global name 'seq_id' is not defined error

AlefNeem commented 8 years ago

I get this error when I use SRST2, How can I resolve it .

katholt commented 8 years ago

Hi Alef, will need a bit more info to help you. Can you please provide

version number
command you are using
contents of log file
full text of the error Thanks

AlefNeem commented 8 years ago

Hi here is the version that I used

command you are using -srst2 --input_pe *.fastq --output strain_serotypeVI__Ant --log --gene_db /home/data/SRST_2/database/all_databases.fsa --forward _R1 --reverse _R2
version number-srst2 0.1.2
content oc tther error-0.11% overall alignment rate [samopen] SAM header is present: 2139 sequences. [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 Traceback (most recent call last): File "/usr/local/bin/srst2", line 9, in load_entry_point('srst2==0.1.2', 'console_scripts', 'srst2')() File "/usr/local/lib/python2.7/dist-packages/srst2/srst2.py", line 1316, in main db_reports, db_results = run_srst2(args,fileSets,args.gene_db,"genes") File "/usr/local/lib/python2.7/dist-packages/srst2/srst2.py", line 937, in run_srst2 db_reports, db_results_list = process_fasta_db(args, fileSets, run_type, db_reports, db_results_list, fasta) File "/usr/local/lib/python2.7/dist-packages/srst2/srst2.py", line 991, in process_fasta_db unique_gene_symbols, unique_allele_symbols,run_type,ST_db,results,gene_list,db_report) File "/usr/local/lib/python2.7/dist-packages/srst2/srst2.py", line 1101, in map_fileSet_to_db unique_gene_symbols, unique_allele_symbols) File "/usr/local/lib/python2.7/dist-packages/srst2/srst2.py", line 679, in parse_scores gene_name = get_allele_name_from_db(allele,unique_allele_symbols,unique_cluster_symbols,run_type,args)[0] File "/usr/local/lib/python2.7/dist-packages/srst2/srst2.py", line 649, in get_allele_name_from_db allele_name += "_" + seq_id NameError: global name 'seq_id' is not defined

I have attached the log file for you to see. I hope you can help me solve this problem. thanks

From: Kat Holt [notifications@github.com] Sent: January-19-16 5:03 PM To: katholt/srst2 Subject: Re: [srst2] global name 'seq_id' is not defined error (#54)

Hi Alef, will need a bit more info to help you. Can you please provide

version number
command you are using
contents of log file
full text of the error Thanks

— Reply to this email directly or view it on GitHubhttps://github.com/katholt/srst2/issues/54#issuecomment-173002645.

katholt / srst2

global name 'seq_id' is not defined error #54