Bam output from SMRT Portal

[cascoamarillo]

Hi,
I don't know what's going on; after running RS_Resequencing.1 from SMART Portal (because the protocol BAM_Resequencing_Beta.1 did't work), I get a mapping report of ca. 90K reads mapped. But when I select to download the aligned reads BAM file (down in Resequencing panel) I get a lousy file:

samtools flagstat pacbio.bam
418 in total
0 QC failure
0 duplicates
418 mapped (100.00%)

I guess there is something I missed, but what?

PS. the H5 aligned reads file looks bigger, at least in size.
PS2. I set Max. divergence 30%

Thanks

[rhall]

What version and patch level is your SMRT Analysis install?
Do you have access to the job directory? Can you run the same test without downloading through SMRT Portal, and use the SMRT Analysis version of samtools?

[cascoamarillo]

smrtanalysis_2.3.0.140936.run with smrtanalysis-patch_2.3.0.140936.p3.run.
Samtools flagstat from the file aligned_reads.bam in the job directory has the same outcome.
Sorry, what's the "SMRT Analysis version of samtools"?
Thanks

[rhall]

SMRT Analysis comes with it's own version of samtools, `which samtools` should point to the SMRT Analysis directory. To make sure you are using it, `source <SMRT Analysis>/etc/setup.sh`
I see very different output:

samtools flagstat aligned_reads.bam
199382 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
199382 + 0 mapped (100.00%:nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (nan%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (nan%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)