[2023-03-17 16:13:55,248] [INFO] DFAST_QC pipeline started.
[2023-03-17 16:13:55,249] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 16:13:55,249] [INFO] DQC Reference Directory: /var/lib/cwl/stg2515e3de-5155-4248-8e0b-1a39dae62863/dqc_reference
[2023-03-17 16:13:56,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 16:13:56,399] [INFO] Task started: Prodigal
[2023-03-17 16:13:56,399] [INFO] Running command: cat /var/lib/cwl/stgf47106aa-9909-4f02-94bf-80d3b48bea11/OceanDNA-b4058.fa | prodigal -d OceanDNA-b4058/cds.fna -a OceanDNA-b4058/protein.faa -g 11 -q > /dev/null
[2023-03-17 16:14:10,744] [INFO] Task succeeded: Prodigal
[2023-03-17 16:14:10,745] [INFO] Task started: HMMsearch
[2023-03-17 16:14:10,745] [INFO] Running command: hmmsearch --tblout OceanDNA-b4058/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2515e3de-5155-4248-8e0b-1a39dae62863/dqc_reference/reference_markers.hmm OceanDNA-b4058/protein.faa > /dev/null
[2023-03-17 16:14:10,933] [INFO] Task succeeded: HMMsearch
[2023-03-17 16:14:10,934] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf47106aa-9909-4f02-94bf-80d3b48bea11/OceanDNA-b4058.fa]
[2023-03-17 16:14:10,953] [INFO] Query marker FASTA was written to OceanDNA-b4058/markers.fasta
[2023-03-17 16:14:10,954] [INFO] Task started: Blastn
[2023-03-17 16:14:10,954] [INFO] Running command: blastn -query OceanDNA-b4058/markers.fasta -db /var/lib/cwl/stg2515e3de-5155-4248-8e0b-1a39dae62863/dqc_reference/reference_markers.fasta -out OceanDNA-b4058/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:14:11,511] [INFO] Task succeeded: Blastn
[2023-03-17 16:14:11,512] [INFO] Selected 23 target genomes.
[2023-03-17 16:14:11,512] [INFO] Target genome list was writen to OceanDNA-b4058/target_genomes.txt
[2023-03-17 16:14:11,524] [INFO] Task started: fastANI
[2023-03-17 16:14:11,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgf47106aa-9909-4f02-94bf-80d3b48bea11/OceanDNA-b4058.fa --refList OceanDNA-b4058/target_genomes.txt --output OceanDNA-b4058/fastani_result.tsv --threads 1
[2023-03-17 16:14:30,875] [INFO] Task succeeded: fastANI
[2023-03-17 16:14:30,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2515e3de-5155-4248-8e0b-1a39dae62863/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 16:14:30,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2515e3de-5155-4248-8e0b-1a39dae62863/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 16:14:30,882] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 16:14:30,882] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 16:14:30,882] [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 spongicola	strain=UST030701-084	GCA_001592965.1	333140	333140	type	True	79.2316	239	508	95	below_threshold
Roseivirga thermotolerans	strain=CGMCC 1.15111	GCA_014653175.1	1758176	1758176	type	True	77.6699	171	508	95	below_threshold
Roseivirga pacifica	strain=CGMCC 1.12402	GCA_900111145.1	1267423	1267423	type	True	77.2293	79	508	95	below_threshold
Roseivirga pacifica	strain=DSM 100771	GCA_003633845.1	1267423	1267423	type	True	77.1954	80	508	95	below_threshold
Roseivirga ehrenbergii	strain=DSM 102268	GCA_004340805.1	279360	279360	type	True	76.3841	51	508	95	below_threshold
Roseivirga ehrenbergii	strain=KMM 6017	GCA_001593005.1	279360	279360	type	True	76.3334	51	508	95	below_threshold
Roseivirga echinicomitans	strain=KMM 6058	GCA_001592935.1	296218	296218	type	True	75.8943	51	508	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 16:14:30,882] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4058/tc_result.tsv
[2023-03-17 16:14:30,882] [INFO] ===== Taxonomy check completed =====
[2023-03-17 16:14:30,882] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 16:14:30,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2515e3de-5155-4248-8e0b-1a39dae62863/dqc_reference/checkm_data
[2023-03-17 16:14:30,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 16:14:30,887] [INFO] Task started: CheckM
[2023-03-17 16:14:30,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4058/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4058/checkm_input OceanDNA-b4058/checkm_result
[2023-03-17 16:15:28,503] [INFO] Task succeeded: CheckM
[2023-03-17 16:15:28,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.24%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 16:15:28,506] [INFO] ===== Completeness check finished =====
[2023-03-17 16:15:28,506] [INFO] ===== Start GTDB Search =====
[2023-03-17 16:15:28,506] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4058/markers.fasta)
[2023-03-17 16:15:28,507] [INFO] Task started: Blastn
[2023-03-17 16:15:28,507] [INFO] Running command: blastn -query OceanDNA-b4058/markers.fasta -db /var/lib/cwl/stg2515e3de-5155-4248-8e0b-1a39dae62863/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4058/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:15:29,506] [INFO] Task succeeded: Blastn
[2023-03-17 16:15:29,507] [INFO] Selected 23 target genomes.
[2023-03-17 16:15:29,507] [INFO] Target genome list was writen to OceanDNA-b4058/target_genomes_gtdb.txt
[2023-03-17 16:15:29,770] [INFO] Task started: fastANI
[2023-03-17 16:15:29,770] [INFO] Running command: fastANI --query /var/lib/cwl/stgf47106aa-9909-4f02-94bf-80d3b48bea11/OceanDNA-b4058.fa --refList OceanDNA-b4058/target_genomes_gtdb.txt --output OceanDNA-b4058/fastani_result_gtdb.tsv --threads 1
[2023-03-17 16:15:45,120] [INFO] Task succeeded: fastANI
[2023-03-17 16:15:45,124] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 16:15:45,125] [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_013373005.1	s__Fabibacter sp013373005	79.9364	268	508	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	79.2518	238	508	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	77.6699	171	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	98.67	98.61	0.92	0.91	4	-
GCF_001747095.1	s__Fabibacter sp001747095	76.8134	68	508	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	76.6738	68	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593005.1	s__Roseivirga ehrenbergii	76.3334	51	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 16:15:45,125] [INFO] GTDB search result was written to OceanDNA-b4058/result_gtdb.tsv
[2023-03-17 16:15:45,125] [INFO] ===== GTDB Search completed =====
[2023-03-17 16:15:45,126] [INFO] DFAST_QC result json was written to OceanDNA-b4058/dqc_result.json
[2023-03-17 16:15:45,126] [INFO] DFAST_QC completed!
[2023-03-17 16:15:45,126] [INFO] Total running time: 0h1m50s