PASA align and assembly stopped prematurely

[Baiwei Lo]

Dear Brian,

I was running alignment assembly pipeline using sqlite with the following command

Launch_PASA_pipeline.pl \
 -c alignAssembly.config -C -R -g genome.fa \
-t Trinity-GG.fasta.clean -T -u Trinity-GG.fasta --ALIGNERS blat --CPU 30

However, PASA stopped automatically when trying to generate the

*pasa_alignment_assembly_building.ascii_illustrations.out file 

I tried to rerun the command many times but it will eventually stop at some point

The last line of the _SQLite_chkpts.cmds_log file is

/project/bat_analysis/baiwei/software/PASApipeline-master/scripts/assemble_clusters.dbi -G ../../01_hisat2_stringtie/ateAlb2_rm.fa  -M '/project/zoo/hedgehog_annotation/02_RNAseq/02_trinity/PASA/hedgehog.sqlite'  -T 30  > hedgehog.sqlite.pasa_alignment_assembly_building.ascii_illustrations.out

The last line of the stderr is

It appears that some assemblies were generated from an earlier pass.  Only contigs w/o existing alignment assemblies will be pursued.  Otherwise, kill this process and remove the 'assemblies' directory, then restart.

I also tried to remove the assemblies folder but the problem is the same

Also the pipeline works perfectly on the sample dataset.

Thanks!

Baiwei