bam2cns error: Odd number of elements in hash assignment at bam2cns line 67

[sean-la]

I've been testing proovread on PBSim simulated long reads and ART simulated short reads of a tuberculosis genome and I've encountered this error when running the tool on the data:

...
[Wed Jun 15 10:32:34 2016] Batch 4/20
perl -I/home/seanla/Software/proovread/bin/../lib/ /home/seanla/Software/proovr\
ead/bin/bam2cns --append 1 --bam proovread/bwa-sr-1/proovread.bam --bin-size 20\
 --cfg ../proovread.cfg --coverage 11.25 --ignore-weak-reads 0 --mask-weak-read\
s 0 --max-ins-length 0 --max-ref-seqs 100 --prefix proovread/bwa-sr-1/proovread\
.3 --qv-offset 33 --ref proovread/read-long/proovread.fq --ref-offset 7022806 
#------------------------------------------------------------------------------#
Odd number of elements in hash assignment at /home/seanla/Software/proovread/bi\
n/bam2cns line 67.
#------------------------------------------------------------------------------#
[Wed Jun 15 10:32:34 2016] bam2cns unexpectedly returned
    Exited at 'main'
    './proovread', line 1634
    Last call 'main::correct_sr_mt'
    './proovread', line 868

I've attached a text file containing the output from stdout, the configuration file, and files containing a few reads from my short reads and long reads files.

ecoli-long-d5_0001-sample.fastq.txt ecoli-short-single-d50-sample.fq.txt proovread-out.txt proovread.cfg.txt

Any ideas on how I can fix this? Thanks.

[sean-la]

The command I used is ./proovread -c ../proovread.cfg in the proovread/bin folder

[sean-la]

I changed deleted the paths for blast and samtools from my configuration file and added the paths to the binaries to PATH as suggested in my previous issue and running the program again yielded the same error. The output and my new config file are attached below:

proovread_out.txt proovread.cfg.txt

[thackl]

I ran your .cfg on my installation without problems. There is, however, something odd about your usage. If I am correct, you modified the proovread.cfg file in the proovread installation folder? That file ideally should not be changed - it is used in any run kind of as the default config and is read without being specified by -c.

To create your own config, run proovread --create-cfg my.cfg, change my.cfg and than run proovread -c my.cfg ...

Let me know if using the original proovread.cfg + a customized my.cfg fixes your problem. And sorry about the inconvenience!

Cheers Thomas

On 15.06.2016 14:29, Sean La wrote:

I changed deleted the paths for blast and samtools from my configuration file and added the paths to the binaries to PATH as suggested in my previous issue and running the program again yielded the same error. The output and my new config file are attached below:

proovread_out.txt https://github.com/BioInf-Wuerzburg/proovread/files/316878/proovread_out.txt proovread.cfg.txt https://github.com/BioInf-Wuerzburg/proovread/files/316879/proovread.cfg.txt

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[sean-la]

Hi Thomas,

Thanks for letting me know, I generated my own config file as you suggested and ran my tests using it. Unfortunately I encountered the same error. I have attached a copy of my output and my config file.

my.cfg.txt proovread-out.txt

[thackl]

Did you restore the original config file?

On 15.06.2016 16:13, Sean La wrote:

Hi Thomas,

Thanks for letting me know, I generated my own config file as you suggested and ran my tests using it. Unfortunately I encountered the same error. I have attached a copy of my output and my config file.

my.cfg.txt https://github.com/BioInf-Wuerzburg/proovread/files/317101/my.cfg.txt proovread-out.txt https://github.com/BioInf-Wuerzburg/proovread/files/317102/proovread-out.txt

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[sean-la]

Yes, I did.

[thackl]

weird. To possible fixes:

1) try using a full path to your config file -c /full/path/to/config 2) if 1) fails, try to avoid using a custom config and just supply everything on command line -l long_reads.fq -s short_reads.fq -p prefix

On 15.06.2016 16:21, Sean La wrote:

Yes, I did.

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[sean-la]

Providing the full path to the config file worked! Thank you so much!