Just another example why python's misleadingly simple idioms are quite
dangerous in production code (couldn't help myself from teasing about python...
sorry about that).
Seems like line 150 in "sam_to_bam.py" tries to read the entire BAM file into
memory just to find out if it's empty or not...
As a stop gap solution with minimal changes, change line 150 from:
if len( open( tmp_aligns_file_name ).read() ) == 0:
to
if len( open( tmp_aligns_file_name ).read(10) ) == 0:
Which will read up to the first 10 bytes (instead of the entire file).
A slightly better (but still wrong) solution is to simply check the file size,
with:
if os.path.getsize(tmp_aligns_file_name) == 0:
But it's still wrong because even an invalid sam file will create a non-empty BAM file
(when using "samtools view -bt") - the BAM file will still contain the
chromosome names and sizes.
Example:
========
$ cat mm9.fa.fai
chr1 197195432 6 50 51
chr10 129993255 201139354 50 51
chr11 121843856 333732482 50 51
chr12 121257530 458013223 50 51
chr13 120284312 581695911 50 51
chr13_random 400311 704385924 50 51
chr14 125194864 704794249 50 51
chr15 103494974 832493018 50 51
...
...
$ cat 1.sam
Hello World
This is not a SAM file
$ samtools view -bt mm9.fa.fai -o 1.bam 1.sam
[sam_header_read2] 35 sequences loaded.
[sam_read1] reference 'This is not a SAM file' is recognized as '*'.
[main_samview] truncated file.
$ ls -l 1.*
-rw-r--r-- 1 gordon hannon 348 Apr 7 00:57 1.bam
-rw-r--r-- 1 gordon hannon 35 Apr 7 00:57 1.sam
========
So in short, this whole sam-to-bam wrapper tool is not suitable for large SAM
files (if they don't fit entirely in memory), and not for error checking of
invalid SAM files.
-gordon
On 04/07/2011 12:30 AM, Ryan Golhar wrote:
Here's what I get:
(galaxy_env)[galaxy@vail pbs]$ sh ./big.sh
Samtools Version: 0.1.14 (r933:170)
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/tools/samtools/sam_to_bam.py", line 150,
in __main__
if len( open( tmp_aligns_file_name ).read() ) == 0:
MemoryError
Error extracting alignments from
(/home/galaxy/galaxy-dist/database/files/000/dataset_785.dat),
(galaxy_env)[galaxy@vail pbs]$
On 4/6/11 7:29 PM, Assaf Gordon wrote:
Ryan,
Since we're shooting in the dark here, best to try and understand
what's the exception.
Add the following line to the beginning of "sam_to_bam.py":
import traceback
and add the following line to "sam_to_bam.py" line 156 (before the
call to "stop_err"):
traceback.print_exc()
Hopefully this will print out which exception you're getting, and
where is it thrown from.
-gordon
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