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Hi,
I am trying to assemble a 124kb BAC and I am new to PacBio data. I have installed SMRT analysis 2.3. I have started a HGAP_Assembly.3 though the SMRT portal, but it keep failing at P_PreAssemblerDagcon/hgapAlignForCorrection step. The issue is that the scattered fasta files required do not exist. The preceding step hgapAlignForCorrection.target.Scatter get completed without any error. I am attaching the log as well as my settings.xml file for your reference.
Few other questions:
1. Is there a way to change the setting for the job queues. I tried updating the files in $SMRT_ROOT/current/analysis/etc/cluster/LSF/ but they are not reflected in the run.
2. Why do I need to supply a reference genome file to HGAP_Assembly when I intend to do a de-novo assembly.
Thanks a ton for the help.
I am trying to assemble a 124kb BAC and I am new to PacBio data. I have installed SMRT analysis 2.3. I have started a HGAP_Assembly.3 though the SMRT portal, but it keep failing at P_PreAssemblerDagcon/hgapAlignForCorrection step. The issue is that the scattered fasta files required do not exist. The preceding step hgapAlignForCorrection.target.Scatter get completed without any error. I am attaching the log as well as my settings.xml file for your reference.
Few other questions:
1. Is there a way to change the setting for the job queues. I tried updating the files in $SMRT_ROOT/current/analysis/etc/cluster/LSF/ but they are not reflected in the run.
2. Why do I need to supply a reference genome file to HGAP_Assembly when I intend to do a de-novo assembly.
Thanks a ton for the help.