Installation issue

[vasilislenis]

Hello and a happy new year!

I have installed SalmonTE and seems everything went well. However, when I tried to run the example in order to test it, I am receiving the following error:

2019-01-07 14:29:47,305 Starting quantification mode 2019-01-07 14:29:47,305 Collecting FASTQ files... 2019-01-07 14:29:47,306 The input dataset is considered as a single-end dataset. 2019-01-07 14:29:47,306 The input dataset is considered as a single-end dataset. Traceback (most recent call last): File "/home/x.v.l.01/SalmonTE/SalmonTE.py", line 285, in <module> run(args) File "/home/x.v.l.01/SalmonTE/SalmonTE.py", line 231, in run param = {**args, **collect_FASTQ_files(args['FILE'])} File "/home/x.v.l.01/SalmonTE/SalmonTE.py", line 125, in collect_FASTQ_files os.symlink(os.path.abspath(file), file_name) FileExistsError: [Errno 17] File exists: '/lustrehome/home/x.v.l.01/SalmonTE/example/CTRL_2_R1.fastq' -> '/tmp/tmp0vsal2pn/x.fastq'

It looks like it has an issue in parsing the fastq files. Any help with this would be much appreciated.

Kind regards, Vasilis.

[hyunhwan-jeong]

@vasilislenis,

This looks like the error is because of the file /tmp/tmp0vsal2pn/x.fastq exists in your machine, so can you purge /tmp/tmp0vsal2pn/ and execute SalmonTE again? Can you also tell me what exact command line you used and which OS you are using?

Thank you,

Hyun-Hwan Jeong

[vasilislenis]

Hi Hyun,

Thank you very much for answering me.

I have purge the /tmp/tmp0vsal2pn/ folder but the error still remains.

I am running it on an HPC cluster (linux OS) with R/3.5.1, python/3.7.0 and anaconda/3

The command that I am trying is for the testing example:

SalmonTE.py quant --reference=hs example

Many thanks, Vasilis.

On 7 Jan 2019, at 18:19, Hyun-Hwan Jeong notifications@github.com wrote:

@vasilislenis https://github.com/vasilislenis,

This looks like the error is because of the file /tmp/tmp0vsal2pn/x.fastq exists in your machine, so can you purge /tmp/tmp0vsal2pn/ and execute SalmonTE again? Can you also tell me what exact command line you used and which OS you are using?

Thank you,

Hyun-Hwan Jeong

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/hyunhwaj/SalmonTE/issues/25#issuecomment-452030318, or mute the thread https://github.com/notifications/unsubscribe-auth/AGhlf_wdpliSkM47pepx0KxsBRQleiY6ks5vA4-fgaJpZM4ZzmuY.

[hyunhwan-jeong]

@vasilislenis Can you pull this github repository and run the command again? I did a minor change and believe it works with you.

Best Regards,

Hyun-Hwan Jeong