When we run tb-profiler in ubuntu 14.04, we got exception

[yujun2017]

When we run tb-profiler in Ubuntu v14.04, we got exception. The error message is:
set([])
Traceback (most recent call last):
File "TBProfiler/tb-profiler", line 538, in
args.func(args)
File "TBProfiler/tb-profiler", line 500, in main_run_pipeline
lin = assign_lin(args.prefix)
File "TBProfiler/tb-profiler", line 91, in assign_lin
dict_sample_lin[sample_lin[0].split(".")[0]] = sorted([x for x in sample_lin if "." in x and sample_lin[0].split(".")[0] in x])[-1]
IndexError: list index out of range

it works fine in Mac machine using same sample files.

By the way, is it possible to use Bam files as input file instead of fastq file? It is too slow to use when we input fastq files.

[jodyphelan]

Hi YuJun,

I suspect that there is a difference in the way SNAP and BWA have created the bams. I will look into this. Great idea to include a bam input option. I will include this in the next release.

Best,
Jody

[jodyphelan]

Hi YuJun,

I have now added an option to use existing bam files with the -a option.
I have also updated the lineage prediction so please let me know if you have any more issues.

Best,
Jody

[yujun2017]

Jody: Thank you so much. I think this option will help us lot. By the way, we do find a big problem when we are using TBProfiler. The simple test is: using the same fastq file in Mac OS and Ubuntu, the result is different. This is why I got error when I am running same fastq file in Ubuntu. Can you try to downsampling using seqtk to 100K or 200K to do test? You will find result is different. I guess the SNAP filter is different. Thank you so much! Jun Yu

…

On 15 July 2017 at 04:36, jodyphelan ***@***.***> wrote: Hi YuJun, I suspect that there is a difference in the way SNAP and BWA have created the bams. I will look into this. Great idea to include a bam input option. I will include this in the next release. Best, Jody — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYaDTJD5oOZtM7YSXqh8OKUNw0KW7AA1ks5sOHnzgaJpZM4OUJIm> .

-- John Yu

[jodyphelan]

Hi Jun,

Yes I this is definitely because of the different mapping tools used. I will look into it.

Jody

[yujun2017]

jody: I got the latest code from git hub and now I got the error : No module named numpy. Thanks! John

…

On 17 July 2017 at 12:31, jodyphelan ***@***.***> wrote: Hi Jun, Yes I this is definitely because of the different mapping tools used. I will look into it. Jody — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYaDTIMNy9YIwuqfXjfIUF4fc6gO0rVFks5sO4s_gaJpZM4OUJIm> .

-- John Yu

[jodyphelan]

Hi John,

Sorry forgot to remove that dependancy. Should be working now.

Jody