Program stopped after Bowtie process about nucmerge

[kseniakh]

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

[FelipeMelis]

the processes are:

bowtie2-build
bowtie2-align-s 
samtools
python Nucbreak

after Nucbreak there is not more processes related to NucMerge.

[kseniakh]

Can you also look what directories were created and which of them are not empty?

[FelipeMelis]

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?

[kseniakh]

are they all empty or not?

[FelipeMelis]

The folders from NucBreak and Pilon are not empty only the NucDiff one.

[kseniakh]

Do Pilon_1 and Pilon_2 folders have <file_name>.out and <file_name>.changes files?
Do NucBreak_1 and NucBreak_2 folders have <file_name>_breakpoints.bedgraph files?

[FelipeMelis]

Pilon_1 and Pilon_2 doesn't have those files (only a bwa folder).
NucBreak_1 and NucBreak_2 they have those <file_name>_breakpoints.bedgraph files.

[kseniakh]

are bwa folders empty?

[FelipeMelis]

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

[kseniakh]

than it means that bwa has failed and Pilon was not able to do anything.
are contigs files large?

[FelipeMelis]

They are contigs from bacterial genomes and have a genome length of ~6000000 (and the file size are like 6mb)

[kseniakh]

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> <assembly_file>
bwa mem -o <work_dir+prefix>_all.sam <work_dir+prefix> PE_reads_1 PE_reads_2

[Prakroothi]

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

[FelipeMelis]

@Prakroothi you have the same problem? try not using the --proc option

[mshrngci118]

@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.