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Old 05-15-2018, 07:55 PM   #1
onsh
Junior Member
 
Location: Japan

Join Date: May 2018
Posts: 2
Post tophat-fusion-post result sam_header empty

Hi all,

I’m having a problem with tophat-fusion-post. I run it, but the output is empty.
I think a sam_header file may cause that problem.

I use the version of
tophat : 2.1.0
bowtie : 1.2.2
on Windows Subsystem for Linux.

My command like this:

tophat-fusion-post -o /home/onsh/src/tophat-2.1.0/tophat_SRR064286/post_out/ \
--num-threads 16 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 \
/home/onsh/src/tophat-2.1.0/Homo_sapiens.GRCh38.small

Bowtie indexes are downloaded from Ensembl. In the original file,
I added a word “chr” to each chromosome numbers because the chromosome number is just a number.

My directory structure like this:

[email protected]:~/src/tophat-2.1.0$ ll
drwxrwxrwx 0 onsh onsh 512 May 14 16:22 blast/
-rwxrwxrwx 1 onsh onsh 22661379 May 14 16:02 ensGene.txt
-rwxrwxrwx 1 onsh onsh 982498668 May 14 15:12 Homo_sapiens.GRCh38.small.1.bt2
-rwxrwxrwx 1 onsh onsh 842742636 May 14 15:12 Homo_sapiens.GRCh38.small.1.ebwt
-rwxrwxrwx 1 onsh onsh 733719256 May 14 15:12 Homo_sapiens.GRCh38.small.2.bt2
-rwxrwxrwx 1 onsh onsh 366859632 May 14 15:12 Homo_sapiens.GRCh38.small.2.ebwt
-rwxrwxrwx 1 onsh onsh 8945 May 14 15:12 Homo_sapiens.GRCh38.small.3.bt2
-rwxrwxrwx 1 onsh onsh 8945 May 14 15:12 Homo_sapiens.GRCh38.small.3.ebwt
-rwxrwxrwx 1 onsh onsh 733719249 May 14 15:12 Homo_sapiens.GRCh38.small.4.bt2
-rwxrwxrwx 1 onsh onsh 733719249 May 14 15:12 Homo_sapiens.GRCh38.small.4.ebwt
-rwxrwxrwx 1 onsh onsh 3150052344 May 14 15:12 Homo_sapiens.GRCh38.small.fa
-rwxrwxrwx 1 onsh onsh 982498668 May 14 17:15 Homo_sapiens.GRCh38.small.rev.1.bt2
-rwxrwxrwx 1 onsh onsh 842742636 May 14 17:15 Homo_sapiens.GRCh38.small.rev.1.ebwt
-rwxrwxrwx 1 onsh onsh 733719256 May 14 17:15 Homo_sapiens.GRCh38.small.rev.2.bt2
-rwxrwxrwx 1 onsh onsh 366859632 May 14 17:15 Homo_sapiens.GRCh38.small.rev.2.ebwt
-rwxrwxrwx 1 onsh onsh 20767330 May 14 16:02 refGene.txt
-rwxr-xr-x 1 onsh onsh 171175 Jul 23 2015 tophat
-rwxr-xr-x 1 onsh onsh 233 Jul 23 2015 tophat2
-rwxr-xr-x 1 onsh onsh 118420 May 15 13:39 tophat-fusion-post
drwxrwxrwx 0 onsh onsh 512 May 15 15:06 tophat_SRR064286/

In the tophat_SRR064286/ directory, I have some files:

[email protected]:~/src/tophat-2.1.0/tophat_SRR064286$ ll
-rw-rw-rw- 1 onsh onsh 2754640914 May 14 15:04 accepted_hits.bam
-rw-rw-rw- 1 onsh onsh 569 May 14 15:04 align_summary.txt
-rw-rw-rw- 1 onsh onsh 1646739 May 14 15:04 deletions.bed
-rw-rw-rw- 1 onsh onsh 16228495 May 14 15:04 fusions.out
-rw-rw-rw- 1 onsh onsh 1380426 May 14 15:04 insertions.bed
-rw-rw-rw- 1 onsh onsh 6025364 May 14 15:04 junctions.bed
drwxrwxrwx 0 onsh onsh 512 May 15 13:58 post_out/ # <— output directory
-rw-rw-rw- 1 onsh onsh 180 May 14 15:04 prep_reads.info
-rw-rw-rw- 1 onsh onsh 75130369 May 14 15:04 unmapped.bam

I dig the tophat-fusion-post code, it seems that “get_chromosome_order()” function doesn’t work.
A sam_header file is empty.

bowtie_header_filename = tmp_dir + "sam_header"
subprocess.call(bowtie_header_cmd,
stdout=open(bowtie_header_filename, "w"),
stderr=open("/dev/null"))

The chrs variable which the function returns is also empty in spite of using chrs variable in the subsequent processes.

Could you anybody solve this?

Thank you all,

onsh

Last edited by onsh; 05-15-2018 at 09:28 PM.
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Old 05-15-2018, 09:21 PM   #2
onsh
Junior Member
 
Location: Japan

Join Date: May 2018
Posts: 2
Post

Quote:
Originally Posted by onsh View Post
Bowtie indexes are downloaded from Ensembl. In the original file,
I added a word “chr” to each chromosome numbers because the chromosome number is just a number.
onsh
I'm sorry that the sentence above is not correct.

<CORRECTION>
FASTA of genome sequences are downloaded from Ensembl. In the original file, I added a word “chr” to each chromosome numbers because the chromosome number is just number.
Bowtie indexes were built by bowtie 1.2.2.
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