Tophat 2.0.12 compatibility with Samtools 1.0

[Vincent Butty]

Hello,

As several of you will probably have noticed by now, it looks like Tophat 2.0.12 cannot interface with Samtools 1.0, because of its inability to recognize a 2-digit version number (or so it is looking like).

vbutty@n36h:~$ samtools --version                                                                                                                                                                        

samtools 1.0

Using htslib 1.0

Copyright (C) 2014 Genome Research Ltd.

vbutty@n36h:~$ module load bowtie2/2.2.3

vbutty@n36h:~$ /home/software/tophat/tophat-2.0.12/tophat -o test_samtools /home/Genomes/hg19_bowtie2/hg19_bwt2 test.fastq

[2014-08-16 20:48:20] Beginning TopHat run (v2.0.12)

-----------------------------------------------

[2014-08-16 20:48:20] Checking for Bowtie

     Bowtie version:     2.2.3.0

[2014-08-16 20:48:21] Checking for Samtools

Traceback (most recent call last):

  File "/home/software/tophat/tophat-2.0.12/tophat", line 4087, in <module>

    sys.exit(main())

  File "/home/software/tophat/tophat-2.0.12/tophat", line 3885, in main

    check_samtools()

  File "/home/software/tophat/tophat-2.0.12/tophat", line 1559, in check_samtools

    samtools_version_str, samtools_version_arr = get_samtools_version()

  File "/home/software/tophat/tophat-2.0.12/tophat", line 1541, in get_samtools_version

    samtools_version_arr = [int(version_match.group(x)) for x in [1,2,3]]

AttributeError: 'NoneType' object has no attribute 'group'

Any chance this could be fixed to allow Tophat to smoothly interface with Samtools 1.0 in the near future?

Thank you very much in advance,

Sincerely, 

Vincent Butty

Vincent Butty, MD, PhD
Research Scientist
BioMicroCenter @ MIT Biology 68-317A
http://openwetware.org/wiki/BioMicroCenter
77 Massachusetts Avenue
Cambridge MA 02139
Phone: +1 (617) 324-9603

[Jeff Hussmann]

Vincent - 

I have also run into this issue. If you are interested, I've attached a workaround patch to tophat's samtools version detection.

- Jeff

[Vincent Butty]

Thank you Jeff for sharing your patch. 

- Vincent

[Margrét Ásgeirsdóttir]

When my Tophat was installed the --with-bam flag was used configuring it to use a specific installation of Samtools 0.1.19. All the same I get this same error.

[Akarsu Hatice]

Thanks a lot Jeff, I had the same issue as described above and your patch solved it!


H.

[Stephane Plaisance]

Thanks Jeff for the patch.

However, since I never patched in my life, could you please comment on the few steps I should go (if possible with code) while building tophat from source to add your corrections?

Thanks in advance

[Mónica Fabbro]

You have to use an older version of Samtools, the patch didn't work for me..

With Samtools 0.1.19.0 works just fine. Add this version to your PATH and Tophat will use it!

Regards!

MF

[Stephane Plaisance]

thanks Monica, 

This is what I do now and I use 1.0 for some applications and 0.1.19 for others while I would 'prefer' to have only ONE samtools on my system to keep it simple. Who knows what differences the two version introduce in the output as they work on different code after all...

I am only a biologist, sorry for my simplistic mind

;-)

[Daehwan Kim]

Sorry for the problem.  We've been working to fix this problem and will release a fixed version sometime soon (within two weeks).

Thanks,
Daehwan

[Yueqi Wang]

I'm new to Tophat and also encountered this issue with Samtools 1.0. I'm using the pre-compiled binary release of Tophat 2.0.12 . 

My temporary solution is to disable the Samtools version detection module. So I commented out the line "check_samtools()" in the tophat script as shown below:

    check_bowtie(params)

    # check_samtools()

Now I'm able to run Tophat with Samtools 1.0 .

My question is, does this change affect the output of TopHat run? 

Thanks!

[joey zhong]

I got same problem.

source  code of function check_samtools().

I think comment it will not affect the output of TopHat run.

# Make sure the SAM tools are installed and are recent enough to be useful

def check_samtools():

    th_log("Checking for Samtools")

    global samtools_path

    samtools_path=prog_path("samtools")

    samtools_version_str, samtools_version_arr = get_samtools_version()

    if samtools_version_str == None:

        die("Error: Samtools not found on this system")

    elif  samtools_version_arr[1] < 1 or samtools_version_arr[2] < 7:

        die("Error: TopHat requires Samtools 0.1.7 or later")

    th_logp("\t\tSamtools version:\t %s" % ".".join([str(x) for x in samtools_version_arr]))

[Yueqi Wang]

Thanks Joey.

It turns out that "# check_samtools()" does affect the program, because the value of "samtools_path" (default value is None) is assigned in "check_samtools()" function, and that "samtools_path" will be used later when Tophat reports output tracks. So comment "check_samtools()" will cause Tophat to fail later on. See below

 

           ........ 

[2014-09-22 20:38:41] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie (1/1)

[2014-09-22 20:45:33] Joining segment hits

[2014-09-22 20:50:42] Reporting output tracks

Traceback (most recent call last):

  File "/home/moon/app/tophat-2.0.12.Linux_x86_64/tophat", line 4087, in <module>

    sys.exit(main())

  File "/home/moon/app/tophat-2.0.12.Linux_x86_64/tophat", line 4061, in main

    params.gff_annotation)

  File "/home/moon/app/tophat-2.0.12.Linux_x86_64/tophat", line 2679, in compile_reports

    report_cmd.extend(["--samtools="+samtools_path])

TypeError: cannot concatenate 'str' and 'NoneType' objects

While it's not hard to solve this (simply copy "samtools_path=prog_path("samtools")" to somewhere outside the function), it's still better to use Samtools 0.1.19 before the next Tophat release. Because I run into another error earlier, which is the exact same one as described in this thread: https://www.biostars.org/p/112749/ , and the author solved it by using Samtools 0.1.19 instead of 1.0 . 

 

[Alexandra Vatsiou]

Make sure you have set the path only for the older version of samtools. otherwise it is getting confused. with samtools 0.1.19 it worked for me