[2023-03-16 09:23:09,461] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:23:09,461] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:23:09,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg930b13f0-f94a-4e31-a408-70c6b7b513a5/dqc_reference
[2023-03-16 09:23:11,216] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:23:11,217] [INFO] Task started: Prodigal
[2023-03-16 09:23:11,217] [INFO] Running command: cat /var/lib/cwl/stg228de05b-94a8-4076-a22a-1e4d9496481c/OceanDNA-b6832.fa | prodigal -d OceanDNA-b6832/cds.fna -a OceanDNA-b6832/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:23:37,260] [INFO] Task succeeded: Prodigal
[2023-03-16 09:23:37,260] [INFO] Task started: HMMsearch
[2023-03-16 09:23:37,260] [INFO] Running command: hmmsearch --tblout OceanDNA-b6832/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg930b13f0-f94a-4e31-a408-70c6b7b513a5/dqc_reference/reference_markers.hmm OceanDNA-b6832/protein.faa > /dev/null
[2023-03-16 09:23:37,478] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:23:37,479] [INFO] Found 6/6 markers.
[2023-03-16 09:23:37,507] [INFO] Query marker FASTA was written to OceanDNA-b6832/markers.fasta
[2023-03-16 09:23:37,508] [INFO] Task started: Blastn
[2023-03-16 09:23:37,508] [INFO] Running command: blastn -query OceanDNA-b6832/markers.fasta -db /var/lib/cwl/stg930b13f0-f94a-4e31-a408-70c6b7b513a5/dqc_reference/reference_markers.fasta -out OceanDNA-b6832/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:23:38,133] [INFO] Task succeeded: Blastn
[2023-03-16 09:23:38,136] [INFO] Selected 11 target genomes.
[2023-03-16 09:23:38,136] [INFO] Target genome list was writen to OceanDNA-b6832/target_genomes.txt
[2023-03-16 09:23:38,144] [INFO] Task started: fastANI
[2023-03-16 09:23:38,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg228de05b-94a8-4076-a22a-1e4d9496481c/OceanDNA-b6832.fa --refList OceanDNA-b6832/target_genomes.txt --output OceanDNA-b6832/fastani_result.tsv --threads 1
[2023-03-16 09:23:46,144] [INFO] Task succeeded: fastANI
[2023-03-16 09:23:46,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg930b13f0-f94a-4e31-a408-70c6b7b513a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:23:46,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg930b13f0-f94a-4e31-a408-70c6b7b513a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:23:46,152] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:23:46,152] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:23:46,152] [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 jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	85.6878	1070	1430	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	81.4733	786	1430	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	81.467	787	1430	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	80.7922	738	1430	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	79.8111	683	1430	95	below_threshold
Flavobacterium gelidilacus	strain=DSM 15343	GCA_000422685.1	206041	206041	type	True	78.8263	462	1430	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	78.6003	345	1430	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.43	387	1430	95	below_threshold
Flavobacterium bernardetii	strain=F-372	GCA_011305415.1	2813823	2813823	type	True	77.8239	321	1430	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.3168	258	1430	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.6805	143	1430	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:23:46,153] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6832/tc_result.tsv
[2023-03-16 09:23:46,156] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:23:46,156] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:23:46,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg930b13f0-f94a-4e31-a408-70c6b7b513a5/dqc_reference/checkm_data
[2023-03-16 09:23:46,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:23:46,198] [INFO] Task started: CheckM
[2023-03-16 09:23:46,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6832/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6832/checkm_input OceanDNA-b6832/checkm_result
[2023-03-16 09:24:49,999] [INFO] Task succeeded: CheckM
[2023-03-16 09:24:50,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:24:50,021] [INFO] ===== Completeness check finished =====
[2023-03-16 09:24:50,021] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:24:50,021] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6832/markers.fasta)
[2023-03-16 09:24:50,023] [INFO] Task started: Blastn
[2023-03-16 09:24:50,023] [INFO] Running command: blastn -query OceanDNA-b6832/markers.fasta -db /var/lib/cwl/stg930b13f0-f94a-4e31-a408-70c6b7b513a5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6832/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:24:50,945] [INFO] Task succeeded: Blastn
[2023-03-16 09:24:50,953] [INFO] Selected 8 target genomes.
[2023-03-16 09:24:50,953] [INFO] Target genome list was writen to OceanDNA-b6832/target_genomes_gtdb.txt
[2023-03-16 09:24:50,989] [INFO] Task started: fastANI
[2023-03-16 09:24:50,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg228de05b-94a8-4076-a22a-1e4d9496481c/OceanDNA-b6832.fa --refList OceanDNA-b6832/target_genomes_gtdb.txt --output OceanDNA-b6832/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:24:57,702] [INFO] Task succeeded: fastANI
[2023-03-16 09:24:57,708] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:24:57,708] [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_006491595.2	s__Flavobacterium jejuense	85.7086	1068	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491645.1	s__Flavobacterium sp006491645	81.4816	785	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004303025.1	s__Flavobacterium sp004303025	81.2855	814	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715085.1	s__Flavobacterium sp002715085	81.2278	714	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862755.1	s__Flavobacterium sp002862755	81.036	756	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032075.1	s__Flavobacterium sp012032075	80.977	563	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	80.911	714	1430	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	80.6584	807	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:24:57,710] [INFO] GTDB search result was written to OceanDNA-b6832/result_gtdb.tsv
[2023-03-16 09:24:57,712] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:24:57,716] [INFO] DFAST_QC result json was written to OceanDNA-b6832/dqc_result.json
[2023-03-16 09:24:57,716] [INFO] DFAST_QC completed!
[2023-03-16 09:24:57,716] [INFO] Total running time: 0h1m48s