Open FelipeMelis opened 4 years ago
Hello,
I assume that there is no problems with NucMerge. It shouldn't output many messages. But to be sure, can you check with the "top" command that it is still running and what tool is exactly running?
Ksenia
the processes are:
bowtie2-build
bowtie2-align-s
samtools
python Nucbreak
after Nucbreak there is not more processes related to NucMerge.
Can you also look what directories were created and which of them are not empty?
The folders inside the NucMerge output:
NucBreak_1/:
Results
NucBreak_2/:
Results
NucDiff/:
Pilon_1/:
bwa
Pilon_2/:
bwa
Do you need more info about the folders inside?
are they all empty or not?
The folders from NucBreak and Pilon are not empty only the NucDiff one.
Do Pilon_1 and Pilon_2 folders have
Pilon_1 and Pilon_2 doesn't have those files (only a bwa folder).
NucBreak_1 and NucBreak_2 they have those
are bwa folders empty?
No, both Pilon's folders have
TEST_2.amb TEST_2.ann TEST_2.bwt TEST_2.pac TEST_2.sa
And also the Bowtie folders from NucBreak contains the bowtie files
than it means that bwa has failed and Pilon was not able to do anything. are contigs files large?
They are contigs from bacterial genomes and have a genome length of ~6000000 (and the file size are like 6mb)
From this point it is quite difficult for me to understand what is going on without data on hands and without any error messages. They only that I can propose is to run bwa yourself to see if it produces any error messages.
bwa index -p <work_dir+prefix>
Hi I Have the same issue. I tried to run the commands above. bwa mem -o <work_dir+prefix>_all.sam <work_dir+prefix> PE_reads_1 PE_reads_2 bwa mem is throwing an error saying -o option is illegal i am using bwa version 0.7.5.a
Do you have any idea why ?
Thank you for your time!!
Kroo
@Prakroothi you have the same problem? try not using the --proc
option
@Prakroothi It seems like BWA MEM does not have -o option. I think you just need to redirect to output file.
mem: invalid option -- 'h'
Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]
Algorithm options:
-t INT number of threads [1]
-k INT minimum seed length [19]
-w INT band width for banded alignment [100]
-d INT off-diagonal X-dropoff [100]
-r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]
-c INT skip seeds with more than INT occurrences [10000]
-S skip mate rescue
-P skip pairing; mate rescue performed unless -S also in use
-A INT score for a sequence match [1]
-B INT penalty for a mismatch [4]
-O INT gap open penalty [6]
-E INT gap extension penalty; a gap of size k cost {-O} + {-E}*k [1]
-L INT penalty for clipping [5]
-U INT penalty for an unpaired read pair [17]
Input/output options:
-p first query file consists of interleaved paired-end sequences
-R STR read group header line such as '@RG\tID:foo\tSM:bar' [null]
-v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3]
-T INT minimum score to output [30]
-a output all alignments for SE or unpaired PE
-C append FASTA/FASTQ comment to SAM output
-H hard clipping
-M mark shorter split hits as secondary (for Picard/GATK compatibility)
Note: Please read the man page for detailed description of the command line and options.
@FelipeMelis '--proc' option is actually only meant for multiprocessing in this tool. It does not affect to threading for external tools. In the multiprocess, there're only 5 processes running, so even if you give more than 5, it still won't speed up. Also, I noticed that Bowtie2 uses 5 threads in NucBreak process. I don't know how it's gonna affect to the other processes. For pilon process, default memory setting may not be enough for running it. It's better to increase it by giving option like '-Xmx10g'. I rewrote some part of the code, but it seems like the last process is still not running properly.
Hello, I already clone the repo and run NucMerge with my data with the following command.
nucmerge.py --proc 50 Contigs1.fasta Contigs2.fasta fw.fastq rv.fastq TEST
But the program stopped after a few minutes and for hours doesn't change the prompt I'm in Ubuntu 16.04 Ram 125gb, 64bits os and I have all the required Software in my $PATH
Thanks in advance