[2023-03-19 01:33:26,239] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:33:26,240] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:33:26,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e415da4-9ef3-4f74-835c-b5c524130e49/dqc_reference
[2023-03-19 01:33:27,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:33:27,382] [INFO] Task started: Prodigal
[2023-03-19 01:33:27,382] [INFO] Running command: cat /var/lib/cwl/stg7d17ea7e-f606-4bf8-8cc0-151b4616ced2/OceanDNA-b6657.fa | prodigal -d OceanDNA-b6657/cds.fna -a OceanDNA-b6657/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:33:45,245] [INFO] Task succeeded: Prodigal
[2023-03-19 01:33:45,246] [INFO] Task started: HMMsearch
[2023-03-19 01:33:45,246] [INFO] Running command: hmmsearch --tblout OceanDNA-b6657/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e415da4-9ef3-4f74-835c-b5c524130e49/dqc_reference/reference_markers.hmm OceanDNA-b6657/protein.faa > /dev/null
[2023-03-19 01:33:45,444] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:33:45,444] [INFO] Found 6/6 markers.
[2023-03-19 01:33:45,460] [INFO] Query marker FASTA was written to OceanDNA-b6657/markers.fasta
[2023-03-19 01:33:45,461] [INFO] Task started: Blastn
[2023-03-19 01:33:45,461] [INFO] Running command: blastn -query OceanDNA-b6657/markers.fasta -db /var/lib/cwl/stg7e415da4-9ef3-4f74-835c-b5c524130e49/dqc_reference/reference_markers.fasta -out OceanDNA-b6657/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:33:46,052] [INFO] Task succeeded: Blastn
[2023-03-19 01:33:46,053] [INFO] Selected 27 target genomes.
[2023-03-19 01:33:46,053] [INFO] Target genome list was writen to OceanDNA-b6657/target_genomes.txt
[2023-03-19 01:33:46,070] [INFO] Task started: fastANI
[2023-03-19 01:33:46,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d17ea7e-f606-4bf8-8cc0-151b4616ced2/OceanDNA-b6657.fa --refList OceanDNA-b6657/target_genomes.txt --output OceanDNA-b6657/fastani_result.tsv --threads 1
[2023-03-19 01:34:00,500] [INFO] Task succeeded: fastANI
[2023-03-19 01:34:00,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e415da4-9ef3-4f74-835c-b5c524130e49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:34:00,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e415da4-9ef3-4f74-835c-b5c524130e49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:34:00,507] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:34:00,507] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:34:00,507] [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
Planktosalinus lacus	strain=CGMCC 1.12924	GCA_014640155.1	1526573	1526573	type	True	79.9434	358	835	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	76.1957	62	835	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.1085	71	835	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.1085	71	835	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	75.9555	50	835	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	75.9156	57	835	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	75.898	65	835	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	75.3904	59	835	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	75.3639	50	835	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:34:00,508] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6657/tc_result.tsv
[2023-03-19 01:34:00,508] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:34:00,508] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:34:00,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e415da4-9ef3-4f74-835c-b5c524130e49/dqc_reference/checkm_data
[2023-03-19 01:34:00,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:34:00,512] [INFO] Task started: CheckM
[2023-03-19 01:34:00,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6657/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6657/checkm_input OceanDNA-b6657/checkm_result
[2023-03-19 01:34:48,185] [INFO] Task succeeded: CheckM
[2023-03-19 01:34:48,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:34:48,229] [INFO] ===== Completeness check finished =====
[2023-03-19 01:34:48,229] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:34:48,229] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6657/markers.fasta)
[2023-03-19 01:34:48,230] [INFO] Task started: Blastn
[2023-03-19 01:34:48,230] [INFO] Running command: blastn -query OceanDNA-b6657/markers.fasta -db /var/lib/cwl/stg7e415da4-9ef3-4f74-835c-b5c524130e49/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6657/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:34:49,064] [INFO] Task succeeded: Blastn
[2023-03-19 01:34:49,066] [INFO] Selected 20 target genomes.
[2023-03-19 01:34:49,066] [INFO] Target genome list was writen to OceanDNA-b6657/target_genomes_gtdb.txt
[2023-03-19 01:34:49,082] [INFO] Task started: fastANI
[2023-03-19 01:34:49,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d17ea7e-f606-4bf8-8cc0-151b4616ced2/OceanDNA-b6657.fa --refList OceanDNA-b6657/target_genomes_gtdb.txt --output OceanDNA-b6657/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:35:00,528] [INFO] Task succeeded: fastANI
[2023-03-19 01:35:00,536] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:35:00,536] [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_018402385.1	s__Planktosalinus sp018402385	89.4775	619	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640155.1	s__Planktosalinus lacus	79.9434	358	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842575.1	s__Planktosalinus sp002842575	77.4824	182	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360635.1	s__Marixanthomonas sp002360635	76.3715	73	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCA_002375695.1	s__Aequorivita sp002375695	76.1293	60	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016649715.1	s__Aequorivita sp016649715	76.0406	60	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	75.9483	53	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016469035.1	s__Gelidibacter salicanalis_A	75.6346	57	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222875.1	s__Psychroserpens sp018222875	75.59	58	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	75.5726	61	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	75.519	54	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:35:00,537] [INFO] GTDB search result was written to OceanDNA-b6657/result_gtdb.tsv
[2023-03-19 01:35:00,538] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:35:00,539] [INFO] DFAST_QC result json was written to OceanDNA-b6657/dqc_result.json
[2023-03-19 01:35:00,540] [INFO] DFAST_QC completed!
[2023-03-19 01:35:00,540] [INFO] Total running time: 0h1m34s