[FATAL] No overlaps were loaded

[544728460]

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 max_overhang_ 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

[ricardo-aaron]

Wrote a comment under issue #27