gt_pro gtpro_db_optimized/sckmer_db 4 force_overwrite
1684353832830: [Info] Starting to load DB: gtpro_db_optimized/sckmer_db
1684353832830: [Info] MMAPPING gtpro_db_optimized/sckmer_db_optimized_db_snps.bin
1684353832830: [Info] MMAPPING gtpro_db_optimized/sckmer_db_optimized_db_kmer_index.bin
1684353832838: [Info] Using -l 32 -m 36 as optimal for system RAM
1684353832838: [Info] MMAPPING gtpro_db_optimized/sckmer_db_optimized_db_mmer_bloom_36.bin
1684353833141: [Info] MMAPPING gtpro_db_optimized/sckmer_db_optimized_db_lmer_index_32.bin
1684353834698: [Info] Done with init for optimized DB with 175132 kmers. That took 1 seconds.
1684353834736: [Info] Waiting for all readers to quiesce
1684353840417: [Progress] 1.02 million reads scanned after 5 seconds, and 0 files output.
1684353845542: [Done] searching is completed for the 998803 reads input from SRR13068812_R2.fq
1684353845542: [Done] searching is completed for the 998803 reads input from SRR13068812_R1.fq
1684353845544: [Stats] 2667 snps, 998803 reads, 1.79 hits/snp, for SRR13068812_R2.fq
1684353845545: [Stats] 2754 snps, 998803 reads, 1.79 hits/snp, for SRR13068812_R1.fq
1684353845548: 1.99 million reads were scanned after 10 seconds
1684353845548: Successfully processed 2 input files containing 1997606 reads.
1684353845558: Totally done: 10 seconds elapsed processing reads, after DB was loaded.
Traceback (most recent call last):
File "/opt/gt-pro/scripts/gtp_parse.py", line 124, in <module>
main()
File "/opt/gt-pro/scripts/gtp_parse.py", line 120, in main
gtp_array = read_gtp_out(gtp_fpath)
File "/opt/gt-pro/scripts/gtp_parse.py", line 44, in read_gtp_out
snp_type = int(items[0][6])
IndexError: string index out of range
Command:
Error: