simoncchu / gappadder Goto Github PK

Hi back

I am opening a new issue, as gappadder isn't working yet with me:
I have recompile TERefiner_1 and ContigsMerger (see previous closed issue).
I am testing the program on a subset of denovo assembled scaffold (8 sequences with total of 6 gaps), as well as subset of miseq read pairs.
Gappadder apparently runs fine but apparently halts in its final steps. Could you help me going through the whole program?

Here is the end of my log file:

Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa_no_dup.fa -c 0.99 -g ...
Running command: ./ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merge.info /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa_no_dup.fa > /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.99 -g ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.99 ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa_no_dup.fa -c 0.99 -g ...
Running command: ./ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa_no_dup.fa.merge.info /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa_no_dup.fa > /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa_no_dup.fa.merged.fa ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa_no_dup.fa.merged.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.99 -g ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.99 ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa_no_dup.fa -c 0.99 -g ...
Running command: ./ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa_no_dup.fa.merge.info /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa_no_dup.fa > /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa_no_dup.fa.merged.fa ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa_no_dup.fa.merged.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.99 -g ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.99 ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa_no_dup.fa -c 0.99 -g ...
Running command: ./ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa_no_dup.fa.merge.info /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa_no_dup.fa > /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa_no_dup.fa.merged.fa ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa_no_dup.fa.merged.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.99 -g ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.99 ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa_no_dup.fa -c 0.99 -g ...
Running command: ./ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa_no_dup.fa.merge.info /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa_no_dup.fa > /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa_no_dup.fa.merged.fa ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa_no_dup.fa.merged.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.99 -g ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.99 ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa_no_dup.fa -c 0.99 -g ...
Running command: ./ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa_no_dup.fa.merge.info /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa_no_dup.fa > /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa_no_dup.fa.merged.fa ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa_no_dup.fa.merged.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.99 -g ...
Running command: ./TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.99 ...
[bwa_index] Pack FASTA... [bwa_index] Pack FASTA... [bwa_index] Pack FASTA... [bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa index /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa
[main] Real time: 0.010 sec; CPU: 0.014 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2 sequences (590 bp)...
[M::mem_process_seqs] Processed 2 reads in 0.001 CPU sec, 0.001 real sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa mem -T 30 -a /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_1/contigs.fa /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/../flank_regions/1_1.fa
[main] Real time: 0.004 sec; CPU: 0.007 sec
0.02 sec
[bwa_index] Construct BWT for the packed sequence...
0.01 sec
[bwa_index] Construct BWT for the packed sequence...
0.47 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=53854680, availableWord=15789224
1.56 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=166442510, availableWord=23711200
[bwa_index] 2.31 seconds elapse.
[bwa_index] Update BWT... 0.01 sec
[bwa_index] Pack forward-only FASTA... 0.02 sec
[bwa_index] Construct SA from BWT and Occ... 2.47 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=71479196, availableWord=17029476
0.20 sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa index /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa
[main] Real time: 2.617 sec; CPU: 2.570 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2 sequences (590 bp)...
[M::mem_process_seqs] Processed 2 reads in 0.062 CPU sec, 0.061 real sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa mem -T 30 -a /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_2/contigs.fa /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/../flank_regions/2_2.fa
[main] Real time: 0.074 sec; CPU: 0.071 sec
[bwa_index] 3.83 seconds elapse.
[bwa_index] Update BWT... 0.02 sec
[bwa_index] Pack forward-only FASTA... 0.01 sec
[bwa_index] Construct SA from BWT and Occ... 0.18 sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa index /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa
[main] Real time: 4.307 sec; CPU: 4.062 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2 sequences (590 bp)...
[M::mem_process_seqs] Processed 2 reads in 0.072 CPU sec, 0.151 real sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa mem -T 30 -a /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_2/contigs.fa /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/../flank_regions/1_2.fa
[main] Real time: 0.191 sec; CPU: 0.088 sec
[BWTIncConstructFromPacked] 10 iterations done. 28090220 characters processed.
[BWTIncConstructFromPacked] 10 iterations done. 26044312 characters processed.
[BWTIncConstructFromPacked] 10 iterations done. 39112382 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 48112776 characters processed.
[bwa_index] 54.90 seconds elapse.
[bwa_index] Update BWT... 0.41 sec
[bwa_index] Pack forward-only FASTA... 0.31 sec
[bwa_index] Construct SA from BWT and Occ... [BWTIncConstructFromPacked] 20 iterations done. 51892636 characters processed.
7.16 sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa index /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa
[main] Real time: 96.273 sec; CPU: 63.264 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2 sequences (590 bp)...
[M::mem_process_seqs] Processed 2 reads in 0.053 CPU sec, 0.101 real sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa mem -T 30 -a /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/4_1/contigs.fa /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/../flank_regions/4_1.fa
[main] Real time: 0.302 sec; CPU: 0.143 sec
[BWTIncConstructFromPacked] 30 iterations done. 71479196 characters processed.
[bwa_index] 63.42 seconds elapse.
[bwa_index] Update BWT... 0.56 sec
[bwa_index] Pack forward-only FASTA... 0.44 sec
[bwa_index] Construct SA from BWT and Occ... 11.47 sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa index /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa
[main] Real time: 117.312 sec; CPU: 78.371 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2 sequences (590 bp)...
[M::mem_process_seqs] Processed 2 reads in 0.089 CPU sec, 0.185 real sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa mem -T 30 -a /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/2_1/contigs.fa /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/../flank_regions/2_1.fa
[main] Real time: 0.337 sec; CPU: 0.203 sec
[BWTIncConstructFromPacked] 20 iterations done. 72256094 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 101710254 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 127885182 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 151145470 characters processed.
[bwa_index] 150.23 seconds elapse.
[bwa_index] Update BWT... 1.37 sec
[bwa_index] Pack forward-only FASTA... 0.95 sec
[bwa_index] Construct SA from BWT and Occ... 27.63 sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa index /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa
[main] Real time: 257.168 sec; CPU: 181.747 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2 sequences (590 bp)...
[M::mem_process_seqs] Processed 2 reads in 0.062 CPU sec, 0.137 real sec
[main] Version: 0.7.15-r1140
[main] CMD: /media/physio/home/pganot/anaconda2/envs/genomeQC/bin/bwa mem -T 30 -a /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/velvet_temp/1_3/contigs.fa /media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/../flank_regions/1_3.fa
[main] Real time: 0.567 sec; CPU: 0.305 sec
Traceback (most recent call last):
File "/media/physio/home/pganot/finisher/GAPPadder/main.py", line 283, in
main_func(scommand,sfconfig)
File "/media/physio/home/pganot/finisher/GAPPadder/main.py", line 274, in main_func
gap_assembler.assemble_pipeline()
File "/media/physio/home/pganot/finisher/GAPPadder/assemble_gaps.py", line 339, in assemble_pipeline
id_remain=self.pick_already_constructed(contigs_select, fa_list, sf_picked)
File "/media/physio/home/pganot/finisher/GAPPadder/assemble_gaps.py", line 321, in pick_already_constructed
m_picked=contigs_select.get_already_picked(sf_picked)
File "/media/physio/home/pganot/finisher/GAPPadder/pick_contigs.py", line 576, in get_already_picked
with open(sf_picked) as fin_picked:
IOError: [Errno 2] No such file or directory: u'/media/physio/home/pganot/finisher/GAPPadder/v143_sample/merged/../picked_seqs.fa'

Thanks
Philippe

Hi,

I am trying to run your GAPPadder software.
However, I get an error that we can not figure out. Could you please give some advice?
Do we need a specific version of samtools?

(py27) nesbocam@silicon:~/GAPPadder-master$ python ./main.py -c Collect -g configuration_bathy1.json

samtools view /nfs/homes/nesbocam/ReAssemble-0.6/ctbRA/MWAHD1170726bathy_rMAG1/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected.curated/BBmap/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected_Ra_sorted.bam "MWAHD1170726pbOP_mb_MAG_00021V2_16S" | python collect_reads_for_gaps.py MWAHD1170726bathy_rMAG1Gappadder/gap_positions.txt 30 MWAHD1170726bathy_rMAG1Gappadder/1_is500/ 500 50 250 -

Traceback (most recent call last):

File "collect_reads_for_gaps.py", line 278, in

grc.parse_reads_fall_in_gaps_one_scaffold_short_is(sf_gap_pos, anchor_mapq, working_folder)

File "collect_reads_for_gaps.py", line 178, in parse_reads_fall_in_gaps_one_scaffold_short_is

flag=int(sam_fields[1])

ValueError: invalid literal for int() with base 10: '1:N:0:0'

samtools view: writing to standard output failed: Broken pipe

samtools view: error closing standard output: -1

Traceback (most recent call last):

File "./main.py", line 283, in

main_func(scommand,sfconfig)

File "./main.py", line 244, in main_func

mtrc.dispath_collect_jobs(nthreads, samtools_path, insert_size, derivation, clip_dist, folder)

File "/nfs/homes/nesbocam/GAPPadder-master/run_multi_threads_collect_reads.py", line 36, in dispath_collect_jobs

pool.map(run_cmd_reads_collect, cmd_list)

File "/nfs/homes/nesbocam/miniconda3/envs/py27/lib/python2.7/multiprocessing/pool.py", line 253, in map

return self.map_async(func, iterable, chunksize).get()

File "/nfs/homes/nesbocam/miniconda3/envs/py27/lib/python2.7/multiprocessing/pool.py", line 572, in get

raise self._value

subprocess.CalledProcessError: Command 'samtools view /nfs/homes/nesbocam/ReAssemble-0.6/ctbRA/MWAHD1170726bathy_rMAG1/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected.curated/BBmap/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected_Ra_sorted.bam "MWAHD1170726pbOP_mb_MAG_00021V2_16S" | python collect_reads_for_gaps.py MWAHD1170726bathy_rMAG1Gappadder/gap_positions.txt 30 MWAHD1170726bathy_rMAG1Gappadder/1_is500/ 500 50 250 -' returned non-zero exit status 1

Hi

I am currently running GAPPadder on some short reads assembly but getting this error at merge_dispatch_reads_for_gaps_v2 step

python ./GAPPadder/main.py -c All -g GAPPadder_configuration_CLC.json

Traceback (most recent call last):
File "./GAPPadder/main.py", line 283, in
main_func(scommand,sfconfig)
File "./GAPPadder/main.py", line 257, in main_func
drc.merge_dispatch_reads_for_gaps_v2(left_reads, right_reads)
File "./GAPPadder/run_multi_threads_discordant.py", line 213, in merge_dispatch_reads_for_gaps_v2
temp_field=id_fields[0].split("/")
IndexError: list index out of range

Any idea why this error occured?

Thanks in advance

I'm trying to run gappadder on my data, but run into problems at the Collect stage. This is the error I receive:

Traceback (most recent call last):
  File "/camp/lab/turnerj/working/jasmin/software/GAPPadder/main.py", line 283, in <module>
    main_func(scommand,sfconfig)
  File "/camp/lab/turnerj/working/jasmin/software/GAPPadder/main.py", line 254, in main_func
    drc.collect_discordant_regions_v2(sfout_discord_pos)
  File "/camp/lab/turnerj/working/jasmin/software/GAPPadder/run_multi_threads_discordant.py", line 122, in collect_discordant_regions_v2
    ftemp.close()
AttributeError: 'NoneType' object has no attribute 'close'

My config file looks like this:

{
    "draft_genome": {
        "fa": "/camp/lab/turnerj/working/jasmin/data/Dovetail/data/DT2_majorScfs_chrUn.fasta"
    },
    "raw_reads": [
		    {
		        "left": "/camp/lab/turnerj/working/shared_projects/Dovetail_opossum_WGS/raw_data/DTG_DNA_465_S61_L003_R1_001.fastq.gz",
		        "right": "/camp/lab/turnerj/working/shared_projects/Dovetail_opossum_WGS/raw_data/DTG_DNA_465_S61_L003_R2_001.fastq.gz"
		    }
	  ],
    "alignments": [
		    {
		        "bam": "/camp/lab/turnerj/working/jasmin/data/Dovetail/bams/10x_reads_to_DT2.bam",
		        "is": "300",
		        "std": "120"
		    }
	  ],
    "software_path": {
        "bwa": "/camp/apps/eb/software/BWA/0.7.17-foss-2018b/bin/bwa",
        "samtools": "/camp/apps/eb/software/SAMtools/1.3.1-foss-2016b/bin/samtools",
        "velvet": "/camp/apps/eb/dev/software/Velvet/1.2.10-foss-2016b-mt-kmer_37/bin",
        "kmc": "/camp/apps/eb/software/khmer/1.4.1-foss-2016b-Python-2.7.12/bin",
        "TERefiner": "/camp/lab/turnerj/working/jasmin/software/GAPPadder/TERefiner_1",
        "ContigsMerger": "/camp/lab/turnerj/working/jasmin/software/GAPPadder/ContigsMerger"
    },
    "parameters": {
    		"working_folder": "/camp/lab/turnerj/working/jasmin/data/Dovetail/gappadder",
        "min_gap_size": "1000",
        "flank_length": "300",
        "nthreads": "1",
        "verbose": "1"
		},
		"kmer_length": [{
						"k": 30,
						"k_velvet": [{
								"k": 29
						}, 
						{
								"k": 27
						}]
				}, 
				{
						"k": 40,
						"k_velvet": [{
								"k": 39
						}, 
						{
								"k": 37
						}]
				},
				{
						"k": 50,
						"k_velvet": [{
								"k": 49
						}, 
						{
								"k": 47
						}]
				}]
}

Any idea how to fix this? Thanks!

Hi,

I am sorry if the question that I am asking has been in the paper, and I just missed the point but:

I have two types of reads and I want to to fill the gaps in Chromium 10x assembly -

1. Illumina PE reads
2. PacBio reads.
   Gappadder needs the alignments of the reads to be done before it fills the gaps. Therefore I am going to run bwa/bowtie on the Illumina reads (10x assembler does not output bam alignment files).
   What about the long reads? Can I use them to fill the gaps too?

Thanks

Hi @simoncchu

I was able to run the Preprocess and Collect steps, but during assembly this is the error message that I get:

First round assembly and merger...
**
***
*
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**
Stage 1: 0%
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Start merging...
Could not build fai index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa.fai
Could not build fai index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa.fai
[bwa_index] Pack FASTA... [bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... [bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa
[main] Real time: 0.015 sec; CPU: 0.009 sec
0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa
[main] Real time: 0.021 sec; CPU: 0.011 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bwa_index] 0.01 seconds elapse.
[bwa_index] Update BWT... [main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa
[main] Real time: 0.003 sec; CPU: 0.005 sec
0.00 sec
[bwa_index] Pack forward-only FASTA... [M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 42 sequences (6250 bp)...
0.00 sec
[bwa_index] Construct SA from BWT and Occ... [M::mem_process_seqs] Processed 42 reads in 0.007 CPU sec, 0.007 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa
[main] Real time: 0.012 sec; CPU: 0.011 sec
0.01 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa
[main] Real time: 0.041 sec; CPU: 0.031 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 420 sequences (55464 bp)...
[M::mem_process_seqs] Processed 420 reads in 0.058 CPU sec, 0.058 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa
[main] Real time: 0.062 sec; CPU: 0.063 sec
rm: cannot remove ‘/hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa.fai’: No such file or directory
[fai_build_core] malformed line
Could not build fai index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.fai
[fai_build_core] malformed line
Could not build fai index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.fai
[fai_build_core] malformed line
Could not build fai index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.fai
[bwa_index] Pack FASTA... [fai_build_core] malformed line
Could not build fai index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.fai
0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] Pack FASTA... [bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa
[main] Real time: 0.024 sec; CPU: 0.007 sec
0.00 sec
[bwa_index] Construct SA from BWT and Occ... [M::bwa_idx_load_from_disk] read 0 ALT contigs
0.00 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa
[main] Real time: 0.021 sec; CPU: 0.007 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa
[main] Real time: 0.004 sec; CPU: 0.003 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa
[main] Real time: 0.003 sec; CPU: 0.003 sec
rm: cannot remove ‘/hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.fai’: No such file or directory
rm: cannot remove ‘/hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.fai’: No such file or directory
[fai_build_core] malformed line
Could not build fai index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai
[fai_build_core] malformed line
Could not build fai index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai
[fai_build_core] malformed line
Could not build fai index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai
[fai_build_core] malformed line
Could not build fai index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai
[bwa_index] Pack FASTA... [bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
[main] Real time: 0.017 sec; CPU: 0.007 sec
0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
[main] Real time: 0.015 sec; CPU: 0.008 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
[main] Real time: 0.002 sec; CPU: 0.003 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
[main] Real time: 0.002 sec; CPU: 0.003 sec
rm: cannot remove ‘/hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai’: No such file or directory
rm: cannot remove ‘/hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai’: No such file or directory
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa
[main] Real time: 0.030 sec; CPU: 0.018 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 82 sequences (21702 bp)...
[M::mem_process_seqs] Processed 82 reads in 0.100 CPU sec, 0.099 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa
[main] Real time: 0.103 sec; CPU: 0.104 sec
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
[main] Real time: 0.035 sec; CPU: 0.016 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 47 sequences (12377 bp)...
[M::mem_process_seqs] Processed 47 reads in 0.020 CPU sec, 0.020 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
[main] Real time: 0.023 sec; CPU: 0.024 sec
Running command: ./TERefiner_1 -P -b /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa.itself.sort.bam -r /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa -c 0.99 -g ...
Running command: ./ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merge.info /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa > /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa ...
Running command: ./TERefiner_1 -P -b /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.99 -g ...
Running command: ./TERefiner_1 -P -b /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.99 ...
Running command: ./TERefiner_1 -P -b /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa.itself.sort.bam -r /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa -c 0.99 -g ...
Running command: ./ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merge.info /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa > /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa ...
Running command: ./TERefiner_1 -P -b /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.99 -g ...
Running command: ./TERefiner_1 -P -b /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.99 ...
Running command: ./TERefiner_1 -P -b /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa.itself.sort.bam -r /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa -c 0.99 -g ...
Running command: ./ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merge.info /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa > /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa ...
Running command: ./TERefiner_1 -P -b /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.99 -g ...
Running command: ./TERefiner_1 -P -b /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.99 ...
[bwa_index] Pack FASTA... [bwa_index] Pack FASTA... [bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
0.00 sec
[bwa_index] Construct BWT for the packed sequence...
0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... [bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Pack forward-only FASTA... [bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
0.00 sec
[bwa_index] Pack forward-only FASTA... [main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/1_1/contigs.fa
[main] Real time: 0.017 sec; CPU: 0.012 sec
0.00 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa
[main] Real time: 0.018 sec; CPU: 0.012 sec
0.01 sec
[bwa_index] Construct SA from BWT and Occ... [M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
0.00 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa
[main] Real time: 0.029 sec; CPU: 0.018 sec
[M::process] read 2 sequences (590 bp)...
[M::process] read 2 sequences (590 bp)...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2 sequences (590 bp)...
[M::mem_process_seqs] Processed 2 reads in 0.002 CPU sec, 0.002 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -T 30 -a /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/64_1/contigs.fa /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/../flank_regions/64_1.fa
[main] Real time: 0.004 sec; CPU: 0.007 sec
Traceback (most recent call last):
  File "./main.py", line 283, in <module>
    main_func(scommand,sfconfig)
  File "./main.py", line 274, in main_func
    gap_assembler.assemble_pipeline()
  File "/hpcdata/bcbb/homc/conda_envs/envs/GAPPadder/assemble_gaps.py", line 339, in assemble_pipeline
    id_remain=self.pick_already_constructed(contigs_select, fa_list, sf_picked)
  File "/hpcdata/bcbb/homc/conda_envs/envs/GAPPadder/assemble_gaps.py", line 321, in pick_already_constructed
    m_picked=contigs_select.get_already_picked(sf_picked)
  File "/hpcdata/bcbb/homc/conda_envs/envs/GAPPadder/pick_contigs.py", line 576, in get_already_picked
    with open(sf_picked) as fin_picked:
IOError: [Errno 2] No such file or directory: u'/hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/../picked_seqs.fa'

Going back to the first error which is Could not build fai index /hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout/merged/velvet_temp/9_1/contigs.fa.fai I went to this file and found that of course it can't index the fasta, it looks like this:

velvet_temp/9_1/contigs.fa.fai:

(GAPPadder) [homc@ai-hpcn106 9_1]$ less contigs.fa
Arrange error! 0 5

Tracing backwards, this is an error provided by ContigsCompactor.cpp

However, I don't know how to troubleshoot further. Why is Contigs Compactor returning an Arange error and how can I fix the pipeline?

This is my json file. SAMTools, BWA were installed using Conda, I recompiled Velvet during install to use MAXKMERLENGTH=99.

{
    "draft_genome": {
        "fa": "/hpcdata/bcbb/homc/multipilon_pb_gIllumina/Tcas_blobtools_round3_gIlluminabasecovatleast1_or_RNAseqgt1.pilon10.fasta"
    },
    "raw_reads": [
		    {
		        "left": "/hpcdata/bcbb/homc/Tcas_gIllumina.trim.1.fastq",
		        "right": "/hpcdata/bcbb/homc/Tcas_gIllumina.trim.2.fastq"
		    }	  ],
    "alignments": [
		    {
            "bam": "/hpcdata/bcbb/homc/multipilon_pb_gIllumina/Tcas_HISAT2_trim_gIllumina_map_Tcas_blobtools_round3_gIlluminabasecovatleast1_or_RNAseqgt1_pilon10/Tcas_HISAT2_trim_gIllumina_map_Tcas_blobtools_round3_gIlluminabasecovatleast1_or_RNAseqgt1_pilon10.bam",
		        "is": "148",
		        "std": "50"
        }
	  ],
    "software_path": {
        "bwa": "bwa",
        "samtools": "samtools",
        "velvet": "/hpcdata/bcbb/homc/conda_envs/envs/GAPPadder/velvet",
        "kmc": "/hpcdata/bcbb/homc/conda_envs/envs/GAPPadder/bin/",
        "TERefiner": "./TERefiner_1",
        "ContigsMerger": "./ContigsMerger"
    },
    "parameters": {
    		"working_folder": "/hpcdata/bcbb/homc/multipilon_pb_gIllumina/GAPPadderout",
        "min_gap_size": "100",
        "flank_length": "300",
        "nthreads": "15",
        "verbose": "1"
		},
		"kmer_length": [{
						"k": 30,
						"k_velvet": [{
								"k": 29
						}, 
						{
								"k": 27
						}]
				}, 
				{
						"k": 40,
						"k_velvet": [{
								"k": 39
						}, 
						{
								"k": 37
						}]
				},
				{
						"k": 50,
						"k_velvet": [{
								"k": 49
						}, 
						{
								"k": 47
						}]
				}]
}

Please let me know what you think. Would really like to use this tool, and have spent several hours troubleshooting and I am running up against a wall.

Sincerely,
Margaret

Hi

I have tried to run gappdder on my draft genome with a sample (2X 1000000 reads) of a miseq library, as a program-test.
The 2 first steps (Preprocess & Collect) went apparently OK, However, it crushed during the assembly step. In my log file, I have a lot of similar error messages(14Mb text file)
recurrently :
[E::fai_insert_index] Malformed line
[E::bwa_idx_load] fail to locate the index files
[bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success

Below is the part of the log file.

Running command: /media/physio/home/pganot/finisher/GAPPadder/ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/579_1/contigs.fa_no_dup.fa.merge.info /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/579_1/contigs.fa_no_dup.fa > /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/579_1/contigs.fa_no_dup.fa.merged.fa ...
Running command: /media/physio/home/pganot/finisher/GAPPadder/TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/579_1/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/579_1/contigs.fa_no_dup.fa.merged.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/579_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.99 -g ...
Running command: /media/physio/home/pganot/finisher/GAPPadder/TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/579_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/579_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/579_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.99 ...
Running command: /media/physio/home/pganot/finisher/GAPPadder/TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa_no_dup.fa -c 0.99 -g ...
Running command: /media/physio/home/pganot/finisher/GAPPadder/ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa_no_dup.fa.merge.info /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa_no_dup.fa > /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa_no_dup.fa.merged.fa ...
Running command: /media/physio/home/pganot/finisher/GAPPadder/TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa_no_dup.fa.merged.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.99 -g ...
Running command: /media/physio/home/pganot/finisher/GAPPadder/TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/597_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.99 ...
Running command: /media/physio/home/pganot/finisher/GAPPadder/TERefiner_1 -P -b /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/618_2/contigs.fa.itself.sort.bam -r /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/618_2/contigs.fa -o /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/618_2/contigs.fa_no_dup.fa -c 0.99 -g ...
Running command: /media/physio/home/pganot/finisher/GAPPadder/ContigsMerger -s 0.4 -i1 -2.0 -i2 -2.0 -x 12 -y 50 -k 10 -t 5 -m 1 -o /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/618_2/contigs.fa_no_dup.fa.merge.info /media/physio/home/pganot/finisher/GAPPadder/v143_ssparm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/613_2/contigs.fa_no_dup.fa.merged.fa.fai': No such file or directory [E::fai_insert_index] Malformed line Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/616_1/contigs.fa_no_dup.fa.merged.fa.fai [E::bwa_idx_load] fail to locate the index files [bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success [E::fai_insert_index] Malformed line Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/613_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/626_4/contigs.fa.fai [E::fai_insert_index] Malformed line Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/615_4/contigs.fa_no_dup.fa.merged.fa.fai rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/607_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.sa': No such file or directory
rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/604_4/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai': No such file or directory [E::fai_insert_index] Malformed line Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/617_7/contigs.fa_no_dup.fa.merged.fa.fai [E::bwa_idx_load] fail to locate the index files [E::fai_insert_index] Malformed line Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/618_2/contigs.fa_no_dup.fa.merged.fa.fai [bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/626_4/contigs.fa.fai [E::fai_insert_index] Malformed line Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/613_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/607_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.bwt': No such file or directory
[E::fai_insert_index] Malformed line
Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/615_4/contigs.fa_no_dup.fa.merged.fa.fai
[E::bwa_idx_load] fail to locate the index files
[bwa_index] Pack FASTA... rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/607_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai'[bwa_index] Pack FASTA... : No such file or directory rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/610_3/contigs.fa_no_dup.fa.merged.fa.fai': No such file or directory
[bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success
[bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success
rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/607_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.ann': No such file or directory [bwa_index] Pack FASTA... [E::fai_insert_index] Malformed line Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/618_2/contigs.fa_no_dup.fa.merged.fa.fai 0.00 sec [bwa_index] Construct BWT for the packed sequence... rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/607_2/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.amb': No such file or directory
[E::fai_build3] Failed to open the FASTA file /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/610_3/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/610_3/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... [E::bwa_idx_load] fail to locate the index files
0.00 sec
[bwa_index] Pack forward-only FASTA... [E::bwa_idx_load] fail to locate the index files
[bwa_index] Pack FASTA... rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/620_2/contigs.fa.sa': No such file or directory rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/622_3/contigs.fa.sa': No such file or directory
rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/614_1/contigs.fa_no_dup.fa.merged.fa.sa': No such file or directory [E::bwa_idx_load] fail to locate the index files 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.00 sec [main] Version: 0.7.10-r789 [main] CMD: /media/physio/build/bwa-0.7.10/bwa index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/615_4/contigs.fa_no_dup.fa.merged.fa [main] Real time: 0.018 sec; CPU: 0.009 sec [E::fai_build3] Failed to open the FASTA file /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/610_3/contigs.fa_no_dup.fa.merged.fa.no_dup.fa Could not build fai index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/610_3/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.fai rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/620_2/contigs.fa.bwt': No such file or directory
rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/610_1/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.sa': No such file or directory [bwa_index] Pack FASTA... rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/614_1/contigs.fa_no_dup.fa.merged.fa.bwt': No such file or directory
rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/622_3/contigs.fa.bwt': No such file or directory [bwa_index] fail to open file '/media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/610_3/contigs.fa_no_dup.fa.merged.fa.no_dup.fa' : No such file or directory [M::main_mem] read 1 sequences (188 bp)... rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/620_2/contigs.fa.ann': No such file or directory
[bwa_index] Pack FASTA... [M::mem_process_seqs] Processed 1 reads in 0.002 CPU sec, 0.001 real sec
[main] Version: 0.7.10-r789
[main] CMD: /media/physio/build/bwa-0.7.10/bwa mem -a /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/615_4/contigs.fa_no_dup.fa.merged.fa /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/615_4/contigs.fa_no_dup.fa.merged.fa
[main] Real time: 0.002 sec; CPU: 0.003 sec
0.00 sec
[bwa_index] Construct BWT for the packed sequence...
rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/614_1/contigs.fa_no_dup.fa.merged.fa.ann': No such file or directory rm: cannot remove /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/622_3/contigs.fa.ann': No such file or directory
rm: cannot remove `/media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/615_2/contigs.fa_no_dup.fa.merged.fa.sa': No such file or directory

the end of log file:
[main] CMD: /media/physio/build/bwa-0.7.10/bwa index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/5052_1/contigs.fa
[main] Real time: 0.005 sec; CPU: 0.007 sec
[E::bwa_idx_load] fail to locate the index files
[M::main_mem] read 2 sequences (590 bp)...
[E::bwa_idx_load] fail to locate the index files
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... [bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Pack forward-only FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success
[M::mem_process_seqs] Processed 2 reads in 0.004 CPU sec, 0.003 real sec
[main] Version: 0.7.10-r789
[main] CMD: /media/physio/build/bwa-0.7.10/bwa mem -T 30 -a /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/4682_1/contigs.fa /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/../flank_regions/4682_1.fa
[main] Real time: 0.003 sec; CPU: 0.004 sec
0.00 sec
[bwa_index] Construct SA from BWT and Occ... [E::bwa_idx_load] fail to locate the index files
[E::bwa_idx_load] fail to locate the index files
[bwa_index] Pack FASTA... 0.00 sec
[main] Version: 0.7.10-r789
[main] CMD: /media/physio/build/bwa-0.7.10/bwa index /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/5109_1/contigs.fa
[main] Real time: 0.005 sec; CPU: 0.008 sec
[bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success
[bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success
[M::main_mem] read 2 sequences (590 bp)...
[M::main_mem] read 2 sequences (590 bp)...
[bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success
[bwa_index] Pack FASTA... [M::mem_process_seqs] Processed 2 reads in 0.002 CPU sec, 0.002 real sec
[bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success
[main] Version: 0.7.10-r789
[main] CMD: /media/physio/build/bwa-0.7.10/bwa mem -T 30 -a /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/4956_1/contigs.fa /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/../flank_regions/4956_1.fa
[main] Real time: 0.002 sec; CPU: 0.003 sec
[bwa_index] Pack FASTA... [E::bwa_idx_load] fail to locate the index files
[bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success
[E::bwa_idx_load] fail to locate the index files
[M::mem_process_seqs] Processed 2 reads in 0.002 CPU sec, 0.002 real sec
[bwa_index] Pack FASTA... [main] Version: 0.7.10-r789
[main] CMD: /media/physio/build/bwa-0.7.10/bwa mem -T 30 -a /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/5052_1/contigs.fa /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/../flank_regions/5052_1.fa
[main] Real time: 0.002 sec; CPU: 0.003 sec
[bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success
[bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 270: Success
[E::bwa_idx_load] fail to locate the index files
[M::main_mem] read 2 sequences (590 bp)...
[E::bwa_idx_load] fail to locate the index files
[M::mem_process_seqs] Processed 2 reads in 0.003 CPU sec, 0.002 real sec
[main] Version: 0.7.10-r789
[main] CMD: /media/physio/build/bwa-0.7.10/bwa mem -T 30 -a /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/velvet_temp/5109_1/contigs.fa /media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/../flank_regions/5109_1.fa
[main] Real time: 0.002 sec; CPU: 0.003 sec
[E::bwa_idx_load] fail to locate the index files
[E::bwa_idx_load] fail to locate the index files
[E::bwa_idx_load] fail to locate the index files
[E::bwa_idx_load] fail to locate the index files
[E::bwa_idx_load] fail to locate the index files
Traceback (most recent call last):
File "/media/physio/home/pganot/finisher/GAPPadder/main.py", line 283, in
main_func(scommand,sfconfig)
File "/media/physio/home/pganot/finisher/GAPPadder/main.py", line 274, in main_func
gap_assembler.assemble_pipeline()
File "/media/physio/home/pganot/finisher/GAPPadder/assemble_gaps.py", line 339, in assemble_pipeline
id_remain=self.pick_already_constructed(contigs_select, fa_list, sf_picked)
File "/media/physio/home/pganot/finisher/GAPPadder/assemble_gaps.py", line 321, in pick_already_constructed
m_picked=contigs_select.get_already_picked(sf_picked)
File "/media/physio/home/pganot/finisher/GAPPadder/pick_contigs.py", line 576, in get_already_picked
with open(sf_picked) as fin_picked:
IOError: [Errno 2] No such file or directory: u'/media/physio/home/pganot/finisher/GAPPadder/v143_sspace/merged/../picked_seqs.fa'

I have tried to recompile TERefiner, but I got the folling error file after make:
g++ -O3 -Wall -static -I/media/physio/build/bamtools/include -L/media/physio/build/bamtools/lib -Wl,-rpath,/media/physio/build/bamtools/lib -o TERefiner_1 public_func.o StrOperation.o local_alignment.o Alignment.o bam_parse.o fai_parser.o contigs.o Coverage.o scaffolding.o RepeatsClassifier.o refiner.o main.o -lbamtools -lz -lm
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
make: *** [TERefiner] Error 1

Could you help ?
Thanks

Hi,
I assembled my genome using MITObim. I haven't managed to run GAPPadder due to IndexError: string index out of range after trying to 'Preprocess the draft genome to get the gap positions and flank regions'. Can you help me on tracing what seems to be a problem?

Hi,

Just noticed that I was getting a "string index out of range" error when KMC was already set to my PATH (so I left it as "" in the configuration.json). The reason seems to be that in Utility.py we always run

if pkmc[-1]!="/":
        pkmc=pkmc+"/"
    if pvelvet[-1]!="/":
        pvelvet=pvelvet+"/"

But these only work if the strings are at least length 1. We should probably add a check like pkmc and pkmc[-1] != "/".

I am trying to make TERefiner using the following command:

cd TERefiner  &&  make  &&  cd ..

but i get:

./bam_parse.h:4:10: fatal error: 'api/BamReader.h' file not found

I have tried installing bamtools and changing its path in TERefiner Makefile. But still facing the similar issue.

PLease help.

Hello, i was running the collect part of the pipeline and i get this error:
"Traceback (most recent call last):
File "./main.py", line 283, in
main_func(scommand,sfconfig)
File "./main.py", line 257, in main_func
drc.merge_dispatch_reads_for_gaps_v2(left_reads, right_reads)
File "/home/software/GAPPadder/run_multi_threads_discordant.py", line 213, in merge_dispatch_reads_for_gaps_v2
temp_field=id_fields[0].split("/")
IndexError: list index out of range"

My configuration.json is below:
"{
"draft_genome": {
"fa": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/ZuCrist_sspace/ZuCrist_sspace.final.scaffolds.fasta"
},
"raw_reads": [
{
"left": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/300_pairs.4_25.h.R1.fq.gz",
"right": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/300_pairs.4_25.h.R2.fq.gz"
},
{
"left": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/550_pairs.4_25.h.R1.fq.gz",
"right": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/550_pairs.4_25.h.R2.fq.gz"
}
],
"alignments": [
{
"bam": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/BWA_sspace/Zu_300p.sorted.bam",
"is": "293",
"std": "119"
},
{
"bam": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/BWA_sspace/Zu_550p.sorted.bam",
"is": "406",
"std": "149"
}
],
"software_path": {
"bwa": "bwa",
"samtools": "samtools",
"velvet": "/home/software/anaconda3/pkgs/velvet-1.2.10-hed695b0_3/bin/",
"kmc": "/usr/local/bin/",
"TERefiner": "/home/software/GAPPadder/TERefiner_1",
"ContigsMerger": "/home/software/GAPPadder/ContigsMerger"
},
"parameters": {
"working_folder": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/GAPPadder_out",
"min_gap_size": "1",
"flank_length": "300",
"nthreads": "35",
"verbose": "1"
},
"kmer_length": [{
"k": 30,
"k_velvet": [{
"k": 29
},
{
"k": 27
}]
},
{
"k": 40,
"k_velvet": [{
"k": 39
},
{
"k": 37
}]
},
{
"k": 50,
"k_velvet": [{
"k": 49
},
{
"k": 47
}]
},
{
"k": 60,
"k_velvet": [{
"k": 59
},
{
"k": 57
}]
}]
}"

Can you help me to understand the problem and to fix it?

#python ./main.py -c Preprocess -g configuration_phage.json

File "./main.py", line 16
print 'Usage: python {0} -c Options -g configure_file\n'.format(sys.argv[0]),
^

I ran the Preprocess and Collect steps according the ReadMe with no apparent errors. However, it seems like some expected output was not produced because when I run the Assembly step, I get the following error:

First round assembly and merger...
Start merging...
Traceback (most recent call last):
  File "./main.py", line 283, in <module>
    main_func(scommand,sfconfig)
  File "./main.py", line 274, in main_func
    gap_assembler.assemble_pipeline()
  File "/home/progs/GAPPadder/assemble_gaps.py", line 339, in assemble_pipeline
    id_remain=self.pick_already_constructed(contigs_select, fa_list, sf_picked)
  File "/home/progs/GAPPadder/assemble_gaps.py", line 321, in pick_already_constructed
    m_picked=contigs_select.get_already_picked(sf_picked)
  File "/home/progs/GAPPadder/pick_contigs.py", line 576, in get_already_picked
    with open(sf_picked) as fin_picked:
IOError: [Errno 2] No such file or directory: u'/<path to results dir>/gappadder/results/merged/../picked_seqs.fa'

Here are the commands that I ran:

python ./main.py -c Preprocess -g /<my path>/gappadder/gappadder_config.json
python ./main.py -c Collect -g /<my path>/gappadder/gappadder_config.json
python ./main.py -c Assembly -g /<my path>/gappadder/gappadder_config.json

Any ideas what could be going wrong?
Thanks!
Dave

Is it possible to post an example of a json file that is needed for GapPadder run?
I do not mean a general json format which I can obviously google, but a specific one... I am pretty new in the field of bioinfo, so if possible would appreciate some help..
Many thanks!

I get several errors during the complete run (-c All) as well as using -c Collect, as you can see below.

Can you please help to fix it, or to understaind what is creating the issue?

`python2.7 ./main.py -c Collect -g configuration.json
samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr1A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -
samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr2A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr4A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -

samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr3A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -
samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr5A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -
samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr6A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -
samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr7A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -
samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chrM" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -
samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chrRA" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -
Traceback (most recent call last):
File "collect_reads_for_gaps.py", line 278, in
grc.parse_reads_fall_in_gaps_one_scaffold_short_is(sf_gap_pos, anchor_mapq, working_folder)
File "collect_reads_for_gaps.py", line 193, in parse_reads_fall_in_gaps_one_scaffold_short_is
focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref)
File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2
if focal_region.has_key(start-i)==False:
AttributeError: 'dict' object has no attribute 'has_key'
Traceback (most recent call last):
File "collect_reads_for_gaps.py", line 278, in
grc.parse_reads_fall_in_gaps_one_scaffold_short_is(sf_gap_pos, anchor_mapq, working_folder)
File "collect_reads_for_gaps.py", line 193, in parse_reads_fall_in_gaps_one_scaffold_short_is
focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref)
File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2
if focal_region.has_key(start-i)==False:
AttributeError: 'dict' object has no attribute 'has_key'
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Traceback (most recent call last):
File "./main.py", line 283, in
Traceback (most recent call last):
File "collect_reads_for_gaps.py", line 278, in
grc.parse_reads_fall_in_gaps_one_scaffold_short_is(sf_gap_pos, anchor_mapq, working_folder)
File "collect_reads_for_gaps.py", line 193, in parse_reads_fall_in_gaps_one_scaffold_short_is
focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref)
File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2
main_func(scommand,sfconfig)
if focal_region.has_key(start-i)==False:
AttributeError: 'dict' object has no attribute 'has_key'
File "./main.py", line 244, in main_func
mtrc.dispath_collect_jobs(nthreads, samtools_path, insert_size, derivation, clip_dist, folder)
File "/home/software/GAPPadder/run_multi_threads_collect_reads.py", line 36, in dispath_collect_jobs
pool.map(run_cmd_reads_collect, cmd_list)
File "/usr/lib/python2.7/multiprocessing/pool.py", line 253, in map
return self.map_async(func, iterable, chunksize).get()
File "/usr/lib/python2.7/multiprocessing/pool.py", line 572, in get
Traceback (most recent call last):
File "collect_reads_for_gaps.py", line 278, in
grc.parse_reads_fall_in_gaps_one_scaffold_short_is(sf_gap_pos, anchor_mapq, working_folder)
File "collect_reads_for_gaps.py", line 193, in parse_reads_fall_in_gaps_one_scaffold_short_is
raise self._value
subprocess.CalledProcessError: Command 'samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr2A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -' returned non-zero exit status 1 focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref)
File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2

if focal_region.has_key(start-i)==False:

AttributeError: 'dict' object has no attribute 'has_key'
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Traceback (most recent call last):
File "collect_reads_for_gaps.py", line 278, in
grc.parse_reads_fall_in_gaps_one_scaffold_short_is(sf_gap_pos, anchor_mapq, working_folder)
File "collect_reads_for_gaps.py", line 193, in parse_reads_fall_in_gaps_one_scaffold_short_is
focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref)
File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2
if focal_region.has_key(start-i)==False:
AttributeError: 'dict' object has no attribute 'has_key'
Traceback (most recent call last):
File "collect_reads_for_gaps.py", line 278, in
grc.parse_reads_fall_in_gaps_one_scaffold_short_is(sf_gap_pos, anchor_mapq, working_folder)
File "collect_reads_for_gaps.py", line 193, in parse_reads_fall_in_gaps_one_scaffold_short_is
focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref)
File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2
if focal_region.has_key(start-i)==False:
samtools view: AttributeError: 'dict' object has no attribute 'has_key'
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Traceback (most recent call last):
File "collect_reads_for_gaps.py", line 278, in
grc.parse_reads_fall_in_gaps_one_scaffold_short_is(sf_gap_pos, anchor_mapq, working_folder)
File "collect_reads_for_gaps.py", line 193, in parse_reads_fall_in_gaps_one_scaffold_short_is
focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref)
File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2
if focal_region.has_key(start-i)==False:
AttributeError: 'dict' object has no attribute 'has_key'
Traceback (most recent call last):
File "collect_reads_for_gaps.py", line 278, in
grc.parse_reads_fall_in_gaps_one_scaffold_short_is(sf_gap_pos, anchor_mapq, working_folder)
File "collect_reads_for_gaps.py", line 193, in parse_reads_fall_in_gaps_one_scaffold_short_is
focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref)
File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2
if focal_region.has_key(start-i)==False:
AttributeError: 'dict' object has no attribute 'has_key'
samtools view: writing to standard output failed: Broken pipe
samtools view: Traceback (most recent call last):
error closing standard output: -1
File "collect_reads_for_gaps.py", line 278, in
grc.parse_reads_fall_in_gaps_one_scaffold_short_is(sf_gap_pos, anchor_mapq, working_folder)
File "collect_reads_for_gaps.py", line 193, in parse_reads_fall_in_gaps_one_scaffold_short_is
focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref)
File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2
if focal_region.has_key(start-i)==False:
AttributeError: 'dict' object has no attribute 'has_key'
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
`

Hi,
In configuration.json at lines 18-19 there are 2 parameters for the bam file. I suppose that "is" means insertion dimension, but I really can't unterstand the meaning of "std".
I want to run GAPPadder to its full potential, what I have to put for std?
Thank you in advance