Code:
$ python3 atram.py --max-processes=12 \
--blast-db=/dgxb_home/se23plsc009/Project/results/aTRAM_db/T1.sqlite.db \
--query-split=/dgxb_home/se23plsc009/Project/data/ref_orthologs/2395_query_file \
--output-prefix=/dgxb_home/se23plsc009/Project/results/Temporary/Output.fasta-unitigs.fa \
--assembler=abyss \
--path=/dgxb_home/se23plsc009/softwares/aTRAM/lib/assemblers/velvet.py \
--iterations=3 \
--max-target-seqs=3000 \
--log-file=/dgxb_home/se23plsc009/Project/results/aTRAM_assembly1/log_file \
--temp-dir=/dgxb_home/se23plsc009/Project/results/aTRAM_assembly1/Temporary/ \
--keep-temp-dir \
--protein
Output:
2024-03-29 08:21:29.100271 INFO : aTRAM blast DB = "/dgxb_home/se23plsc009/Thrips_Project/results/aTRAM_db/T1", query = "2395_query_file_RPRC015459_PA_2395.fasta", iteration 1
2024-03-29 08:21:29.101075 INFO : Blasting query against shards: iteration 1
2024-03-29 08:23:00.952156 INFO : All 93 blast results completed
2024-03-29 08:23:00.954933 INFO : 72 blast hits in iteration 1
2024-03-29 08:23:00.954965 INFO : Writing assembler input files: iteration 1
2024-03-29 08:23:01.258918 INFO : Assembling shards with abyss: iteration 1
2024-03-29 08:23:01.406976 ERROR: Exception: [Errno 2] No such file or directory: '/dgxb_home/se23plsc009/Thrips_Project/results/aTRAM_assembly/Temporary/atram_nowsbxk1/T1_2395_query_file_RPRC015459_PA_2395.fasta_01_clkdfnle/output.fasta-unitigs.fa'
2024-03-29 08:23:01.409907 INFO : Writing 0 filtered contigs after iteration 1
2024-03-29 08:23:01.412235 INFO : 0 total contigs after iteration 1
I have tried running the job with different assembler, gave the path to "Output.fasta-unitigs.fa" as output folder but nothing is working.
I've attached below the github link of the tool for reference: https://github.com/juliema/aTRAM/blob/master/doc/atram_reference.md
I have checked to make sure that each output directory exists.
Here is the github issue that I think is related to my problem:
