I'm getting the error shown below. The proximal cause seems to be that hic_exp.py populates the dictionary dict_fragments from a file in the main output directory named "list_contig_names.txt". The reason for the error is the file in my directory is empty, thus the dictionary is empty, and on line 76 we therefore get a key error. I can see on line 39 that this file is generated from a call to bowtie2-inspect -n . The problem for me is there is no genome index.
This is where some more detailed documentation would come in handy. Am I supposed to generate the index myself? If so, this needs to be explicitly stated in the readme. Also what is "Bowtie folder" in the advanced options? When I enter stuff into the advanced options and click "apply" it gives the warning message "Could not find bowtie folder". This also needs to be explained.
Also, as an urelated side-note, 22270 seconds (i.e. 6 hours) seems like a long time for just making a restriction map of a 1.2 Gb genome. This should probably be optimized. I'm guessing your problem is the biopython restriction module. In the past I've noticed that some (but not all) of those functions were super slow, to the point that I just used regular expressions as a workaround. Just an idea.
Restriction map generated in 22270.876373 s
filling list of contigs ..
[]
filling dictionnary of fragments ...
Traceback (most recent call last):
File "main.py", line 278, in OnAlign
ncpu=self.ncpu)
File "/home/tom/Desktop/HiC-Box-master/analysis_main.py", line 102, in analyze
len_paired_wise_fastq)
File "/home/tom/Desktop/HiC-Box-master/hic_exp.py", line 76, in init
dict_fragments[a_tmp[1]].append(int(a_tmp[0]))
KeyError: 'gi|526059867|ref|NW_004823088.1| Melopsittacus undulatus
unplaced genomic scaffold, Melopsittacus_undulatus_6.3
budgerigar_v6.3_scf900160251875, whole genome shotgun sequence'
I'm getting the error shown below. The proximal cause seems to be that hic_exp.py populates the dictionary dict_fragments from a file in the main output directory named "list_contig_names.txt". The reason for the error is the file in my directory is empty, thus the dictionary is empty, and on line 76 we therefore get a key error. I can see on line 39 that this file is generated from a call to bowtie2-inspect -n . The problem for me is there is no genome index.
This is where some more detailed documentation would come in handy. Am I supposed to generate the index myself? If so, this needs to be explicitly stated in the readme. Also what is "Bowtie folder" in the advanced options? When I enter stuff into the advanced options and click "apply" it gives the warning message "Could not find bowtie folder". This also needs to be explained.
Also, as an urelated side-note, 22270 seconds (i.e. 6 hours) seems like a long time for just making a restriction map of a 1.2 Gb genome. This should probably be optimized. I'm guessing your problem is the biopython restriction module. In the past I've noticed that some (but not all) of those functions were super slow, to the point that I just used regular expressions as a workaround. Just an idea.
Restriction map generated in 22270.876373 s
filling list of contigs ..
[]
filling dictionnary of fragments ...
Traceback (most recent call last):
File "main.py", line 278, in OnAlign
ncpu=self.ncpu)
File "/home/tom/Desktop/HiC-Box-master/analysis_main.py", line 102, in analyze
len_paired_wise_fastq)
File "/home/tom/Desktop/HiC-Box-master/hic_exp.py", line 76, in init
dict_fragments[a_tmp[1]].append(int(a_tmp[0]))
KeyError: 'gi|526059867|ref|NW_004823088.1| Melopsittacus undulatus
unplaced genomic scaffold, Melopsittacus_undulatus_6.3
budgerigar_v6.3_scf900160251875, whole genome shotgun sequence'