Error Running on Examples

[lsplf]

Hi, Dr Li. I installed transflow on ubantu 22.04 using mamba. When i ran transflow.sh, i got error as follows. Could you help me to solve this problem? Thanks !

(transflow) plf@plf-linux:~/transflow$ bash transflow.sh --configfile config/configfile.yaml --cores 1 1st step: Generate quality control statistics (based on fastqc and MultiQC) ... [*] Parsing all samples from the metadata file.

=> Total number of samples: 10

=> Samples are:

['S1', 'S2', 'S3', 'S4', 'S5', 'S6', 'S7', 'S8', 'S9', 'S10'] Wildcard constraints in inputs are ignored. (rule: clip) Building DAG of jobs... InputFunctionException in rule merge_reads in file /home/plf/transflow/workflow/rules/transition.smk, line 24: Error: NameError: name 'subprocess' is not defined Wildcards: smp=S1 Traceback: File "/home/plf/transflow/workflow/rules/transition.smk", line 38, in File "/home/plf/transflow/workflow/quality_control.snakefile", line 73, in read_length_from_name File "/home/plf/transflow/workflow/quality_control.snakefile", line 63, in read_length_from_file 2nd step: variants calling (based on MTB pan-genome & bwa + GATK3) ... FileNotFoundError in file /home/plf/transflow/workflow/variant_calling.snakefile, line 19: [Errno 2] No such file or directory: '2.MTBC_identification/MTBC_samples.txt' File "/home/plf/transflow/workflow/variant_calling.snakefile", line 19, in 3rd step: sample clustering and transmission events predicting (based on transcluster + SeqTrack) ... FileNotFoundError in file /home/plf/transflow/workflow/transmission_analysis.snakefile, line 13: [Errno 2] No such file or directory: '2.MTBC_identification/MTBC_samples.txt' File "/home/plf/transflow/workflow/transmission_analysis.snakefile", line 13, in

[jloubser]

I get this same subprocess issue. I tried recreating the environment as well. Same problem.

[jloubser]

any updates on this..? It appears to be a Snakemake issue?