[2023-03-16 17:03:09,051] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:03:09,051] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:03:09,052] [INFO] DQC Reference Directory: /var/lib/cwl/stge15577db-c29d-4a78-a46d-0668ea1b51a0/dqc_reference
[2023-03-16 17:03:11,162] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:03:11,162] [INFO] Task started: Prodigal
[2023-03-16 17:03:11,163] [INFO] Running command: cat /var/lib/cwl/stgb26cd229-8df0-41cf-9d10-2a54908ee738/OceanDNA-b6424.fa | prodigal -d OceanDNA-b6424/cds.fna -a OceanDNA-b6424/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:03:31,379] [INFO] Task succeeded: Prodigal
[2023-03-16 17:03:31,379] [INFO] Task started: HMMsearch
[2023-03-16 17:03:31,379] [INFO] Running command: hmmsearch --tblout OceanDNA-b6424/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge15577db-c29d-4a78-a46d-0668ea1b51a0/dqc_reference/reference_markers.hmm OceanDNA-b6424/protein.faa > /dev/null
[2023-03-16 17:03:31,632] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:03:31,632] [INFO] Found 6/6 markers.
[2023-03-16 17:03:31,659] [INFO] Query marker FASTA was written to OceanDNA-b6424/markers.fasta
[2023-03-16 17:03:31,674] [INFO] Task started: Blastn
[2023-03-16 17:03:31,674] [INFO] Running command: blastn -query OceanDNA-b6424/markers.fasta -db /var/lib/cwl/stge15577db-c29d-4a78-a46d-0668ea1b51a0/dqc_reference/reference_markers.fasta -out OceanDNA-b6424/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:03:32,417] [INFO] Task succeeded: Blastn
[2023-03-16 17:03:32,418] [INFO] Selected 9 target genomes.
[2023-03-16 17:03:32,418] [INFO] Target genome list was writen to OceanDNA-b6424/target_genomes.txt
[2023-03-16 17:03:32,436] [INFO] Task started: fastANI
[2023-03-16 17:03:32,436] [INFO] Running command: fastANI --query /var/lib/cwl/stgb26cd229-8df0-41cf-9d10-2a54908ee738/OceanDNA-b6424.fa --refList OceanDNA-b6424/target_genomes.txt --output OceanDNA-b6424/fastani_result.tsv --threads 1
[2023-03-16 17:03:38,419] [INFO] Task succeeded: fastANI
[2023-03-16 17:03:38,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge15577db-c29d-4a78-a46d-0668ea1b51a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:03:38,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge15577db-c29d-4a78-a46d-0668ea1b51a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:03:38,476] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:03:38,476] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:03:38,476] [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
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	79.9155	307	466	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	79.9071	312	466	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	79.7992	298	466	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	79.4116	303	466	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	79.3749	278	466	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	79.3019	311	466	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	79.0698	269	466	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	78.5947	216	466	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	77.8578	171	466	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:03:38,476] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6424/tc_result.tsv
[2023-03-16 17:03:38,476] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:03:38,476] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:03:38,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge15577db-c29d-4a78-a46d-0668ea1b51a0/dqc_reference/checkm_data
[2023-03-16 17:03:38,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:03:38,480] [INFO] Task started: CheckM
[2023-03-16 17:03:38,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6424/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6424/checkm_input OceanDNA-b6424/checkm_result
[2023-03-16 17:04:15,606] [INFO] Task succeeded: CheckM
[2023-03-16 17:04:15,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:04:15,608] [INFO] ===== Completeness check finished =====
[2023-03-16 17:04:15,608] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:04:15,608] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6424/markers.fasta)
[2023-03-16 17:04:15,610] [INFO] Task started: Blastn
[2023-03-16 17:04:15,610] [INFO] Running command: blastn -query OceanDNA-b6424/markers.fasta -db /var/lib/cwl/stge15577db-c29d-4a78-a46d-0668ea1b51a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6424/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:04:17,081] [INFO] Task succeeded: Blastn
[2023-03-16 17:04:17,082] [INFO] Selected 12 target genomes.
[2023-03-16 17:04:17,082] [INFO] Target genome list was writen to OceanDNA-b6424/target_genomes_gtdb.txt
[2023-03-16 17:04:17,122] [INFO] Task started: fastANI
[2023-03-16 17:04:17,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgb26cd229-8df0-41cf-9d10-2a54908ee738/OceanDNA-b6424.fa --refList OceanDNA-b6424/target_genomes_gtdb.txt --output OceanDNA-b6424/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:04:23,866] [INFO] Task succeeded: fastANI
[2023-03-16 17:04:23,873] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:04:23,873] [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_001641085.1	s__Aequorivita soesokkakensis	79.9334	306	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCF_007997135.1	s__Aequorivita lipolytica	79.9071	312	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007997155.1	s__Aequorivita antarctica	79.7992	298	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900489465.1	s__Aequorivita sp900489465	79.5928	286	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364215.1	s__Aequorivita sp002364215	79.592	303	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_016757735.1	s__Aequorivita sp016757735	79.4116	303	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649715.1	s__Aequorivita sp016649715	79.3567	274	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733915.1	s__Aequorivita sp002733915	79.3455	290	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715485.1	s__Aequorivita sp002715485	79.2825	275	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_000265385.1	s__Aequorivita sublithincola	79.0532	270	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375695.1	s__Aequorivita sp002375695	78.6417	240	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000429125.1	s__Aequorivita capsosiphonis	78.5947	216	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:04:23,874] [INFO] GTDB search result was written to OceanDNA-b6424/result_gtdb.tsv
[2023-03-16 17:04:23,874] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:04:23,875] [INFO] DFAST_QC result json was written to OceanDNA-b6424/dqc_result.json
[2023-03-16 17:04:23,875] [INFO] DFAST_QC completed!
[2023-03-16 17:04:23,875] [INFO] Total running time: 0h1m15s