Empty output files

[vania fonseca]

Dear members,

Me and a colleague are trying to use MafFilter version 1.1.1 for sliding window analysis. My main objective is to calculate diversity metrics on sliding windows in two genomes I aligned to evaluate the regions that are more divergent between the two.

For now, I have tried two different filters of the program with my data, the "Concatenate", the WindowSplit, and I additionally tried some script examples posted here in the forum, exactly as it was but just changing for my data, of course.

However it can`t seem to work, I only get blank output files whenever I try. I checked the example .maf input and mine looks fine as well, so I can`t figure out what is wrong, and as I am a beginner in bioinformatics, maybe I am doing some mistake... I attach here my input file and one of the parameter file with the script I tried to run

I get results like this when I run the program, and the output file is created, but is always blank.

Parsing options:

Parsing file teste.bpp for options.

WARNING!!! Parameter input.format not specified. Default used instead: Maf

Reading file...........................: ferret_otter_ids_score.maf.gz as Maf(gzip)

Output log file........................: teste.maffilter.log

-------------------------------------------------------------------

Adding filter..........................: AlnFilter

WARNING!!! Parameter verbose not specified. Default used instead: 1

-- Verbose.............................: yes

WARNING!!! Parameter max.ent not specified. Default used instead: 0

-- Window size.........................: 1000

-- Window step.........................: 10

-- Max. gaps allowed in Window.........: 20

-- Max. total entropy in Window........: 0

-- Missing sequence replaced by gaps...: no

-- Output removed blocks...............: yes

-- File compression for removed blocks.: gzip

-------------------------------------------------------------------

Adding filter..........................: MinBlockSize

WARNING!!! Parameter verbose not specified. Default used instead: 1

-- Verbose.............................: yes

-- Minimum block size required.........: 2

-------------------------------------------------------------------

Adding filter..........................: MinBlockLength

WARNING!!! Parameter verbose not specified. Default used instead: 1

-- Verbose.............................: yes

-- Minimum block length required.......: 5000

-------------------------------------------------------------------

Adding filter..........................: Output

WARNING!!! Parameter verbose not specified. Default used instead: 1

-- Verbose.............................: yes

-- Output file.........................: teste.filtered.maf.gz

-- File compression....................: gzip

-- Output mask.........................: yes

-------------------------------------------------------------------

Adding filter..........................: SequenceStatistics

WARNING!!! Parameter verbose not specified. Default used instead: 1

-- Verbose.............................: yes

-- Adding statistic....................: Number of sites. <BlockLength>

-- Adding statistic....................: Sequence length for species ferret <SequenceLengthForferret>

-- Adding statistic....................: Sequence length for species otter <SequenceLengthForotter>

-- Adding statistic....................: Site statistics. <SiteStatistics>

-- Adding statistic....................: Site statistics. <SiteStatistics>

-- Adding statistic....................: Alignment score. <AlnScore>

-- Adding statistic....................: Pairwise divergence between ferret and otter. <Div.ferret-otter>

-- Output file.........................: teste.filtered.statistics.blocks.csv

-- Reference species...................: ferret

Parsing...

MafFilter's done. Bye.

I appreciate any help on this.

Best regards

Vania

[Julien Yann Dutheil]

Dear Vania,

It is currently difficult to judge as the example option file you provide only split into windows, without generating any output... so nothing unexpected. Could you provide the option file corresponding to the output in your message?

Best,

Julien.

[vania fonseca]

Yes, sorry, this was just one of the examples I tried but maybe not the best one indeed. In the meantime, maybe my colleague found out what is going wrong (a detail in the input file, just to change the species names) but the job crashed as the program tried to use all the memory in our server. We will figure out how to avoid that and if the analysis still not works after that I will get back to you :)

Thanks

Vania