Crashed with SPAdes error

[ad3002]

Output:

2020-11-19 15:52:37,727 - INFO: Extending ...
2020-11-19 15:52:37,727 - INFO: Adding initial words ...
2020-11-19 15:52:41,010 - INFO: AW 1157586
2020-11-19 15:52:42,466 - INFO: Round 1: 240758/240758 AI 48459 AW 1194647
2020-11-19 15:52:43,200 - INFO: Round 2: 240758/240758 AI 50521 AW 1210915
2020-11-19 15:52:43,883 - INFO: Round 3: 240758/240758 AI 51479 AW 1220253
2020-11-19 15:52:44,612 - INFO: Round 4: 240758/240758 AI 52154 AW 1226555
2020-11-19 15:52:45,304 - INFO: Round 5: 240758/240758 AI 52492 AW 1230191
2020-11-19 15:52:45,988 - INFO: Round 6: 240758/240758 AI 52700 AW 1232685
2020-11-19 15:52:46,639 - INFO: Round 7: 240758/240758 AI 52856 AW 1234869
2020-11-19 15:52:47,376 - INFO: Round 8: 240758/240758 AI 52972 AW 1236239
2020-11-19 15:52:48,066 - INFO: Round 9: 240758/240758 AI 53023 AW 1236643
2020-11-19 15:52:48,771 - INFO: Round 10: 240758/240758 AI 53034 AW 1236685
2020-11-19 15:52:49,454 - INFO: Round 11: 240758/240758 AI 53039 AW 1236753
2020-11-19 15:52:50,123 - INFO: Round 12: 240758/240758 AI 53042 AW 1236821
2020-11-19 15:52:50,788 - INFO: Round 13: 240758/240758 AI 53042 AW 1236821
2020-11-19 15:52:50,788 - INFO: No more reads found and terminated ...
2020-11-19 15:52:51,528 - INFO: Extending finished.

2020-11-19 15:52:51,555 - INFO: Separating filtered fastq file ... 
2020-11-19 15:52:51,889 - INFO: Setting '-k 21,55,85'
2020-11-19 15:52:51,890 - INFO: Assembling using SPAdes ...
2020-11-19 15:52:51,924 - INFO: spades.py -t 100  -1 duni_sample_15_76_ref_lacertida_mtDNA/filtered_1_paired.fq -2 duni_sample_15_76_ref_lacertida_mtDNA/filtered_2_paired.fq --s1 duni_sample_15_76_ref_lacertida_mtDNA/filtered_1_unpaired.fq --s2 duni_sample_15_76_ref_lacertida_mtDNA/filtered_2_unpaired.fq -k 21,55,85 -o duni_sample_15_76_ref_lacertida_mtDNA/filtered_spades
2020-11-19 15:53:12,323 - ERROR: Error in SPAdes: 
== Error ==  system call for: "['/home/akomissarov/libs/anaconda2/bin/spades-core', '/media/eternus1/data/lizards/forNCBI/mtDNA/duni_sample_15_76_ref_lacertida_mtDNA/filtered_spades/K55/configs/config.info']" finished abnormally, OS return value: -6


2020-11-19 15:53:12,323 - ERROR: Assembling failed.

Total cost 154.74 s

[Kinggerm]

Could you please provide the spades.log file for troubleshooting? Thanks.

BTW, complete get_org.log.txt will be preferred.

[WEIGUO93]

I have the same problem
spades.log

[Kinggerm]

@WEIGUO93
get_org.log.txt required!!

[WEIGUO93]

get_org.log.txt
spades.log
Problems I encountered while testing my own data

[Kinggerm]

@WEIGUO93
The issue you encountered may be different from above, which is due to the insufficient target coverage. SPAdes barely found overlaps from the limited reads.