assembly error

[AstrMary]

Dear Xiao,
Thank you for your tool!
I managed to run the correction step with success, but when I tried to run the assemble step I got the following error.

Can you please help me?

Smartmatch is experimental at /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/Plgd/Project.pm line 263.
2021-12-08 08:14:47 [Info] Skip correcting rawreads for outputs are newer.
2021-12-08 08:14:47 [Info] Skip trimming reads for outputs are newer.
2021-12-08 08:14:47 [Info] Start assembling.
2021-12-08 08:14:47 [Info] Run script: /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/scripts/ass_job.sh 2>&1 |tee /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/scripts/ass_job.sh.log
2021-12-08 08:14:47 [INFO] Start
2021-12-08 08:14:47 [INFO] Arguments:
overlaps = /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/3-assembly/pm.m4.gz
filtered_overlaps = /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/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 = 5000000
coverage = 40
output_directory = /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/4-fsa
thread_size = 20
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

2021-12-08 08:14:47 [INFO] Auto select parameters
2021-12-08 08:14:47 [INFO] Actual coverage = 4
2021-12-08 08:14:47 [INFO] Auto Select min_length = 2500
2021-12-08 08:14:47 [INFO] Stat identity median=93.119592, mad=5.288957
2021-12-08 08:14:47 [WARNING] Estimated min_identity is less than 90.0
2021-12-08 08:14:47 [INFO] Auto select min_identity = 90.000000
2021-12-08 08:14:47 [INFO] Stat overhang: median=217.000000, mad=217.000000
2021-12-08 08:14:47 [WARNING] Estimated max_overhang_ is greater than 500
2021-12-08 08:14:47 [INFO] Auto select max_overhang = 500
2021-12-08 08:14:47 [INFO] Load overlap file
2021-12-08 08:14:47 [INFO] Overlap size: 12842
2021-12-08 08:14:47 [INFO] Group overlaps and remove duplicated
2021-12-08 08:14:47 [INFO] Filter low-quality overlaps
2021-12-08 08:14:47 [INFO] Check Coverage
2021-12-08 08:14:47 [INFO] min_coverage = 30, max_coverage = 66, max_diff_coverage = 39
2021-12-08 08:14:47 [INFO] min_coverage = 9, max_coverage = 66, max_diff_coverage = 39
2021-12-08 08:14:47 [INFO] Check Support
2021-12-08 08:14:47 [INFO] Remove contained reads
2021-12-08 08:14:47 [INFO] Select BestN overlaps
2021-12-08 08:14:47 [INFO] Save Overlaps: /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/4-fsa/filter.m4
2021-12-08 08:14:47 [INFO] Dump
2021-12-08 08:14:47 [INFO] End
2021-12-08 08:14:47 [INFO] Arguments:
filterd_overlaps = /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/4-fsa/filter.m4
min_length = 0
min_identity = 0
min_aligned_length = 0
min_contig_length = 500
read_file = /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/trimReads.fasta.gz
overlap_file_type =
output_directory = /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/4-fsa
select_branch = no
thread_size = 20
dump = 0
run_mode = 4
lfc = 0
remove_chimer = 0
max_spur_length = 50000

2021-12-08 08:14:47 [INFO] Start
2021-12-08 08:14:47 [INFO] Load Overlaps
2021-12-08 08:14:47 [INFO] Start Load Overlaps
2021-12-08 08:14:47 [INFO] End Load Overlaps: size = 0
2021-12-08 08:14:47 [FATAL] No overlaps were loaded
/data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/scripts/ass_job.sh: line 29: 3611071 Aborted (core dumped) /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/fsa_assemble /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/4-fsa/filter.m4 --read_file=/data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/trimReads.fasta.gz --thread_size=20 --output_directory=/data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/4-fsa
2021-12-08 08:14:47 [Warning] Failed to run script, 134, /data-nfs/maria/necat_assembler/NECAT/Linux-amd64/bin/athiri/scripts/ass_job.sh
2021-12-08 08:14:47 [Error] Reached to maximum number of script errors
Thank you,
Maria

[ricardo-aaron]

Wrote a comment under issue #27