[FATAL] No overlaps were loaded

I have successfully install necat with anoconda command like this : conda install -c bioconda necat -y. After smoothly finishing the config and correct steps with these command : necat config ecoli_config.txt, necat correct ecoli_config.txt, I met an error when running the assemble command : necat assemble ecoli_config.txt.

The error information and related files are as follows and attached:

Smartmatch is experimental at /home/evl-shr/software/miniconda3/envs/ngs/share/necat-0.0.1_update20200803-1/bin/Plgd/Project.pm line 263. 2021-05-07 10:35:55 [Info] Skip correcting rawreads for outputs are newer. 2021-05-07 10:35:55 [Info] Skip trimming reads for outputs are newer. 2021-05-07 10:35:55 [Info] Start assembling. 2021-05-07 10:35:55 [Info] Run script: /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/scripts/ass_job.sh 2>&1 |tee /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/scripts/ass_job.sh.log 2021-05-07 10:35:55 [INFO] Start 2021-05-07 10:35:55 [INFO] Arguments: overlaps = /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/3-assembly/pm.m4.gz filtered_overlaps = /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/4-fsa/filter.m4 min_length = 2500 max_length = 2147483647 min_identity = -1 min_aligned_length = 2500 max_overhang = -1 min_coverage = -1 max_coverage = -1 max_diff_coverage = -1 coverage_discard = 0.01 overlap_file_type = bestn = 10 genome_size = 35000 coverage = 40 output_directory = /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/4-fsa thread_size = 64 identity_global_deviation1 = 98 identity_global_deviation2 = 6 overhang_global_deviation1 = 30 overhang_global_deviation2 = 6 identity_local_deviation1 = 99 identity_local_deviation2 = 6 overhang_local_deviation1 = 10 overhang_local_deviation2 = 6 identity_local_condition = 0 local_low_coverage = 25

2021-05-07 10:35:55 [INFO] Auto select parameters 2021-05-07 10:35:55 [INFO] Actual coverage = 26 2021-05-07 10:35:55 [INFO] Auto Select min_length = 2645 2021-05-07 10:35:55 [INFO] Stat identity median=93.174074, mad=2.176584 2021-05-07 10:35:55 [WARNING] Estimated min_identity is less than 90.0 2021-05-07 10:35:55 [INFO] Auto select min_identity = 90.000000 2021-05-07 10:35:55 [INFO] Stat overhang: median=507.000000, mad=308.000000 2021-05-07 10:35:55 [WARNING] Estimated maxoverhang is greater than 500 2021-05-07 10:35:55 [INFO] Auto select max_overhang = 500 2021-05-07 10:35:55 [INFO] Load overlap file 2021-05-07 10:35:55 [INFO] Overlap size: 1098 2021-05-07 10:35:55 [INFO] Group overlaps and remove duplicated 2021-05-07 10:35:55 [INFO] Filter low-quality overlaps 2021-05-07 10:35:55 [INFO] Check Coverage 2021-05-07 10:35:55 [INFO] min_coverage = 13, max_coverage = 27, max_diff_coverage = 22 2021-05-07 10:35:55 [INFO] min_coverage = 3, max_coverage = 27, max_diff_coverage = 22 2021-05-07 10:35:55 [INFO] Check Support 2021-05-07 10:35:55 [INFO] Remove contained reads 2021-05-07 10:35:55 [INFO] Select BestN overlaps 2021-05-07 10:35:55 [INFO] Save Overlaps: /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/4-fsa/filter.m4 2021-05-07 10:35:55 [INFO] Dump 2021-05-07 10:35:55 [INFO] End 2021-05-07 10:35:55 [INFO] Arguments: filterd_overlaps = /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/4-fsa/filter.m4 min_length = 0 min_identity = 0 min_aligned_length = 0 min_contig_length = 500 read_file = /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/trimReads.fasta.gz overlap_file_type = output_directory = /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/4-fsa select_branch = no thread_size = 64 dump = 0 run_mode = 4 lfc = 0 remove_chimer = 0 max_spur_length = 50000

2021-05-07 10:35:55 [INFO] Start 2021-05-07 10:35:55 [INFO] Load Overlaps 2021-05-07 10:35:55 [INFO] Start Load Overlaps 2021-05-07 10:35:55 [INFO] End Load Overlaps: size = 0 2021-05-07 10:35:55 [FATAL] No overlaps were loaded /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/scripts/ass_job.sh: 行 29: 3741 已放弃 (核心已转储) /home/evl-shr/software/miniconda3/envs/ngs/share/necat-0.0.1_update20200803-1/bin/fsa_assemble /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/4-fsa/filter.m4 --read_file=/home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/trimReads.fasta.gz --thread_size=64 --output_directory=/home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/4-fsa 2021-05-07 10:35:55 [Warning] Failed to run script, 134, /home/evl-shr/workfiles/shr/LMQ_Nanopore/test/test2/test/scripts/ass_job.sh 2021-05-07 10:35:55 [Error] Reached to maximum number of script errors NECAT_error.zip

xiaochuanle / NECAT

[FATAL] No overlaps were loaded #33