pipeline failing at step A3

aechchiki commented 6 years ago

Hi, I am trying to run haplomerger2.

I got this error at step A3:

aechchik@rserv01:/scratch/beegfs/monthly/aechchik/amphio_genome/HaploMerger2_20161205/project_template$ tail _A3.pathFinder_preparation.log
========== Start at Tue Mar 27 14:16:58 CEST 2018
../bin/HM_pathFinder_preparation.pl --Species amphmasked amphmaskedx --scoreScheme=score --filter=100000 --Force --Delete

Species included:  amphmasked amphmaskedx
Set the scoring scheme to score, and set the filter score/ali_len to 100000 .
Set to OVER-WRITING mode!
Set to DELETING mode!
Produce tsc/qsc_ids, total id are 3237 !
Read the zeroMinSpace.rbest.net.gz file and do some basic node filtering ...
Modification of non-creatable array value attempted, subscript -1 at ../bin/HM_pathFinder_preparation.pl line 252.

any idea how I can fix this?

logs from previous steps did not display any errors.

Best Amina

mapleforest commented 5 years ago

I am sorry to over look this question before. Have you solve the poblem? It looks like some executables are not accessible.

Carol-Symbiomics commented 3 years ago

I have exactly the same issue, any idea of which executables should I look for?

mapleforest commented 3 years ago

First of all, most errors are caused by three major reasons:

1) the script can not find path to the excutatbles;

2) There are not enough file handles for too many scaffolds;

3) the chainNet executables are not compatible with your linux system.

The manual has dicussion on these issues.

Then, have you successfully run example 1 & 2 with correct outputs?

If you did, please pack up the example 1&2 directory and sent it to me.

Also pack up all the log files related to your corrent error and send it to me.

mapleforest / HaploMerger2

pipeline failing at step A3 #16