Error with calculation of read length statistics

[ChloeAmbroset]

Hey,
I've installed SequelTool and when I run the following command,
srun ./SequelTools.sh -t Q -u ../../0_sequelTool/bam_loc_file.txt -n 15 -o ../../0_sequelTool/
the tool crashed and write this error :
Beginning quality control function
Running in NO_SCRAPS mode
/shared/ifbstor1/projects/mbovis_diversity/Mbv-analyze/SequelTools/Scripts/./SequelTools.sh: line 676: generateReadLenStats_noScraps.py: command not found
ERROR: Calculation of read length statistics failed!

Can you help me to solve the problem ?
Thanks a lot in advance

Best Regards

Chloé

[DavidEHufnagel]

Hello Chloé, Thank you for your interest in SequelTools! This error is most likely because SequelTools is not finding Python. Do you have Python installed? If you do, is it in your $PATH? A good way to test whether Python is in your $PATH is to type "python --version" into the command line. It should return "Python" followed by a series of numbers relating to the version of Python on your machine. Let me know if you need any further assistance with this. Best, David

…

On Thu, May 6, 2021 at 8:37 AM ChloeAmbroset ***@***.***> wrote: Hey, I've installed SequelTool and when I run the following command, srun ./SequelTools.sh -t Q -u ../../0_sequelTool/bam_loc_file.txt -n 15 -o ../../0_sequelTool/ the tool crashed and write this error : Beginning quality control function Running in NO_SCRAPS mode /shared/ifbstor1/projects/mbovis_diversity/Mbv-analyze/SequelTools/Scripts/./SequelTools.sh: line 676: generateReadLenStats_noScraps.py: command not found ERROR: Calculation of read length statistics failed! Can you help me to solve the problem ? Thanks a lot in advance Best Regards Chloé — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#13>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABQPE3IO75MWR35BFDTFNLLTMKLSRANCNFSM44HCILOA> .

[ChloeAmbroset]

Thanks David for your reply.
I work on a cluster and Python is installed.I bigan with the module load (python, r and samtools). I've check for python "python --version" as you mentionned and indeed it returns the version of Python. So I've try again to run my command line but the problem still persists ...
Do you have any idea ?
thanks again for your help ... (I didn't mentionned that I'm a biologist and sometimes I'm lost in this dark side of bioinfo ;-))

Chloé

[DavidEHufnagel]

No worries! Are you running the "python --version" check in the same environment you're running SequelTools in? For example are you putting both in the command line directly or is SequelTools running in a job? This error could happen if you are running SequelTools in a job, but doing the module loading in the command-line directly. I'm pretty sure one way or another the issue is that SequelTools can't find Python. If you're running SequelTools in a job and can't get that figured out, maybe try running it directly in the command-line. Unless you have an exceptionally large data set or a slow computer it should finish in less than an hour. Let me know if you're still having trouble and could use some other ideas. Also it would be helpful for me to know more about how you're running SequelTools. Are you running it on a computer locally, or on a cluster? If you are running it within a cluster are you doing it as part of a job, an allocated node, or directly into the master node? What kind of operating system are you using (mac, PC, or linux)? Best, David

…

On Fri, May 7, 2021 at 2:58 AM ChloeAmbroset ***@***.***> wrote: Thanks David for your reply. I work on a cluster and Python is installed.I bigan with the module load (python, r and samtools). I've check for python "python --version" as you mentionned and indeed it returns the version of Python. So I've try again to run my command line but the problem still persists ... Do you have any idea ? thanks again for your help ... (I didn't mentionned that I'm a biologist and sometimes I'm lost in this dark side of bioinfo ;-)) Chloé — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABQPE3KFPHBF7AFFB7ELLQLTMOMSLANCNFSM44HCILOA> .

[msnoon]

Hi David, I am getting a similar error and I am sure all required tools are on the path. Could you help resolve this??

SequelTools.sh -t Q -v -u subFiles.txt
Beginning quality control function

Running in NO_SCRAPS mode
Extracting data from .bam files
Data extraction was sucessful
Beginning calculation of read length statistics
Traceback (most recent call last):
File "/hdd_scratch1/msn/tools/SequelTools/Scripts/generateReadLenStats_noScraps.py", line 94, in
start = int(coord.split("")[0]); stop = int(coord.split("")[1])
ValueError: invalid literal for int() with base 10: 'ccs'
ERROR: Calculation of read length statistics failed!

[ywddwed]

Hi David,
I run the command on Linux and got a similar error and I am sure all requires tools are in conda. I try to run it
directly in the command-line, but but the problem still persists ...
Do you have any idea ?
my command : /nfs_genome1/software/SequelTools/Scripts/SequelTools.sh -t Q -u subFiles.txt
the error:
Beginning quality control function

Running in NO_SCRAPS mode
/nfs_genome1/software/SequelTools/Scripts/SequelTools.sh: line 676: generateReadLenStats_noScraps.py: command not found
ERROR: Calculation of read length statistics failed!

Looking forward to your reply!