On Sun, Oct 5, 2014 at 7:59 PM, Charles Plessy <[email protected]> wrote:
> Le Sun, Oct 05, 2014 at 01:21:57PM -0400, Dominique Belhachemi a écrit : > > > > Based on the changelog I would say that you can skip the 2.0.13 release. > > > > ---------------------------------------------------- > > TopHat 2.0.13 release 10/2/2014 > > Version 2.0.13 is a maintenance release with the following changes: > > > > removed SAMtools as an external dependency in order to avoid > > incompatibility issues with recent and future changes of SAMtools and its > > code library (an older, stable SAMtools version is now packaged with > > TopHat) > > > > fixed a few code compatibility issues when compiling on OSX 10.9 > > ---------------------------------------------------- > > > > I wonder which versions of tophat/samtools are incompatible and why? > > Hi Dominique, > > You can see some reports in the following threads: > > - https://www.biostars.org/p/112749/ > - https://groups.google.com/forum/#!topic/tuxedo-tools-users/BVNDDmInU0A > > If it were just the parsing of Samtool's version number, the solution > would be > trivial, but I worry that TopHat may also be broken by changes in the > default > output of Samtools. I think that if we would patch TopHat 2.0.12, we would > need to rely on somebody doing extensive tests. On my side, I am a BWA > user… > > Are there TopHat users here who could help us testing the possible > alternatives ? > > Hi Charles, I followed the 'Testing the installation' instructions on http://ccb.jhu.edu/software/tophat/tutorial.shtml . wget http://ccb.jhu.edu/software/tophat/downloads/test_data.tar.gz tar zxvf test_data.tar.gz cd test_data tophat -r 20 test_ref reads_1.fq reads_2.fq I am immediately running into the version parser issue. [2014-10-05 20:51:46] Beginning TopHat run (v2.0.12) ----------------------------------------------- [2014-10-05 20:51:46] Checking for Bowtie Bowtie version: 2.2.3.0 [2014-10-05 20:51:46] Checking for Samtools Traceback (most recent call last): File "/usr/bin/tophat", line 4087, in <module> sys.exit(main()) File "/usr/bin/tophat", line 3885, in main check_samtools() File "/usr/bin/tophat", line 1559, in check_samtools samtools_version_str, samtools_version_arr = get_samtools_version() File "/usr/bin/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' You have new mail in /var/mail/ionadmin After a quick&dirty patch ... --- /usr/bin/tophat 2014-09-25 02:29:36.000000000 -0400 +++ /usr/bin/tophat.patch 2014-10-05 20:45:55.900444000 -0400 @@ -1537,10 +1537,10 @@ samtools_out = proc.communicate()[1] # Find the version identifier - version_match = re.search(r'Version:\s+(\d+)\.(\d+).(\d+)([a-zA-Z]?)', samtools_out) - samtools_version_arr = [int(version_match.group(x)) for x in [1,2,3]] - if version_match.group(4): - samtools_version_arr.append(version_match.group(4)) + version_match = re.search(r'Version:\s+(\d+)\.(\d+)([a-zA-Z]?)', samtools_out) + samtools_version_arr = [int(version_match.group(x)) for x in [1,2]] + if version_match.group(3): + samtools_version_arr.append(version_match.group(3)) else: samtools_version_arr.append(0) @@ -1559,8 +1559,8 @@ 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") + #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])) I am getting the same results as with samtools 0.1.19: tophat -r 20 test_ref reads_1.fq reads_2.fq [2014-10-05 20:55:06] Beginning TopHat run (v2.0.12) ----------------------------------------------- [2014-10-05 20:55:06] Checking for Bowtie Bowtie version: 2.2.3.0 [2014-10-05 20:55:06] Checking for Samtools Samtools version: 1.1.0 [2014-10-05 20:55:06] Checking for Bowtie index files (genome).. Found both Bowtie1 and Bowtie2 indexes. [2014-10-05 20:55:06] Checking for reference FASTA file [2014-10-05 20:55:06] Generating SAM header for test_ref [2014-10-05 20:55:06] Preparing reads left reads: min. length=75, max. length=75, 100 kept reads (0 discarded) right reads: min. length=75, max. length=75, 100 kept reads (0 discarded) [2014-10-05 20:55:06] Mapping left_kept_reads to genome test_ref with Bowtie2 [2014-10-05 20:55:06] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3) [2014-10-05 20:55:06] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3) [2014-10-05 20:55:06] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3) [2014-10-05 20:55:06] Mapping right_kept_reads to genome test_ref with Bowtie2 [2014-10-05 20:55:06] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3) [2014-10-05 20:55:06] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3) [2014-10-05 20:55:07] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3) [2014-10-05 20:55:07] Searching for junctions via segment mapping [2014-10-05 20:55:07] Retrieving sequences for splices [2014-10-05 20:55:07] Indexing splices Building a SMALL index [2014-10-05 20:55:07] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/3) [2014-10-05 20:55:07] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/3) [2014-10-05 20:55:07] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/3) [2014-10-05 20:55:07] Joining segment hits [2014-10-05 20:55:07] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/3) [2014-10-05 20:55:07] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/3) [2014-10-05 20:55:07] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/3) [2014-10-05 20:55:07] Joining segment hits [2014-10-05 20:55:07] Reporting output tracks ----------------------------------------------- [2014-10-05 20:55:07] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt Any idea where to find upstreams test suite? Best -Dominique
