[2023-03-19 04:43:18,698] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,698] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,698] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2600984-137d-4f17-88b7-98e920f99224/dqc_reference
[2023-03-19 04:43:19,854] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,854] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,855] [INFO] Running command: cat /var/lib/cwl/stgdd3dd036-e029-4e5e-8851-4479154b20be/OceanDNA-b6846.fa | prodigal -d OceanDNA-b6846/cds.fna -a OceanDNA-b6846/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:40,114] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:40,114] [INFO] Task started: HMMsearch
[2023-03-19 04:43:40,114] [INFO] Running command: hmmsearch --tblout OceanDNA-b6846/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2600984-137d-4f17-88b7-98e920f99224/dqc_reference/reference_markers.hmm OceanDNA-b6846/protein.faa > /dev/null
[2023-03-19 04:43:40,326] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:40,327] [INFO] Found 6/6 markers.
[2023-03-19 04:43:40,348] [INFO] Query marker FASTA was written to OceanDNA-b6846/markers.fasta
[2023-03-19 04:43:40,349] [INFO] Task started: Blastn
[2023-03-19 04:43:40,349] [INFO] Running command: blastn -query OceanDNA-b6846/markers.fasta -db /var/lib/cwl/stgb2600984-137d-4f17-88b7-98e920f99224/dqc_reference/reference_markers.fasta -out OceanDNA-b6846/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:40,975] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:40,976] [INFO] Selected 11 target genomes.
[2023-03-19 04:43:40,976] [INFO] Target genome list was writen to OceanDNA-b6846/target_genomes.txt
[2023-03-19 04:43:40,983] [INFO] Task started: fastANI
[2023-03-19 04:43:40,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd3dd036-e029-4e5e-8851-4479154b20be/OceanDNA-b6846.fa --refList OceanDNA-b6846/target_genomes.txt --output OceanDNA-b6846/fastani_result.tsv --threads 1
[2023-03-19 04:43:48,529] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:48,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2600984-137d-4f17-88b7-98e920f99224/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:48,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2600984-137d-4f17-88b7-98e920f99224/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:48,536] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:43:48,536] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:43:48,536] [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
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	92.322	940	1070	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	92.322	940	1070	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	80.575	714	1070	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	78.9847	507	1070	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	78.3403	486	1070	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.1551	291	1070	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	78.1476	279	1070	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.9773	316	1070	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.7325	307	1070	95	below_threshold
Flavobacterium terrigena	strain=DSM 17934	GCA_900108955.1	402734	402734	type	True	77.1899	222	1070	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.436	105	1070	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:43:48,537] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6846/tc_result.tsv
[2023-03-19 04:43:48,537] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:48,537] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:48,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2600984-137d-4f17-88b7-98e920f99224/dqc_reference/checkm_data
[2023-03-19 04:43:48,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:48,558] [INFO] Task started: CheckM
[2023-03-19 04:43:48,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6846/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6846/checkm_input OceanDNA-b6846/checkm_result
[2023-03-19 04:44:40,086] [INFO] Task succeeded: CheckM
[2023-03-19 04:44:40,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:44:40,089] [INFO] ===== Completeness check finished =====
[2023-03-19 04:44:40,089] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:44:40,089] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6846/markers.fasta)
[2023-03-19 04:44:40,090] [INFO] Task started: Blastn
[2023-03-19 04:44:40,090] [INFO] Running command: blastn -query OceanDNA-b6846/markers.fasta -db /var/lib/cwl/stgb2600984-137d-4f17-88b7-98e920f99224/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6846/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:44:40,985] [INFO] Task succeeded: Blastn
[2023-03-19 04:44:40,986] [INFO] Selected 6 target genomes.
[2023-03-19 04:44:40,986] [INFO] Target genome list was writen to OceanDNA-b6846/target_genomes_gtdb.txt
[2023-03-19 04:44:41,024] [INFO] Task started: fastANI
[2023-03-19 04:44:41,060] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd3dd036-e029-4e5e-8851-4479154b20be/OceanDNA-b6846.fa --refList OceanDNA-b6846/target_genomes_gtdb.txt --output OceanDNA-b6846/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:44:46,432] [INFO] Task succeeded: fastANI
[2023-03-19 04:44:46,436] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:44:46,437] [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_002715085.1	s__Flavobacterium sp002715085	99.9634	1031	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006491645.1	s__Flavobacterium sp006491645	92.322	940	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002862755.1	s__Flavobacterium sp002862755	91.4189	911	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506265.1	s__Flavobacterium sp902506265	84.6772	773	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004303025.1	s__Flavobacterium sp004303025	84.3733	791	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491595.2	s__Flavobacterium jejuense	80.5923	712	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:44:46,437] [INFO] GTDB search result was written to OceanDNA-b6846/result_gtdb.tsv
[2023-03-19 04:44:46,437] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:44:46,438] [INFO] DFAST_QC result json was written to OceanDNA-b6846/dqc_result.json
[2023-03-19 04:44:46,438] [INFO] DFAST_QC completed!
[2023-03-19 04:44:46,438] [INFO] Total running time: 0h1m28s