[2023-03-16 16:26:08,041] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:26:08,041] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:26:08,042] [INFO] DQC Reference Directory: /var/lib/cwl/stg285131e4-d4b2-44ae-b89f-2b47b46e1822/dqc_reference
[2023-03-16 16:26:09,226] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:26:09,226] [INFO] Task started: Prodigal
[2023-03-16 16:26:09,226] [INFO] Running command: cat /var/lib/cwl/stg643924f9-3c48-493f-9ebb-482c352b966e/OceanDNA-b7127.fa | prodigal -d OceanDNA-b7127/cds.fna -a OceanDNA-b7127/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:26:29,951] [INFO] Task succeeded: Prodigal
[2023-03-16 16:26:29,951] [INFO] Task started: HMMsearch
[2023-03-16 16:26:29,951] [INFO] Running command: hmmsearch --tblout OceanDNA-b7127/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg285131e4-d4b2-44ae-b89f-2b47b46e1822/dqc_reference/reference_markers.hmm OceanDNA-b7127/protein.faa > /dev/null
[2023-03-16 16:26:30,143] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:26:30,144] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg643924f9-3c48-493f-9ebb-482c352b966e/OceanDNA-b7127.fa]
[2023-03-16 16:26:30,165] [INFO] Query marker FASTA was written to OceanDNA-b7127/markers.fasta
[2023-03-16 16:26:30,167] [INFO] Task started: Blastn
[2023-03-16 16:26:30,167] [INFO] Running command: blastn -query OceanDNA-b7127/markers.fasta -db /var/lib/cwl/stg285131e4-d4b2-44ae-b89f-2b47b46e1822/dqc_reference/reference_markers.fasta -out OceanDNA-b7127/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:26:30,843] [INFO] Task succeeded: Blastn
[2023-03-16 16:26:30,844] [INFO] Selected 29 target genomes.
[2023-03-16 16:26:30,844] [INFO] Target genome list was writen to OceanDNA-b7127/target_genomes.txt
[2023-03-16 16:26:30,866] [INFO] Task started: fastANI
[2023-03-16 16:26:30,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg643924f9-3c48-493f-9ebb-482c352b966e/OceanDNA-b7127.fa --refList OceanDNA-b7127/target_genomes.txt --output OceanDNA-b7127/fastani_result.tsv --threads 1
[2023-03-16 16:26:48,951] [INFO] Task succeeded: fastANI
[2023-03-16 16:26:48,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg285131e4-d4b2-44ae-b89f-2b47b46e1822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:26:48,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg285131e4-d4b2-44ae-b89f-2b47b46e1822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:26:48,967] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:26:48,967] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:26:48,967] [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
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	76.695	56	702	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.6482	50	702	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	76.6375	55	702	95	below_threshold
Kordia zhangzhouensis	strain=MCCC 1A00726	GCA_001005305.1	1620405	1620405	type	True	76.4258	63	702	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	76.3934	54	702	95	below_threshold
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	76.2512	54	702	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	76.2512	54	702	95	below_threshold
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	76.2472	51	702	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	76.2471	66	702	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.196	52	702	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	76.1684	50	702	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	76.1383	53	702	95	below_threshold
Kordia aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	76.0723	67	702	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	75.7832	53	702	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:26:48,968] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7127/tc_result.tsv
[2023-03-16 16:26:48,968] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:26:48,968] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:26:48,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg285131e4-d4b2-44ae-b89f-2b47b46e1822/dqc_reference/checkm_data
[2023-03-16 16:26:48,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:26:49,004] [INFO] Task started: CheckM
[2023-03-16 16:26:49,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7127/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7127/checkm_input OceanDNA-b7127/checkm_result
[2023-03-16 16:27:48,453] [INFO] Task succeeded: CheckM
[2023-03-16 16:27:48,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.26%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:27:48,456] [INFO] ===== Completeness check finished =====
[2023-03-16 16:27:48,456] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:27:48,457] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7127/markers.fasta)
[2023-03-16 16:27:48,458] [INFO] Task started: Blastn
[2023-03-16 16:27:48,458] [INFO] Running command: blastn -query OceanDNA-b7127/markers.fasta -db /var/lib/cwl/stg285131e4-d4b2-44ae-b89f-2b47b46e1822/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7127/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:27:51,135] [INFO] Task succeeded: Blastn
[2023-03-16 16:27:51,136] [INFO] Selected 28 target genomes.
[2023-03-16 16:27:51,136] [INFO] Target genome list was writen to OceanDNA-b7127/target_genomes_gtdb.txt
[2023-03-16 16:27:51,751] [INFO] Task started: fastANI
[2023-03-16 16:27:51,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg643924f9-3c48-493f-9ebb-482c352b966e/OceanDNA-b7127.fa --refList OceanDNA-b7127/target_genomes_gtdb.txt --output OceanDNA-b7127/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:28:13,277] [INFO] Task succeeded: fastANI
[2023-03-16 16:28:13,288] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:28:13,289] [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_013214425.1	s__DT-35 sp013214425	99.7363	647	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-35	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018860825.1	s__Oceanihabitans sp018860825	77.0456	60	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	76.7667	61	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	76.7214	52	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005315.1	s__Kordia jejudonensis	76.695	56	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944795.1	s__Mangrovimonas spongiae	76.6686	50	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	76.5439	53	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	76.5243	57	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCA_009901575.1	s__Leptobacterium sp009901575	76.4803	63	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154725.1	s__Kordia algicida	76.4705	56	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202195.1	s__Oceanihabitans iliipiscarium	76.4608	53	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005305.1	s__Kordia zhangzhouensis	76.4572	64	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869935.1	s__Winogradskyella algicola	76.3621	51	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	76.2557	54	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	76.2277	67	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007489275.1	s__Aquimarina algiphila	76.1957	62	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.78	98.78	0.88	0.88	2	-
GCF_009901525.1	s__Kordia antarctica	76.1932	55	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114005.1	s__Olleya namhaensis	76.1809	54	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCF_014397005.1	s__Kordia aestuariivivens	76.1331	68	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	75.9364	50	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033385.1	s__Algibacter pacificus	75.8254	56	702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:28:13,289] [INFO] GTDB search result was written to OceanDNA-b7127/result_gtdb.tsv
[2023-03-16 16:28:13,289] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:28:13,291] [INFO] DFAST_QC result json was written to OceanDNA-b7127/dqc_result.json
[2023-03-16 16:28:13,291] [INFO] DFAST_QC completed!
[2023-03-16 16:28:13,291] [INFO] Total running time: 0h2m5s