[2023-03-16 06:49:10,578] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:49:10,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:49:10,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e96784f-97fd-488d-93f8-49835e4f1240/dqc_reference
[2023-03-16 06:49:11,698] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:49:11,699] [INFO] Task started: Prodigal
[2023-03-16 06:49:11,699] [INFO] Running command: cat /var/lib/cwl/stgbc7e69a1-1ddd-4468-806c-6fa86463a560/OceanDNA-b6426.fa | prodigal -d OceanDNA-b6426/cds.fna -a OceanDNA-b6426/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:49:35,015] [INFO] Task succeeded: Prodigal
[2023-03-16 06:49:35,015] [INFO] Task started: HMMsearch
[2023-03-16 06:49:35,015] [INFO] Running command: hmmsearch --tblout OceanDNA-b6426/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e96784f-97fd-488d-93f8-49835e4f1240/dqc_reference/reference_markers.hmm OceanDNA-b6426/protein.faa > /dev/null
[2023-03-16 06:49:35,247] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:49:35,248] [INFO] Found 6/6 markers.
[2023-03-16 06:49:35,269] [INFO] Query marker FASTA was written to OceanDNA-b6426/markers.fasta
[2023-03-16 06:49:35,270] [INFO] Task started: Blastn
[2023-03-16 06:49:35,270] [INFO] Running command: blastn -query OceanDNA-b6426/markers.fasta -db /var/lib/cwl/stg3e96784f-97fd-488d-93f8-49835e4f1240/dqc_reference/reference_markers.fasta -out OceanDNA-b6426/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:49:35,963] [INFO] Task succeeded: Blastn
[2023-03-16 06:49:35,965] [INFO] Selected 11 target genomes.
[2023-03-16 06:49:35,965] [INFO] Target genome list was writen to OceanDNA-b6426/target_genomes.txt
[2023-03-16 06:49:35,983] [INFO] Task started: fastANI
[2023-03-16 06:49:35,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc7e69a1-1ddd-4468-806c-6fa86463a560/OceanDNA-b6426.fa --refList OceanDNA-b6426/target_genomes.txt --output OceanDNA-b6426/fastani_result.tsv --threads 1
[2023-03-16 06:49:43,660] [INFO] Task succeeded: fastANI
[2023-03-16 06:49:43,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e96784f-97fd-488d-93f8-49835e4f1240/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:49:43,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e96784f-97fd-488d-93f8-49835e4f1240/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:49:43,718] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:49:43,718] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:49:43,719] [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	86.7885	841	1059	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	81.6123	747	1059	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	81.5281	646	1059	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	81.2174	668	1059	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	81.1599	693	1059	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	80.835	616	1059	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	80.6065	657	1059	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.7321	137	1059	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.3252	61	1059	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.2831	63	1059	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	75.6889	58	1059	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:49:43,719] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6426/tc_result.tsv
[2023-03-16 06:49:43,720] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:49:43,720] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:49:43,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e96784f-97fd-488d-93f8-49835e4f1240/dqc_reference/checkm_data
[2023-03-16 06:49:43,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:49:44,025] [INFO] Task started: CheckM
[2023-03-16 06:49:44,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6426/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6426/checkm_input OceanDNA-b6426/checkm_result
[2023-03-16 06:50:46,926] [INFO] Task succeeded: CheckM
[2023-03-16 06:50:46,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:50:46,939] [INFO] ===== Completeness check finished =====
[2023-03-16 06:50:46,939] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:50:46,939] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6426/markers.fasta)
[2023-03-16 06:50:46,940] [INFO] Task started: Blastn
[2023-03-16 06:50:46,940] [INFO] Running command: blastn -query OceanDNA-b6426/markers.fasta -db /var/lib/cwl/stg3e96784f-97fd-488d-93f8-49835e4f1240/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6426/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:50:48,142] [INFO] Task succeeded: Blastn
[2023-03-16 06:50:48,145] [INFO] Selected 12 target genomes.
[2023-03-16 06:50:48,145] [INFO] Target genome list was writen to OceanDNA-b6426/target_genomes_gtdb.txt
[2023-03-16 06:50:48,186] [INFO] Task started: fastANI
[2023-03-16 06:50:48,186] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc7e69a1-1ddd-4468-806c-6fa86463a560/OceanDNA-b6426.fa --refList OceanDNA-b6426/target_genomes_gtdb.txt --output OceanDNA-b6426/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:50:56,855] [INFO] Task succeeded: fastANI
[2023-03-16 06:50:56,863] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:50:56,863] [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	86.7908	841	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCF_900489465.1	s__Aequorivita sp900489465	82.7327	781	1059	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	81.7275	695	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_007997155.1	s__Aequorivita antarctica	81.6076	747	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCF_016757735.1	s__Aequorivita sp016757735	81.5281	646	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001573155.1	s__Aequorivita aquimaris	81.2174	668	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997135.1	s__Aequorivita lipolytica	81.1594	693	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002733915.1	s__Aequorivita sp002733915	81.0321	636	1059	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	80.8653	639	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	80.8349	616	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCA_002715485.1	s__Aequorivita sp002715485	80.7581	620	1059	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	80.6093	657	1059	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 06:50:56,865] [INFO] GTDB search result was written to OceanDNA-b6426/result_gtdb.tsv
[2023-03-16 06:50:56,866] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:50:56,868] [INFO] DFAST_QC result json was written to OceanDNA-b6426/dqc_result.json
[2023-03-16 06:50:56,868] [INFO] DFAST_QC completed!
[2023-03-16 06:50:56,868] [INFO] Total running time: 0h1m46s