IndexError: list index out of range during collect

[DomeJoyce]

Hello, i was running the collect part of the pipeline and i get this error: "Traceback (most recent call last): File "./main.py", line 283, in main_func(scommand,sfconfig) File "./main.py", line 257, in main_func drc.merge_dispatch_reads_for_gaps_v2(left_reads, right_reads) File "/home/software/GAPPadder/run_multi_threads_discordant.py", line 213, in merge_dispatch_reads_for_gaps_v2 temp_field=id_fields[0].split("/") IndexError: list index out of range"

My configuration.json is below: "{ "draft_genome": { "fa": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/ZuCrist_sspace/ZuCrist_sspace.final.scaffolds.fasta" }, "raw_reads": [ { "left": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/300_pairs.4_25.h.R1.fq.gz", "right": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/300_pairs.4_25.h.R2.fq.gz" }, { "left": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/550_pairs.4_25.h.R1.fq.gz", "right": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/550_pairs.4_25.h.R2.fq.gz" } ], "alignments": [ { "bam": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/BWA_sspace/Zu_300p.sorted.bam", "is": "293", "std": "119" }, { "bam": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/BWA_sspace/Zu_550p.sorted.bam", "is": "406", "std": "149" } ], "software_path": { "bwa": "bwa", "samtools": "samtools", "velvet": "/home/software/anaconda3/pkgs/velvet-1.2.10-hed695b0_3/bin/", "kmc": "/usr/local/bin/", "TERefiner": "/home/software/GAPPadder/TERefiner_1", "ContigsMerger": "/home/software/GAPPadder/ContigsMerger" }, "parameters": { "working_folder": "/home/domenico/Scrivania/DATA/Projects/Domi/Zu_crist/GAPPadder_out", "min_gap_size": "1", "flank_length": "300", "nthreads": "35", "verbose": "1" }, "kmer_length": [{ "k": 30, "k_velvet": [{ "k": 29 }, { "k": 27 }] }, { "k": 40, "k_velvet": [{ "k": 39 }, { "k": 37 }] }, { "k": 50, "k_velvet": [{ "k": 49 }, { "k": 47 }] }, { "k": 60, "k_velvet": [{ "k": 59 }, { "k": 57 }] }] }"

Can you help me to understand the problem and to fix it?

[Brent-Saylor-Canopy]

I had the same issue. Check this issue page https://github.com/simoncchu/GAPPadder/issues/3