[2023-03-17 09:41:39,970] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:41:39,970] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:41:39,970] [INFO] DQC Reference Directory: /var/lib/cwl/stgd83d874d-8fe8-4ca5-8910-80790cb5653c/dqc_reference
[2023-03-17 09:41:41,759] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:41:41,760] [INFO] Task started: Prodigal
[2023-03-17 09:41:41,760] [INFO] Running command: cat /var/lib/cwl/stg5c058796-eafe-4bb8-b747-93a234a3c705/OceanDNA-b6558.fa | prodigal -d OceanDNA-b6558/cds.fna -a OceanDNA-b6558/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:42:14,369] [INFO] Task succeeded: Prodigal
[2023-03-17 09:42:14,369] [INFO] Task started: HMMsearch
[2023-03-17 09:42:14,370] [INFO] Running command: hmmsearch --tblout OceanDNA-b6558/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd83d874d-8fe8-4ca5-8910-80790cb5653c/dqc_reference/reference_markers.hmm OceanDNA-b6558/protein.faa > /dev/null
[2023-03-17 09:42:14,610] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:42:14,610] [INFO] Found 6/6 markers.
[2023-03-17 09:42:14,670] [INFO] Query marker FASTA was written to OceanDNA-b6558/markers.fasta
[2023-03-17 09:42:14,671] [INFO] Task started: Blastn
[2023-03-17 09:42:14,671] [INFO] Running command: blastn -query OceanDNA-b6558/markers.fasta -db /var/lib/cwl/stgd83d874d-8fe8-4ca5-8910-80790cb5653c/dqc_reference/reference_markers.fasta -out OceanDNA-b6558/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:42:15,245] [INFO] Task succeeded: Blastn
[2023-03-17 09:42:15,251] [INFO] Selected 10 target genomes.
[2023-03-17 09:42:15,251] [INFO] Target genome list was writen to OceanDNA-b6558/target_genomes.txt
[2023-03-17 09:42:15,308] [INFO] Task started: fastANI
[2023-03-17 09:42:15,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c058796-eafe-4bb8-b747-93a234a3c705/OceanDNA-b6558.fa --refList OceanDNA-b6558/target_genomes.txt --output OceanDNA-b6558/fastani_result.tsv --threads 1
[2023-03-17 09:42:25,244] [INFO] Task succeeded: fastANI
[2023-03-17 09:42:25,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd83d874d-8fe8-4ca5-8910-80790cb5653c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:42:25,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd83d874d-8fe8-4ca5-8910-80790cb5653c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:42:25,254] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:42:25,255] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:42:25,255] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	85.4427	1066	1418	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	85.1733	1103	1418	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	84.7673	1057	1418	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	84.5815	1073	1418	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	82.3377	921	1418	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	75.695	71	1418	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	75.5756	89	1418	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:42:25,257] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6558/tc_result.tsv
[2023-03-17 09:42:25,265] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:42:25,265] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:42:25,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd83d874d-8fe8-4ca5-8910-80790cb5653c/dqc_reference/checkm_data
[2023-03-17 09:42:25,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:42:25,359] [INFO] Task started: CheckM
[2023-03-17 09:42:25,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6558/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6558/checkm_input OceanDNA-b6558/checkm_result
[2023-03-17 09:43:42,948] [INFO] Task succeeded: CheckM
[2023-03-17 09:43:42,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:43:43,003] [INFO] ===== Completeness check finished =====
[2023-03-17 09:43:43,003] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:43:43,003] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6558/markers.fasta)
[2023-03-17 09:43:43,005] [INFO] Task started: Blastn
[2023-03-17 09:43:43,005] [INFO] Running command: blastn -query OceanDNA-b6558/markers.fasta -db /var/lib/cwl/stgd83d874d-8fe8-4ca5-8910-80790cb5653c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6558/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:43:43,827] [INFO] Task succeeded: Blastn
[2023-03-17 09:43:43,835] [INFO] Selected 7 target genomes.
[2023-03-17 09:43:43,835] [INFO] Target genome list was writen to OceanDNA-b6558/target_genomes_gtdb.txt
[2023-03-17 09:43:43,928] [INFO] Task started: fastANI
[2023-03-17 09:43:43,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c058796-eafe-4bb8-b747-93a234a3c705/OceanDNA-b6558.fa --refList OceanDNA-b6558/target_genomes_gtdb.txt --output OceanDNA-b6558/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:43:52,538] [INFO] Task succeeded: fastANI
[2023-03-17 09:43:52,543] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:43:52,543] [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
GCF_003201775.1	s__Arenibacter sp003201775	99.1464	1329	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018860365.1	s__Arenibacter algicola_B	86.8878	1131	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259375.1	s__Arenibacter echinorum	85.4427	1066	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129275.1	s__Arenibacter palladensis	85.1617	1104	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_000733925.1	s__Arenibacter algicola	84.7746	1055	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_900177645.1	s__Arenibacter troitsensis	84.5877	1072	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397245.1	s__Arenibacter arenosicollis	82.3653	918	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:43:52,546] [INFO] GTDB search result was written to OceanDNA-b6558/result_gtdb.tsv
[2023-03-17 09:43:52,549] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:43:52,553] [INFO] DFAST_QC result json was written to OceanDNA-b6558/dqc_result.json
[2023-03-17 09:43:52,553] [INFO] DFAST_QC completed!
[2023-03-17 09:43:52,553] [INFO] Total running time: 0h2m13s