: /usr/local/lib/python2.7/dist-packages/_emirge_amplicon.so
Command:
/usr/local/bin/emirge_amplicon.py F3D0_S188_L001_R1_001EMIRGE_output -1 F3D0_S188_L001_R1_001.fastq -2 F3D0_S188_L001_R2_001.fastq -b /home/EMIRGE-master/SSURef_111_candidate_db -f /home/EMIRGE-master/SSURef_111_candidate_db.fasta -i 250 -s 1 -l 251 -a 4 --phred33
EMIRGE started at Tue Oct 27 22:03:03 2015
Rewriting reads with indices in headers at Tue Oct 27 22:03:03 2015...
DONE Rewriting reads with indexes in headers at Tue Oct 27 22:03:03 2015 [0:00:00.074732]...
Number of reads (or read pairs) in input file(s): 7793
Preallocating reads and quals in memory at Tue Oct 27 22:03:03 2015...
DONE Preallocating reads and quals in memory at Tue Oct 27 22:03:03 2015 [0:00:00.091667]...
Performing initial mapping with command:
cat /home/galen/Desktop/test/F3D0_S188_L001_R1_001EMIRGE_output/emirge_tmp_reads_1.fastq | bowtie --phred33-quals -t -p 4 -n 3 -l 20 -e 300 --best --sam --chunkmbs 128 --minins 251 --maxins 253 /home/EMIRGE-master/SSURef_111_candidate_db -1 - -2 /home/galen/Desktop/test/F3D0_S188_L001_R1_001EMIRGE_output/emirge_tmp_reads_2.fastq | samtools view -S -h -u -b -F 0x0004 - > /home/galen/Desktop/test/F3D0_S188_L001_R1_001EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.u.bam
Time loading reference: 00:00:00
Time loading forward index: 00:00:01
Time loading mirror index: 00:00:00
[samopen] SAM header is present: 150807 sequences.
Seeded quality full-index search: 00:00:03
# reads processed: 7793
# reads with at least one reported alignment: 6542 (83.95%)
# reads that failed to align: 1251 (16.05%)
Reported 6542 paired-end alignments to 1 output stream(s)
Time searching: 00:00:04
Overall time: 00:00:04
Beginning initialization at Tue Oct 27 22:03:07 2015...
Reading bam file /home/galen/Desktop/test/F3D0_S188_L001_R1_001EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.u.bam at Tue Oct 27 22:03:07 2015...
Culled 812 sequences in iteration -1 due to low fraction of reference sequence bases covered by >= 1 reads
DONE Reading bam file /home/galen/Desktop/test/F3D0_S188_L001_R1_001EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.u.bam at Tue Oct 27 22:03:07 2015 [0:00:00.507276]...
DONE with initialization at Tue Oct 27 22:03:07 2015...
Starting iteration 0 at Tue Oct 27 22:03:07 2015...
Reading bam file /home/galen/Desktop/test/F3D0_S188_L001_R1_001EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.u.bam at Tue Oct 27 22:03:07 2015...
Culled 812 sequences in iteration 00 due to low fraction of reference sequence bases covered by >= 1 reads
DONE Reading bam file /home/galen/Desktop/test/F3D0_S188_L001_R1_001EMIRGE_output/initial_mapping/initial_bowtie_mapping.PE.u.bam at Tue Oct 27 22:03:08 2015 [0:00:00.567163]...
Calculating likelihood (812, 7793) for iteration 0 at Tue Oct 27 22:03:08 2015...
Calculating Pr(N=n) for iteration 0 at Tue Oct 27 22:03:08 2015...
DONE calculating Pr(N=n) for iteration 0 at Tue Oct 27 22:03:08 2015 [0:00:00.000360]...
DONE Calculating likelihood for iteration 0 at Tue Oct 27 22:03:08 2015 [0:00:00.001159]...
Calculating posteriors for iteration 0 at Tue Oct 27 22:03:08 2015...
DONE Calculating posteriors for iteration 0 at Tue Oct 27 22:03:08 2015 [0.000 seconds]...
/usr/local/bin/emirge_amplicon.py:508: RuntimeWarning: invalid value encountered in divide
self.priors[-1] = numpy.asarray(self.posteriors[-1].sum(axis = 1)).flatten() / self.posteriors[-1].sum()
Writing consensus for iteration 0 at Tue Oct 27 22:03:08 2015...
snp_minor_prob_thresh = 0.100
snp_percentage_thresh = 0.040
Split out 0 new minor strain sequences.
Average time for non-split sequences: [0.000000 seconds]
DONE Writing consensus for iteration 0 at Tue Oct 27 22:03:08 2015 [0:00:00.004475]...
Clustering sequences for iteration 0 at Tue Oct 27 22:03:08 2015...
cluster threshold = 0.970
[fai_load] build FASTA index.
[fai_load] fail to open FASTA index.
Traceback (most recent call last):
File "/usr/local/bin/emirge_amplicon.py", line 1576, in <module>
main()
File "/usr/local/bin/emirge_amplicon.py", line 1568, in main
do_iterations(em, max_iter = options.iterations, save_every = None)
File "/usr/local/bin/emirge_amplicon.py", line 1184, in do_iterations
em.do_iteration(em.current_bam_filename, em.current_reference_fasta_filename)
File "/usr/local/bin/emirge_amplicon.py", line 435, in do_iteration
self.cluster_sequences(consensus_filename) # merges sequences that have evolved to be the same (USEARCH)
File "/usr/local/bin/emirge_amplicon.py", line 759, in cluster_sequences
return self.cluster_sequences_usearch(fastafilename)
File "/usr/local/bin/emirge_amplicon.py", line 789, in cluster_sequences_usearch
num_seqs = self.write_consensus_with_mask(fastafilename, tmp_fastafilename, mask="soft")
File "/usr/local/bin/emirge_amplicon.py", line 725, in write_consensus_with_mask
reference_fastafile = pysam.Fastafile(reference_fastafilename)
File "pysam/cfaidx.pyx", line 81, in pysam.cfaidx.FastaFile.__cinit__ (pysam/cfaidx.c:1674)
File "pysam/cfaidx.pyx", line 105, in pysam.cfaidx.FastaFile._open (pysam/cfaidx.c:2255)
IOError: could not open file '/home/galen/Desktop/test/F3D0_S188_L001_R1_001EMIRGE_output/iter.00/iter.00.cons.fasta'
EDIT 1: resultados ls adicionados
-rw-r--r-- 1 galen galen 0 Oct 27 22:33 /home/galen/Desktop/test/F3D0_S188_L001_R1_001EMIRGE_output/iter.00/iter.00.cons.fasta
drwxr-xr-x 4 galen galen 4096 Oct 27 22:33 /home/galen/Desktop/test/
drwxr-xr-x 4 galen galen 4096 Oct 27 22:33 /home/galen/Desktop/test/F3D0_S188_L001_R1_001EMIRGE_output/
drwxr-xr-x 2 galen galen 4096 Oct 27 22:33 /home/galen/Desktop/test/F3D0_S188_L001_R1_001EMIRGE_output/iter.00/
EDIT 2: fasta e referências de índice:
/ home / EMIRGE-master /
-rw-r--r-- 1 root root 71362262 Oct 27 20:24 SSURef_111_candidate_db.1.ebwt
-rw-r--r-- 1 root root 27269528 Oct 27 20:24 SSURef_111_candidate_db.2.ebwt
-rw-r--r-- 1 root root 1357271 Oct 27 20:18 SSURef_111_candidate_db.3.ebwt
-rw-r--r-- 1 root root 54539044 Oct 27 20:18 SSURef_111_candidate_db.4.ebwt
-rw-r--r-- 1 root root 224443581 Oct 27 20:17 SSURef_111_candidate_db.fasta
-rw-r--r-- 1 root root 71362262 Oct 27 20:30 SSURef_111_candidate_db.rev.1.ebwt
-rw-r--r-- 1 root root 27269528 Oct 27 20:30 SSURef_111_candidate_db.rev.2.ebwt
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