running hm.batchA1.initiation_and_all_lastz didn't produce *.nib file

[wuxiaopei0509]

Dear HaploMerger2 devoloper I use falcon-unzip to assemble my genome and I obtained cns_h_ctg.fasta and cns_p_ctg.fasta,then I cat the two fasta file together. I use the merge fasta file to run HaploMerger2,however the hm.batchA1.initiation_and_all_lastz didn't produce *.nib file at the first stage ,thus it couldn't continue . what's the problem and how can I slove it ? Thank you very much! Best regard

[wuxiaopei0509]

I check the _A1.initiation.log file and found the follows ====faToNib started!==== Checking existing directories ... converting the fa files to nib files ... Converting directory merge_wm.seq.fa/.fa to merge_wm.seq/.nib ... sh: arrow.nib: command not found sh: arrow.fa: command not found faToNib - Convert from .fa to .nib format usage: faToNib [options] in.fa out.nib options: -softMask - create nib that soft-masks lower case sequence -hardMask - create nib that hard-masks lower case sequence

Can not find merge_wm.seq.fa/000000F_003|arrow.fa !

[roylejw]

I am also having this exact error, both starting with A1 and B1. Something is happening at the initiation stage (initiation.pl), where faToNib fails to read files that exist. The contig it is trying to find does exist in my directory with sequence information in it, so not sure why it's throwing this error.

====faToNib started!==== Checking existing directories ... converting the fa files to nib files ... Converting directory hgap_masked.seq.fa/.fa to hgap_masked.seq/.nib ... sh: arrow.nib: command not found sh: arrow.fa: command not found faToNib - Convert from .fa to .nib format usage: faToNib [options] in.fa out.nib options: -softMask - create nib that soft-masks lower case sequence -hardMask - create nib that hard-masks lower case sequence

Can not find hgap_masked.seq.fa/002071F|arrow.fa !

[mapleforest]

If the two examples could be run successfully, the there are two possibiliies: 1) In "hgap_masked.seq.fa/002071F|arrow.fa" the symbol "|" might prevent correct processing of the file name. 2) There are two many sequences but not enough openable file handle, please read the manual for solution, also here is some quote:

1. How to lift the openable file handle limit? Could it cause a problem to the system? The easy way: run as root, to execute the command ulimit –n 655350 (default is 1024). The hard way: run as non-root user. First to modify the limit file /etc/security/limits.conf, add two lines to it and save it (you still need root privilege to do this, or you may have to ask your system administrator to do this): your_user_name soft nofile 655350 your_user_name hard nofile 655350 Then save the file, and logout and login again to left the change take effect. Now you can execute the command ulimit –n 655350. You need to set this each time you re-login or start a new shell, because each time the system will set file handle limit back to the default value (1024). You may want to reverse these changes after finish running HM2. This is just a solution to a small glitch of several third-party executables. HM2 and third-party programs will NOT actually read/write many files simultaneously. So it will not post a problem to your servers.