[2023-03-15 16:15:00,883] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:15:00,883] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:15:00,883] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d91d5a5-ad1f-4f51-a7ae-512b43efc5e8/dqc_reference
[2023-03-15 16:15:02,009] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:15:02,009] [INFO] Task started: Prodigal
[2023-03-15 16:15:02,010] [INFO] Running command: cat /var/lib/cwl/stg4cebd572-5b43-4049-837a-c0c2c6a85299/OceanDNA-b10442.fa | prodigal -d OceanDNA-b10442/cds.fna -a OceanDNA-b10442/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:15:15,684] [INFO] Task succeeded: Prodigal
[2023-03-15 16:15:15,684] [INFO] Task started: HMMsearch
[2023-03-15 16:15:15,684] [INFO] Running command: hmmsearch --tblout OceanDNA-b10442/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d91d5a5-ad1f-4f51-a7ae-512b43efc5e8/dqc_reference/reference_markers.hmm OceanDNA-b10442/protein.faa > /dev/null
[2023-03-15 16:15:15,872] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:15:15,873] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4cebd572-5b43-4049-837a-c0c2c6a85299/OceanDNA-b10442.fa]
[2023-03-15 16:15:15,888] [INFO] Query marker FASTA was written to OceanDNA-b10442/markers.fasta
[2023-03-15 16:15:15,888] [INFO] Task started: Blastn
[2023-03-15 16:15:15,888] [INFO] Running command: blastn -query OceanDNA-b10442/markers.fasta -db /var/lib/cwl/stg9d91d5a5-ad1f-4f51-a7ae-512b43efc5e8/dqc_reference/reference_markers.fasta -out OceanDNA-b10442/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:16,453] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:16,454] [INFO] Selected 15 target genomes.
[2023-03-15 16:15:16,454] [INFO] Target genome list was writen to OceanDNA-b10442/target_genomes.txt
[2023-03-15 16:15:16,462] [INFO] Task started: fastANI
[2023-03-15 16:15:16,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cebd572-5b43-4049-837a-c0c2c6a85299/OceanDNA-b10442.fa --refList OceanDNA-b10442/target_genomes.txt --output OceanDNA-b10442/fastani_result.tsv --threads 1
[2023-03-15 16:15:26,333] [INFO] Task succeeded: fastANI
[2023-03-15 16:15:26,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d91d5a5-ad1f-4f51-a7ae-512b43efc5e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:15:26,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d91d5a5-ad1f-4f51-a7ae-512b43efc5e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:15:26,344] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:15:26,344] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:15:26,344] [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
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	87.3306	625	780	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	82.7184	608	780	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	81.0423	478	780	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	80.9669	476	780	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	80.8695	511	780	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	80.0112	503	780	95	below_threshold
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	79.4006	453	780	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	79.3788	398	780	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	79.3515	453	780	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	79.3473	446	780	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.698	389	780	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.2943	312	780	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.2701	346	780	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.1134	327	780	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.4899	261	780	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:15:26,344] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10442/tc_result.tsv
[2023-03-15 16:15:26,345] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:15:26,345] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:15:26,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d91d5a5-ad1f-4f51-a7ae-512b43efc5e8/dqc_reference/checkm_data
[2023-03-15 16:15:26,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:15:26,350] [INFO] Task started: CheckM
[2023-03-15 16:15:26,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10442/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10442/checkm_input OceanDNA-b10442/checkm_result
[2023-03-15 16:16:03,236] [INFO] Task succeeded: CheckM
[2023-03-15 16:16:03,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:16:03,263] [INFO] ===== Completeness check finished =====
[2023-03-15 16:16:03,263] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:16:03,263] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10442/markers.fasta)
[2023-03-15 16:16:03,265] [INFO] Task started: Blastn
[2023-03-15 16:16:03,265] [INFO] Running command: blastn -query OceanDNA-b10442/markers.fasta -db /var/lib/cwl/stg9d91d5a5-ad1f-4f51-a7ae-512b43efc5e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10442/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:16:04,092] [INFO] Task succeeded: Blastn
[2023-03-15 16:16:04,093] [INFO] Selected 14 target genomes.
[2023-03-15 16:16:04,093] [INFO] Target genome list was writen to OceanDNA-b10442/target_genomes_gtdb.txt
[2023-03-15 16:16:04,106] [INFO] Task started: fastANI
[2023-03-15 16:16:04,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cebd572-5b43-4049-837a-c0c2c6a85299/OceanDNA-b10442.fa --refList OceanDNA-b10442/target_genomes_gtdb.txt --output OceanDNA-b10442/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:16:13,184] [INFO] Task succeeded: fastANI
[2023-03-15 16:16:13,192] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:16:13,193] [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_001693415.1	s__Tenacibaculum soleae	83.5681	612	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	82.7388	606	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_002836595.1	s__Tenacibaculum sp002836595	82.61	614	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239185.1	s__Tenacibaculum finnmarkense_A	81.0474	477	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	96.8963	99.00	98.36	0.95	0.91	6	-
GCF_900239345.1	s__Tenacibaculum dicentrarchi	80.988	488	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
GCF_900239495.1	s__Tenacibaculum finnmarkense	80.9531	477	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	96.8963	98.86	98.40	0.93	0.91	7	-
GCF_014062345.1	s__Tenacibaculum pelagium	80.8609	512	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239505.1	s__Tenacibaculum piscium	80.6811	433	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.64	99.33	0.97	0.95	5	-
GCF_008806755.1	s__Tenacibaculum aiptasiae	80.0216	502	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664185.1	s__Tenacibaculum discolor	79.3789	455	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	-
GCF_003867075.1	s__Tenacibaculum mesophilum	79.3336	451	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
GCF_900105985.1	s__Tenacibaculum sp900105985	78.7864	422	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	78.714	388	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	78.2825	313	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:16:13,193] [INFO] GTDB search result was written to OceanDNA-b10442/result_gtdb.tsv
[2023-03-15 16:16:13,193] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:16:13,195] [INFO] DFAST_QC result json was written to OceanDNA-b10442/dqc_result.json
[2023-03-15 16:16:13,195] [INFO] DFAST_QC completed!
[2023-03-15 16:16:13,195] [INFO] Total running time: 0h1m12s