Runsheet for MACS2

[huipan1973]

I have difficulty in running the test data using MACS2

Here are the first 4 columns of my runsheet:

Here is the error message:
Traceback (most recent call last):
File "/home/panh/.local/bin/henipipe", line 8, in
sys.exit(run_henipipe())
File "/home/panh/.local/pipx/venvs/henipipe/lib/python3.7/site-packages/henipipe/main.py", line 166, in run_henipipe
MACS2job = henipipe.MACS2(runsheet_data = parsed_runsheet, threads = args.threads, gb_ram = args.gb_ram, debug=args.debug, cluster=args.cluster, user=args.user, log=args.log_prefix, out=args.output)
File "/home/panh/.local/pipx/venvs/henipipe/lib/python3.7/site-packages/henipipe/henipipe.py", line 402, in init
self.script = self.environs.generate_job(self,commands, self.job)
NameError: name 'commands' is not defined

[scfurl]

Hi Hui, Sorry for the delay. I haven’t fully developed the MACS2 pipeline. It worked at one point but updates to the cluster have probably broken the workflow. I know that this email is pretty old, but were you able to figure this out? S On February 27, 2021 at 2:19:58 PM, Hui Pan ***@***.***) wrote: I have difficulty in running the test data using MACS2 Here are my first 4 columns of my runsheet: sample SEACR_key MACS2_key MERGE_key 4G1_IgG 4G1_CONTROL 41 4G1_IgG 4G1_H3K27me3 4G1 41_CONTROL 4G1_H3K27me3 4N1_H3K27me3 4N1 41 4N1_H3K27me3 4N2_H3K27me3 4N2 42 4N2_H3K27me3 4G2_IgG 4G2_CONTROL 42 4G2_IgG 4N1_IgG 4N1_CONTROL 41 4N1_IgG 4G2_H3K27me3 4G2 42_CONTROL 4G2_H3K27me3 4N2_IgG 4N2_CONTROL 42 4N2_IgG Here is the error message: Traceback (most recent call last): File "/home/panh/.local/bin/henipipe", line 8, in sys.exit(run_henipipe()) File "/home/panh/.local/pipx/venvs/henipipe/lib/python3.7/site-packages/henipipe/ *main*.py", line 166, in run_henipipe MACS2job = henipipe.MACS2(runsheet_data = parsed_runsheet, threads = args.threads, gb_ram = args.gb_ram, debug=args.debug, cluster=args.cluster, user=args.user, log=args.log_prefix, out=args.output) File "/home/panh/.local/pipx/venvs/henipipe/lib/python3.7/site-packages/henipipe/henipipe.py", line 402, in *init* self.script = self.environs.generate_job(self,commands, self.job) NameError: name 'commands' is not defined — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD4DVMYZ7P3BQNPW3KPNEVDTBFVY3ANCNFSM4YKLWGFQ> .

[huipan1973]

Thanks for the message. I haven't figured out yet. Regards, Hui Get Outlook for Android<https://aka.ms/ghei36>

…

________________________________ From: scfurl ***@***.***> Sent: Tuesday, April 13, 2021 10:42:32 AM To: scfurl/henipipe ***@***.***> Cc: Hui Pan ***@***.***>; Author ***@***.***> Subject: Re: [scfurl/henipipe] Runsheet for MACS2 (#4) Hi Hui, Sorry for the delay. I haven’t fully developed the MACS2 pipeline. It worked at one point but updates to the cluster have probably broken the workflow. I know that this email is pretty old, but were you able to figure this out? S On February 27, 2021 at 2:19:58 PM, Hui Pan ***@***.***) wrote: I have difficulty in running the test data using MACS2 Here are my first 4 columns of my runsheet: sample SEACR_key MACS2_key MERGE_key 4G1_IgG 4G1_CONTROL 41 4G1_IgG 4G1_H3K27me3 4G1 41_CONTROL 4G1_H3K27me3 4N1_H3K27me3 4N1 41 4N1_H3K27me3 4N2_H3K27me3 4N2 42 4N2_H3K27me3 4G2_IgG 4G2_CONTROL 42 4G2_IgG 4N1_IgG 4N1_CONTROL 41 4N1_IgG 4G2_H3K27me3 4G2 42_CONTROL 4G2_H3K27me3 4N2_IgG 4N2_CONTROL 42 4N2_IgG Here is the error message: Traceback (most recent call last): File "/home/panh/.local/bin/henipipe", line 8, in sys.exit(run_henipipe()) File "/home/panh/.local/pipx/venvs/henipipe/lib/python3.7/site-packages/henipipe/ *main*.py", line 166, in run_henipipe MACS2job = henipipe.MACS2(runsheet_data = parsed_runsheet, threads = args.threads, gb_ram = args.gb_ram, debug=args.debug, cluster=args.cluster, user=args.user, log=args.log_prefix, out=args.output) File "/home/panh/.local/pipx/venvs/henipipe/lib/python3.7/site-packages/henipipe/henipipe.py", line 402, in *init* self.script = self.environs.generate_job(self,commands, self.job) NameError: name 'commands' is not defined — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD4DVMYZ7P3BQNPW3KPNEVDTBFVY3ANCNFSM4YKLWGFQ> . — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#4 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABBEJDWTHRMAXSWMYBSZWGTTIRJ5RANCNFSM4YKLWGFQ>.