sureman / pbsim Goto Github PK

What steps will reproduce the problem?
1. simulate fastq reads file from human genome chr20 use PBSIM. 
2. map back fastq reads back to human genome chr20 using BWA-SW with parameter 
bwa bwasw -t 4 -b 5 -q 2 -r 1 -z 20 
3. Use picard tools convert sam to bam and sort.

What is the expected output? What do you see instead?
In step 3 above, the convert and sort should be success. However, there is SAM 
parsing error. There exist '<<DEL>' in the sequence field, which is not in the 
SAM standard. 

What version of the product are you using? On what operating system?
pbsim-1.0.3-Linux-amd64.tar.gz   
Linux  3.2.0-39-generic Ubuntu 

Please provide any additional information below.

What steps will reproduce the problem?
1. I want to reuse a function which introduces errors in reads.
2. I found function mutate.
3. I cannot use it since it has 47242 dependencies on global variables, which 
are undocumented.

What is the expected output? What do you see instead?
I expect clean function which takes correct sequence + error profile as an 
input and produces sequence with errors as an output.
What I see is spaghetti.

What steps will reproduce the problem?
1. created ccs reads using the sample data provided and using the 
sampling-based simulation
2. tried mira on the .fastq file using the sytax 
mira sd_0001.fastq
3.

What is the expected output? What do you see instead?
expected output is a maf file, instead I get the error
k: @S1_1
v:

Fatal error (may be due to problems of the input data or parameters):

"In file sd_0001.fastq: line
@S1_1
Expected keyword 'readgroup'"

->Thrown: void Manifest::slurpInManifest(stringstream & mfin, const string & 
origsource))
->Caught: main

Aborting process, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.

Subscribing / unsubscribing to mira talk, see: 
http://www.freelists.org/list/mira_talk

CWD: /home/amodupe
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.


What version of the product are you using? On what operating system?
version 1.0.2 on unix/linux operating system

Please provide any additional information below.
do u have any suggestions on other pacbio assembliers

What steps will reproduce the problem?
1. converting maf to sam
2. using maf2sam.py script
3.

What is the expected output? What do you see instead?
a sam output, but I get the error
[maf2sam] Identified 0 read groups
Traceback (most recent call last):
  File "maf2sam.py", line 514, in <module>
    assert line.startswith("CO\t"), line
AssertionError: a


What version of the product are you using? On what operating system?
v1.0.2 on unix/linux operating system

Please provide any additional information below.