Lan Wu-Cavener

I am running PBJ to fill gaps of a draft genome assembly using Pacbio long reads on PBS one node 40 cores. The multiple job spun out from the main script has the following error: [INFO] 2019-08-05T11:50:06 [blasr] started. Warning: When attempting to select equivalently scoring reads at random the bestn parameter should be greater than one. And all stopped without any output. Did anyone run into the same problem? Could anyone give me some advice? I'd appreciate any help! Lan

Hi, I have problem with running PBJelly mapping stage on a single node with 40 cores as part of PBS cluster. I used the <cluster> ... </cluster> as shown in xml file (attached). It seems working but having problem to get blasr running. The blasr complained about "bestn" parameter. The run generated mapping_chunkXX.sh for each of the input fasta file. But there is no output (fasta.m4 file, .fasta.out file). I need your advice on how to fix it. Could anyone who successfully get PBJ running with cluster...

Hi, I have problem with running PBJelly mapping stage on a single node with 40 cores as part of PBS cluster. The run generated mapping_chunkXX.sh for each of the input fasta file. But there is no output (fasta.m4 file, .fasta.out file) The same data set was used to run mapping stage without cluster successfully. So the problem should be in those mapping_chunkXX.sh. I need advice on how to fix it. The .err file does not show the early steps such as Extracting tails, Parsing XX reads, etc. Only showes...

Hi, Run PBJelly mapping stage on a single node with 40 cores as part of PBS cluster. It generated mapping_chunkXX.sh for each of the input fasta file. But there is no output (fasta.m4 file, .fasta.out file) The same data set was used to run mapping stage without cluster successfully. Please help me to diagnose the problem. The .err file does not show the early steps such as Extracting tails, Parsing XX reads, etc. Only showes the blasr started. All the mapping_chunkX.err show the same message: I...

Hi, Run PBJelly mapping stage on a single node with 40 cores as part of PBS cluster. It generated mapping_chunkXX.sh for each of the input fasta file. But there is no output (fasta.m4 file, .fasta.out file) Please help me to diagnose the problem. Thanks! Lan All the mapping_chunkX.err show the same message: [INFO] 2019-08-02T16:06:56 [blasr] started. Warning: When attempting to select equivalently scoring reads at random the bestn parameter should be greater than one. The mapping_chunk0.sh is below:...

Have you solved the problem? It looks like you have completed previous stages using cluster. Could you please post your protocol file. I am using PBS cluster and trying to get PBJ to work, yet not successful. Thanks! Lan