[2023-03-15 14:06:11,246] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:06:11,247] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:06:11,247] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2d713af-1a2a-4415-ba24-c324527cfbbe/dqc_reference
[2023-03-15 14:06:12,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:06:12,382] [INFO] Task started: Prodigal
[2023-03-15 14:06:12,383] [INFO] Running command: cat /var/lib/cwl/stg392e9e5f-4fa8-408b-a003-ad735bb0b17b/OceanDNA-b4056.fa | prodigal -d OceanDNA-b4056/cds.fna -a OceanDNA-b4056/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:06:34,349] [INFO] Task succeeded: Prodigal
[2023-03-15 14:06:34,350] [INFO] Task started: HMMsearch
[2023-03-15 14:06:34,350] [INFO] Running command: hmmsearch --tblout OceanDNA-b4056/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2d713af-1a2a-4415-ba24-c324527cfbbe/dqc_reference/reference_markers.hmm OceanDNA-b4056/protein.faa > /dev/null
[2023-03-15 14:06:34,556] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:06:34,557] [INFO] Found 6/6 markers.
[2023-03-15 14:06:34,575] [INFO] Query marker FASTA was written to OceanDNA-b4056/markers.fasta
[2023-03-15 14:06:34,577] [INFO] Task started: Blastn
[2023-03-15 14:06:34,577] [INFO] Running command: blastn -query OceanDNA-b4056/markers.fasta -db /var/lib/cwl/stgd2d713af-1a2a-4415-ba24-c324527cfbbe/dqc_reference/reference_markers.fasta -out OceanDNA-b4056/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:06:35,122] [INFO] Task succeeded: Blastn
[2023-03-15 14:06:35,123] [INFO] Selected 25 target genomes.
[2023-03-15 14:06:35,124] [INFO] Target genome list was writen to OceanDNA-b4056/target_genomes.txt
[2023-03-15 14:06:35,140] [INFO] Task started: fastANI
[2023-03-15 14:06:35,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg392e9e5f-4fa8-408b-a003-ad735bb0b17b/OceanDNA-b4056.fa --refList OceanDNA-b4056/target_genomes.txt --output OceanDNA-b4056/fastani_result.tsv --threads 1
[2023-03-15 14:06:52,345] [INFO] Task succeeded: fastANI
[2023-03-15 14:06:52,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2d713af-1a2a-4415-ba24-c324527cfbbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:06:52,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2d713af-1a2a-4415-ba24-c324527cfbbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:06:52,352] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:06:52,352] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:06:52,352] [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
Roseivirga pacifica	strain=CGMCC 1.12402	GCA_900111145.1	1267423	1267423	type	True	76.7404	139	1074	95	below_threshold
Roseivirga pacifica	strain=DSM 100771	GCA_003633845.1	1267423	1267423	type	True	76.694	143	1074	95	below_threshold
Roseivirga spongicola	strain=UST030701-084	GCA_001592965.1	333140	333140	type	True	76.2814	112	1074	95	below_threshold
Roseivirga thermotolerans	strain=CGMCC 1.15111	GCA_014653175.1	1758176	1758176	type	True	76.2215	80	1074	95	below_threshold
Roseivirga misakiensis	strain=SK-8	GCA_001747105.1	1563681	1563681	type	True	76.1128	89	1074	95	below_threshold
Roseivirga echinicomitans	strain=KMM 6058	GCA_001592935.1	296218	296218	type	True	75.9785	67	1074	95	below_threshold
Roseivirga ehrenbergii	strain=DSM 102268	GCA_004340805.1	279360	279360	type	True	75.9016	70	1074	95	below_threshold
Roseivirga seohaensis subsp. aquiponti	strain=D-25	GCA_001267955.1	1566026	1914963	type	True	75.9005	62	1074	95	below_threshold
Roseivirga ehrenbergii	strain=KMM 6017	GCA_001593005.1	279360	279360	type	True	75.8624	72	1074	95	below_threshold
Roseivirga seohaensis	strain=SW-152	GCA_001592945.1	1914963	1914963	type	True	75.8109	67	1074	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:06:52,353] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4056/tc_result.tsv
[2023-03-15 14:06:52,353] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:06:52,353] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:06:52,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2d713af-1a2a-4415-ba24-c324527cfbbe/dqc_reference/checkm_data
[2023-03-15 14:06:52,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:06:52,381] [INFO] Task started: CheckM
[2023-03-15 14:06:52,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4056/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4056/checkm_input OceanDNA-b4056/checkm_result
[2023-03-15 14:07:48,903] [INFO] Task succeeded: CheckM
[2023-03-15 14:07:48,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:07:48,908] [INFO] ===== Completeness check finished =====
[2023-03-15 14:07:48,908] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:07:48,909] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4056/markers.fasta)
[2023-03-15 14:07:48,910] [INFO] Task started: Blastn
[2023-03-15 14:07:48,910] [INFO] Running command: blastn -query OceanDNA-b4056/markers.fasta -db /var/lib/cwl/stgd2d713af-1a2a-4415-ba24-c324527cfbbe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4056/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:07:49,630] [INFO] Task succeeded: Blastn
[2023-03-15 14:07:49,632] [INFO] Selected 25 target genomes.
[2023-03-15 14:07:49,632] [INFO] Target genome list was writen to OceanDNA-b4056/target_genomes_gtdb.txt
[2023-03-15 14:07:49,686] [INFO] Task started: fastANI
[2023-03-15 14:07:49,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg392e9e5f-4fa8-408b-a003-ad735bb0b17b/OceanDNA-b4056.fa --refList OceanDNA-b4056/target_genomes_gtdb.txt --output OceanDNA-b4056/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:08:07,321] [INFO] Task succeeded: fastANI
[2023-03-15 14:08:07,328] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:08:07,328] [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_900111145.1	s__Fabibacter pacificus	76.7243	140	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002427755.1	s__Fabibacter sp002427755	76.7153	124	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592825.1	s__Fabibacter sp017592825	76.5697	98	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373005.1	s__Fabibacter sp013373005	76.3807	84	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592965.1	s__Fabibacter spongicola	76.2814	112	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	97.73	96.54	0.93	0.88	5	-
GCF_014653175.1	s__Fabibacter thermotolerans	76.2215	80	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	98.67	98.61	0.92	0.91	4	-
GCA_002477595.1	s__Fabibacter sp002477595	76.1309	65	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	99.68	99.60	0.84	0.83	4	-
GCF_001747105.1	s__Fabibacter misakiensis	76.1128	89	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592935.1	s__Roseivirga echinicomitans	75.9785	67	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593005.1	s__Roseivirga ehrenbergii	75.8624	72	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001592945.1	s__Roseivirga seohaensis	75.8109	67	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	97.29	97.29	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-15 14:08:07,330] [INFO] GTDB search result was written to OceanDNA-b4056/result_gtdb.tsv
[2023-03-15 14:08:07,330] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:08:07,333] [INFO] DFAST_QC result json was written to OceanDNA-b4056/dqc_result.json
[2023-03-15 14:08:07,333] [INFO] DFAST_QC completed!
[2023-03-15 14:08:07,333] [INFO] Total running time: 0h1m56s