[ERROR] Exception raised in task NC_008401.2:ErrorCounter - exit

Qincai Li — Wed, 23 May 2018 08:56:03 -0000

2018-05-23 16:15:42,907 [ERROR] Exception raised in task NC_008401.2:ErrorCounter - exit
2018-05-23 16:15:42,928 [ERROR] Dumping Traceback:
Traceback (most recent call last):
File "/xxxx/PBSuite_15.8.24/pbsuite/honey/HSpots.py", line 500, in run
next_task(self.bam, self.reference, self.honH5)
File "/xxxx/PBSuite_15.8.24/pbsuite/honey/HSpots.py", line 597, in call
with honH5.acquireH5('a') as h5dat:
File "/xxxx/Python/2.7.8/lib/python2.7/contextlib.py", line 17, in enter
return self.gen.next()
File "/xxxxxx/PBSuite_15.8.24/pbsuite/honey/HSpots.py", line 439, in acquireH5
with self.__lock:

Please help me !!!!!

Example Fails at blasr

Ch Cu — Tue, 08 May 2018 06:18:16 -0000

Ostensibly this is because I'm using the wrong version of blasr. I've asked how to install the right version here.

Where can I get the right version of blasr?

Ch Cu — Tue, 08 May 2018 06:17:46 -0000

Where can I install blasr 1.3.1.127046 from? It's not available through conda, it doesn't seem to be available on Github, and I can't run PBHoney without it.

Thanks for your help.

Example Fails at blasr

Ch Cu — Tue, 08 May 2018 00:30:49 -0000

At the first step of the PBHoney example, Honey.py pie $inputReads $reference, I'm hitting the error -nproc is not a valid option.

The full output is

/home/users/ccurnin/miniconda3/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters

Please Cite: English, Adam C., William J. Salerno, Jeffery G.
             Reid. "PBHoney: identyfying genomic variants via
             long-read discordance and interrupted mapping."
             BMC Bioinformatics 2014, 15:180 (June 10, 2014).
             doi:10.1186/1471-2105-15-180

2018-05-07 16:05:21,649 [INFO] Running /scratch/pb/PBSuite_15.8.24//bin/Honey.py pie filtered_subreads.fastq lambda_modified.fastq
2018-05-07 16:05:21,649 [INFO] Running Blasr
2018-05-07 16:05:21,707 [ERROR] blasr mapping failed!
2018-05-07 16:05:21,707 [ERROR] RETCODE 1
2018-05-07 16:05:21,707 [ERROR] STDOUT    Options for blasr 
   Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [-options] 
 option Description (default_value).

 <blasr options> 

 In release v5.1 of BLASR, command-line options will use the 
single dash/double dash convention: 
Character options are preceded by a single dash. (Example: -v) 
Word options are preceded by a double dash. (Example: --verbose) 
Please modify your scripts accordingly when BLASR v5.1 is released. 

To cite BLASR, please use: Chaisson M.J., and Tesler G., Mapping 
single molecule sequencing reads using Basic Local Alignment with 
Successive Refinement (BLASR): Theory and Application, BMC 
Bioinformatics 2012, 13:238.
Please report any bugs to 'https://github.com/PacificBiosciences/blasr/issues'.

ERROR: -nproc is not a valid option.

2018-05-07 16:05:21,707 [ERROR] STDERR None
2018-05-07 16:05:21,707 [ERROR] Exiting

I'm using blasr 5.3.9c6f0a5. Thanks!

How PBSuite spots calcualte start and end point for insertion

medhat — Sat, 04 Nov 2017 08:29:39 -0000

Hi,

I'm using PBSuite version 15.8.24

Honey.py spots was used to identify structure variations.

one line from the output
1 1211650 1211854 INS 353 zscore=-11.943;szMean=353.000;sz3rdQ=550.000;szCount=5.000;strandCnt=2,3;szMedian=547.000;groupName=1;coverage=14.000;sz1stQ=60.000;mqfilt=0.000

this means that the start of the insertion in the genome is 1211650 and the end 1211854?!

is not the insertion should happen in one point in the genome (so the start and the end should be the same as in https://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/9b263cf1/), how the tool calculate the start and the end?

Hony spots error

medhat — Fri, 13 Oct 2017 09:56:04 -0000

Hi,
I am running Honey.py spots with 10 threads and I have this error:

2017-10-11 14:46:53,098 [INFO] |6:SpotCaller|RateMean 0.060716  -- RateStd  0.238808
[e0129:31253] *** Process received signal ***
[e0129:31253] Signal: Segmentation fault (11)
[e0129:31253] Signal code: Address not mapped (1)
[e0129:31253] Failing at address: 0x1581078
[e0129:31254] *** Process received signal ***
[e0129:31254] Signal: Segmentation fault (11)
[e0129:31254] Signal code: Address not mapped (1)
[e0129:31254] Failing at address: 0x1581078
2017-10-11 14:46:57,093 [INFO] |3:SpotCaller|COV processing
2017-10-11 14:46:57,093 [INFO] |3:SpotCaller|MaxCov:486 MeanCov:2 StdCov:2 MinCov:2
2017-10-11 14:46:57,095 [INFO] |3:SpotCaller|INS processing
2017-10-11 14:46:58,642 [INFO] |7:SpotCaller|RateMean 0.031061  -- RateStd  0.173483
[e0129:31257] *** Process received signal ***
[e0129:31257] Signal: Segmentation fault (11)
[e0129:31257] Signal code: Address not mapped (1)
[e0129:31257] Failing at address: 0x1581078
2017-10-11 14:47:08,440 [INFO] |3:SpotCaller|RateMean 0.059855  -- RateStd  0.237218
2017-10-11 14:47:11,862 [INFO] |3:SpotCaller|DEL processing

another thing

when using Honey,py pie in bampie.py line 64

cmd = ("blasr %s %s %s -nproc %d -bestn 1 "
           "-sam -clipping subread -out %s ") \
           % (inFile, refFile, sa, nproc, outFile)
    r, o, e = exe(cmd + params)

while the current blasr uses -- instead of- (meaning -nproc not valid paramter any more use --nproc instead)

Thanks,
Medhat

PBHoney spots parameters

Adam English — Tue, 12 Sep 2017 22:12:40 -0000

--minIndelErr, and insertion/deletion in the alignment needs to be over -m basepairs before we consider it for potential SV evaluation. This helps get rid of most of the sequencing errors since pacbio reads' main mistakes are single base pair insertions or deletions.

--threshold, is the minimum number of reads needed to support a varaint before it's considered for SV evaluation

--spanMax, if there's a region longer than this threshold where we have a signal of an SV, we ignore it.
This helps filter out extra-noisy alignment regions

--minIndelSize is the minimum size an evaluated SV needs to be before it's reported.

--minMapQ, correct. I put this at 1 by default because - generally - blasr reports a binary 0/256 MAPQ, so 1 helps filter out the handful of unconfident alignments.

PBHoney reported coverage

Adam English — Tue, 12 Sep 2017 21:57:26 -0000

Not all reads are mapped in an orientation that allows them to confidently span the region of interest. Additionally, sometimes, alignment of the long-noisy reads using blasr can 'hide' the variant (e.g. supurious matches to bases that have been deleted in order to gain a better alignment score).
Alternate supporting reads those supporting the variant and are fed into the assembly process for refinement.
Reference reads are those that confidently span the region of interest.

PBHoney reported coverage

Melanie Lou — Thu, 07 Sep 2017 22:39:35 -0000

Hi Adam,

For each call, coverage is reported. However I notice that there tend to be more reads shown in IGV than what is reported as coverage for a region in a VCF.

How do you calculate coverage (or which reads do you not include and why)?

Best,
Melanie

PBHoney spots parameters

Melanie Lou — Thu, 07 Sep 2017 22:28:17 -0000

Hi Adam,

I checked the documentation (HoneyReadme.txt and the url https://hgsc-vmweb-08.hgsc.bcm.edu/software/honey is down); please let me know if I should have looked elsewhere.

What do the following parameters mean?

-m MININDELERR, --minIndelErr MININDELERR
Minimum size of an indel error to be counted (5)
-e THRESHOLD, --threshold THRESHOLD
Minimum Spot Threshold (3)
--spanMax SPANMAX Maximum Size of spot to be called (3000)

For the following parameters, I believe -q uses MAPQ and -i uses szMean. Can you please confirm?

-q MINMAPQ, --minMapQ MINMAPQ
Minimum map quality of reads considered (1)
-i MININDELSIZE, --minIndelSize MININDELSIZE
Minimum indel SV size (50)

Self-explanatory:
-E MINERRREADS, --minErrReads MINERRREADS
Minimum number of reads with indel (3)
--consensus {pbdagcon,pbbanana,None}
Method for polishing consensus. (pbdagcon)

Much thanks,
Melanie

Recent posts to PBHoney Tickets

[ERROR] Exception raised in task NC_008401.2:ErrorCounter - __exit__

Example Fails at blasr

Where can I get the right version of blasr?

Example Fails at blasr

How PBSuite spots calcualte start and end point for insertion

Hony spots error

PBHoney spots parameters

PBHoney reported coverage

PBHoney reported coverage

PBHoney spots parameters

[ERROR] Exception raised in task NC_008401.2:ErrorCounter - exit