Error running the code

[AmitSharma267]

Hello there,

I am having issues with running the code.

My sample sheet looks like this-

SS3_S143,ss3_lib,sclscl_ref,/home/sharma267/project1/GCF_000146945.2_ASM14694v2_genomic.fna,1,/home/sharma267/project1/SS3_S143_L008_R1_001.fastq.gz,/home/sharma267/project1/SS3_S143_L008_R2_001.fastq.gz

I tried running this command

snakemake -s /home/sharma267/snpArcher/workflow/Snakefile -d /home/sharma267/project1 --cores 4

It shows me this error

Please let me know if more information is needed. Thanks in advance. Amit

[cademirch]

Hi Amit,

Can you please paste or upload the log files specified in the rule error messages?

[AmitSharma267]

Hi Cade,

I says I do not have those files. (base)

[sharma267@ap2002 ~]$ cat logs/sclscl_ref/index_ref/log.txt cat: logs/sclscl_ref/index_ref/log.txt: No such file or directory (base) [sharma267@ap2002 ~]$ cat logs/sclscl_ref/fastp/SS3_S143/1.txt cat: logs/sclscl_ref/fastp/SS3_S143/1.txt: No such file or directory (base) [sharma267@ap2002 ~]$ cat logs/sclscl_ref/genmap/log.txt cat: logs/sclscl_ref/genmap/log.txt: No such file or directory (base) [sharma267@ap2002 ~]$

[cademirch]

Amit, those files should be in the project directory: /home/sharma267/project1

[AmitSharma267]

I tried looking it.

the log.txt file in index_ref says-

(base) [sharma267@ap2002 sclscl_ref]$ ls download_ref fastp genmap index_ref (base) [sharma267@ap2002 sclscl_ref]$ cd index_ref (base) [sharma267@ap2002 index_ref]$ ls log.txt (base) [sharma267@ap2002 index_ref]$ nano log.txt (base) [sharma267@ap2002 index_ref]$

GNU nano 5.6.1 log.txt
/usr/bin/bash: line 2: bwa: command not found

the log.txt file in genmap says-

(base) [sharma267@ap2002 sclscl_ref]$ ls download_ref fastp genmap index_ref (base) [sharma267@ap2002 sclscl_ref]$ cd genmap (base) [sharma267@ap2002 genmap]$ ls log.txt (base) [sharma267@ap2002 genmap]$ nano log.txt

GNU nano 5.6.1 log.txt
/usr/bin/bash: line 2: genmap: command not found

while 1.txt file in fastp is vacant

log.txt in download_ref seems same.

(base) [sharma267@ap2002 sclscl_ref]$ ls download_ref fastp genmap index_ref (base) [sharma267@ap2002 sclscl_ref]$ cd download_ref (base) [sharma267@ap2002 download_ref]$ ls log.txt (base) [sharma267@ap2002 download_ref]$ nano log.txt

Please le me know if more information needed

[cademirch]

Can you try modifying your command to this: snakemake -s /home/sharma267/snpArcher/workflow/Snakefile --profile /home/sharma267/snpArcher/profiles/default -d /home/sharma267/project1 --cores 4