[2023-03-16 19:45:43,019] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:45:43,019] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:45:43,019] [INFO] DQC Reference Directory: /var/lib/cwl/stgff4badd1-2881-4c7a-99be-83a18ccc8b6e/dqc_reference
[2023-03-16 19:45:44,158] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:45:44,159] [INFO] Task started: Prodigal
[2023-03-16 19:45:44,159] [INFO] Running command: cat /var/lib/cwl/stgf9d40aff-1263-4edc-b067-818ccc638bf1/OceanDNA-a2039.fa | prodigal -d OceanDNA-a2039/cds.fna -a OceanDNA-a2039/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:45:51,209] [INFO] Task succeeded: Prodigal
[2023-03-16 19:45:51,209] [INFO] Task started: HMMsearch
[2023-03-16 19:45:51,209] [INFO] Running command: hmmsearch --tblout OceanDNA-a2039/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff4badd1-2881-4c7a-99be-83a18ccc8b6e/dqc_reference/reference_markers.hmm OceanDNA-a2039/protein.faa > /dev/null
[2023-03-16 19:45:51,357] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:45:51,358] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf9d40aff-1263-4edc-b067-818ccc638bf1/OceanDNA-a2039.fa]
[2023-03-16 19:45:51,370] [INFO] Query marker FASTA was written to OceanDNA-a2039/markers.fasta
[2023-03-16 19:45:51,371] [INFO] Task started: Blastn
[2023-03-16 19:45:51,371] [INFO] Running command: blastn -query OceanDNA-a2039/markers.fasta -db /var/lib/cwl/stgff4badd1-2881-4c7a-99be-83a18ccc8b6e/dqc_reference/reference_markers.fasta -out OceanDNA-a2039/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:45:51,830] [INFO] Task succeeded: Blastn
[2023-03-16 19:45:51,830] [INFO] Selected 0 target genomes.
[2023-03-16 19:45:51,831] [INFO] Target genome list was writen to OceanDNA-a2039/target_genomes.txt
[2023-03-16 19:45:51,831] [ERROR] File is empty. [OceanDNA-a2039/target_genomes.txt]
[2023-03-16 19:45:51,831] [ERROR] Task failed. No target genome found.
[2023-03-16 19:45:51,831] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:45:51,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff4badd1-2881-4c7a-99be-83a18ccc8b6e/dqc_reference/checkm_data
[2023-03-16 19:45:51,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:45:51,891] [INFO] Task started: CheckM
[2023-03-16 19:45:51,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2039/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2039/checkm_input OceanDNA-a2039/checkm_result
[2023-03-16 19:46:16,537] [INFO] Task succeeded: CheckM
[2023-03-16 19:46:16,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:46:16,539] [INFO] ===== Completeness check finished =====
[2023-03-16 19:46:16,539] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:46:16,540] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2039/markers.fasta)
[2023-03-16 19:46:16,540] [INFO] Task started: Blastn
[2023-03-16 19:46:16,541] [INFO] Running command: blastn -query OceanDNA-a2039/markers.fasta -db /var/lib/cwl/stgff4badd1-2881-4c7a-99be-83a18ccc8b6e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2039/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:46:17,151] [INFO] Task succeeded: Blastn
[2023-03-16 19:46:17,152] [INFO] Selected 8 target genomes.
[2023-03-16 19:46:17,152] [INFO] Target genome list was writen to OceanDNA-a2039/target_genomes_gtdb.txt
[2023-03-16 19:46:17,163] [INFO] Task started: fastANI
[2023-03-16 19:46:17,163] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9d40aff-1263-4edc-b067-818ccc638bf1/OceanDNA-a2039.fa --refList OceanDNA-a2039/target_genomes_gtdb.txt --output OceanDNA-a2039/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:46:19,889] [INFO] Task succeeded: fastANI
[2023-03-16 19:46:19,894] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:46:19,894] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002727695.1	s__MGIIa-K1 sp002727695	96.6424	313	388	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002498185.1	s__MGIIa-K1 sp002498185	92.3363	333	388	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.51	99.39	0.80	0.77	3	-
GCA_002709705.1	s__MGIIa-K1 sp002709705	83.8418	285	388	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710205.1	s__MGIIa-K1 sp002710205	83.0208	299	388	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902563095.1	s__MGIIa-K1 sp902563095	81.1994	204	388	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.06	97.94	0.61	0.59	4	-
GCA_003602535.1	s__MGIIa-K1 sp003602535	77.8754	121	388	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689565.1	s__MGIIa-K1 sp002689565	77.724	116	388	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706615.1	s__MGIIa-K1 sp002706615	76.2282	58	388	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.10	98.10	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-16 19:46:19,894] [INFO] GTDB search result was written to OceanDNA-a2039/result_gtdb.tsv
[2023-03-16 19:46:19,894] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:46:19,895] [INFO] DFAST_QC result json was written to OceanDNA-a2039/dqc_result.json
[2023-03-16 19:46:19,895] [INFO] DFAST_QC completed!
[2023-03-16 19:46:19,895] [INFO] Total running time: 0h0m37s