[2023-03-15 11:09:10,899] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,899] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,900] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4f23253-c17f-485a-9e25-a7a208083449/dqc_reference
[2023-03-15 11:09:12,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,123] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,123] [INFO] Running command: cat /var/lib/cwl/stge2ce8c2a-55b0-4de5-bed9-7a6028916540/OceanDNA-b4138.fa | prodigal -d OceanDNA-b4138/cds.fna -a OceanDNA-b4138/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:37,679] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:37,680] [INFO] Task started: HMMsearch
[2023-03-15 11:09:37,680] [INFO] Running command: hmmsearch --tblout OceanDNA-b4138/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4f23253-c17f-485a-9e25-a7a208083449/dqc_reference/reference_markers.hmm OceanDNA-b4138/protein.faa > /dev/null
[2023-03-15 11:09:37,922] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:37,922] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge2ce8c2a-55b0-4de5-bed9-7a6028916540/OceanDNA-b4138.fa]
[2023-03-15 11:09:37,945] [INFO] Query marker FASTA was written to OceanDNA-b4138/markers.fasta
[2023-03-15 11:09:37,945] [INFO] Task started: Blastn
[2023-03-15 11:09:37,945] [INFO] Running command: blastn -query OceanDNA-b4138/markers.fasta -db /var/lib/cwl/stgd4f23253-c17f-485a-9e25-a7a208083449/dqc_reference/reference_markers.fasta -out OceanDNA-b4138/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:38,504] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:38,505] [INFO] Selected 7 target genomes.
[2023-03-15 11:09:38,505] [INFO] Target genome list was writen to OceanDNA-b4138/target_genomes.txt
[2023-03-15 11:09:38,509] [INFO] Task started: fastANI
[2023-03-15 11:09:38,509] [INFO] Running command: fastANI --query /var/lib/cwl/stge2ce8c2a-55b0-4de5-bed9-7a6028916540/OceanDNA-b4138.fa --refList OceanDNA-b4138/target_genomes.txt --output OceanDNA-b4138/fastani_result.tsv --threads 1
[2023-03-15 11:09:44,716] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:44,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4f23253-c17f-485a-9e25-a7a208083449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:44,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4f23253-c17f-485a-9e25-a7a208083449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:44,721] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 11:09:44,721] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 11:09:44,721] [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 seohaensis	strain=SW-152	GCA_001592945.1	1914963	1914963	type	True	96.7062	960	1067	95	conclusive
Roseivirga seohaensis subsp. aquiponti	strain=D-25	GCA_001267955.1	1566026	1914963	type	True	96.3965	968	1067	95	conclusive
Roseivirga ehrenbergii	strain=KMM 6017	GCA_001593005.1	279360	279360	type	True	93.001	932	1067	95	below_threshold
Roseivirga ehrenbergii	strain=DSM 102268	GCA_004340805.1	279360	279360	type	True	92.9521	953	1067	95	below_threshold
Roseivirga echinicomitans	strain=KMM 6058	GCA_001592935.1	296218	296218	type	True	85.2337	827	1067	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:44,721] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4138/tc_result.tsv
[2023-03-15 11:09:44,721] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:44,722] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:44,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4f23253-c17f-485a-9e25-a7a208083449/dqc_reference/checkm_data
[2023-03-15 11:09:44,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:44,728] [INFO] Task started: CheckM
[2023-03-15 11:09:44,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4138/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4138/checkm_input OceanDNA-b4138/checkm_result
[2023-03-15 11:10:42,118] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:42,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:42,121] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:42,121] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:42,121] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4138/markers.fasta)
[2023-03-15 11:10:42,121] [INFO] Task started: Blastn
[2023-03-15 11:10:42,122] [INFO] Running command: blastn -query OceanDNA-b4138/markers.fasta -db /var/lib/cwl/stgd4f23253-c17f-485a-9e25-a7a208083449/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4138/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:42,834] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:42,835] [INFO] Selected 10 target genomes.
[2023-03-15 11:10:42,835] [INFO] Target genome list was writen to OceanDNA-b4138/target_genomes_gtdb.txt
[2023-03-15 11:10:42,843] [INFO] Task started: fastANI
[2023-03-15 11:10:42,844] [INFO] Running command: fastANI --query /var/lib/cwl/stge2ce8c2a-55b0-4de5-bed9-7a6028916540/OceanDNA-b4138.fa --refList OceanDNA-b4138/target_genomes_gtdb.txt --output OceanDNA-b4138/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:50,878] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:50,884] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:10:50,884] [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_001592945.1	s__Roseivirga seohaensis	96.7062	960	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	97.29	97.29	0.91	0.91	2	conclusive
GCF_001593005.1	s__Roseivirga ehrenbergii	93.001	932	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001592935.1	s__Roseivirga echinicomitans	85.2339	828	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786855.1	s__Roseivirga sp002786855	77.4136	285	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	99.94	99.94	0.97	0.97	2	-
GCF_001592965.1	s__Fabibacter spongicola	76.4195	112	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	97.73	96.54	0.93	0.88	5	-
GCF_900111145.1	s__Fabibacter pacificus	76.282	110	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001747095.1	s__Fabibacter sp001747095	76.2428	62	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653175.1	s__Fabibacter thermotolerans	75.9699	89	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	98.67	98.61	0.92	0.91	4	-
GCA_002427745.1	s__Roseivirga sp002427745	75.9689	58	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:50,884] [INFO] GTDB search result was written to OceanDNA-b4138/result_gtdb.tsv
[2023-03-15 11:10:50,884] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:50,885] [INFO] DFAST_QC result json was written to OceanDNA-b4138/dqc_result.json
[2023-03-15 11:10:50,886] [INFO] DFAST_QC completed!
[2023-03-15 11:10:50,886] [INFO] Total running time: 0h1m40s