[2023-03-18 04:34:51,153] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:34:51,154] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:34:51,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d682ead-25fc-49aa-87ce-7419aaf54c09/dqc_reference
[2023-03-18 04:34:52,261] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:34:52,262] [INFO] Task started: Prodigal
[2023-03-18 04:34:52,262] [INFO] Running command: cat /var/lib/cwl/stg8708fc6f-6c02-4840-b204-4e3958f4eccb/OceanDNA-b10444.fa | prodigal -d OceanDNA-b10444/cds.fna -a OceanDNA-b10444/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:35:02,919] [INFO] Task succeeded: Prodigal
[2023-03-18 04:35:02,919] [INFO] Task started: HMMsearch
[2023-03-18 04:35:02,919] [INFO] Running command: hmmsearch --tblout OceanDNA-b10444/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d682ead-25fc-49aa-87ce-7419aaf54c09/dqc_reference/reference_markers.hmm OceanDNA-b10444/protein.faa > /dev/null
[2023-03-18 04:35:03,132] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:35:03,132] [INFO] Found 6/6 markers.
[2023-03-18 04:35:03,151] [INFO] Query marker FASTA was written to OceanDNA-b10444/markers.fasta
[2023-03-18 04:35:03,152] [INFO] Task started: Blastn
[2023-03-18 04:35:03,152] [INFO] Running command: blastn -query OceanDNA-b10444/markers.fasta -db /var/lib/cwl/stg7d682ead-25fc-49aa-87ce-7419aaf54c09/dqc_reference/reference_markers.fasta -out OceanDNA-b10444/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:35:03,761] [INFO] Task succeeded: Blastn
[2023-03-18 04:35:03,766] [INFO] Selected 22 target genomes.
[2023-03-18 04:35:03,766] [INFO] Target genome list was writen to OceanDNA-b10444/target_genomes.txt
[2023-03-18 04:35:03,774] [INFO] Task started: fastANI
[2023-03-18 04:35:03,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg8708fc6f-6c02-4840-b204-4e3958f4eccb/OceanDNA-b10444.fa --refList OceanDNA-b10444/target_genomes.txt --output OceanDNA-b10444/fastani_result.tsv --threads 1
[2023-03-18 04:35:15,463] [INFO] Task succeeded: fastANI
[2023-03-18 04:35:15,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d682ead-25fc-49aa-87ce-7419aaf54c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:35:15,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d682ead-25fc-49aa-87ce-7419aaf54c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:35:15,636] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 04:35:15,636] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 04:35:15,636] [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
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	96.6283	490	508	95	conclusive
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	79.2126	294	508	95	below_threshold
Tenacibaculum agarivorans	strain=HZ1	GCA_001936575.1	1908389	1908389	type	True	78.8141	273	508	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	78.2312	199	508	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	78.1957	182	508	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	78.1154	171	508	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	78.1126	191	508	95	below_threshold
Tenacibaculum gallaicum	strain=DSM 18841	GCA_003387615.1	561505	561505	type	True	77.9849	172	508	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_003867075.1	104268	104268	type	True	77.9632	164	508	95	below_threshold
Tenacibaculum adriaticum	strain=DSM 18961	GCA_008124875.1	413713	413713	type	True	77.9252	196	508	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	77.8788	169	508	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	77.8573	170	508	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	77.8552	177	508	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.709	161	508	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.3647	151	508	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	77.3067	150	508	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	77.29	151	508	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	77.2886	150	508	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	77.2591	153	508	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.1448	129	508	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.1072	127	508	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	75.5938	54	508	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:35:15,643] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10444/tc_result.tsv
[2023-03-18 04:35:15,648] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:35:15,648] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:35:15,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d682ead-25fc-49aa-87ce-7419aaf54c09/dqc_reference/checkm_data
[2023-03-18 04:35:15,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:35:15,656] [INFO] Task started: CheckM
[2023-03-18 04:35:15,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10444/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10444/checkm_input OceanDNA-b10444/checkm_result
[2023-03-18 04:35:49,097] [INFO] Task succeeded: CheckM
[2023-03-18 04:35:49,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:35:49,131] [INFO] ===== Completeness check finished =====
[2023-03-18 04:35:49,131] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:35:49,131] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10444/markers.fasta)
[2023-03-18 04:35:49,132] [INFO] Task started: Blastn
[2023-03-18 04:35:49,132] [INFO] Running command: blastn -query OceanDNA-b10444/markers.fasta -db /var/lib/cwl/stg7d682ead-25fc-49aa-87ce-7419aaf54c09/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10444/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:35:49,960] [INFO] Task succeeded: Blastn
[2023-03-18 04:35:49,969] [INFO] Selected 13 target genomes.
[2023-03-18 04:35:49,969] [INFO] Target genome list was writen to OceanDNA-b10444/target_genomes_gtdb.txt
[2023-03-18 04:35:49,988] [INFO] Task started: fastANI
[2023-03-18 04:35:49,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg8708fc6f-6c02-4840-b204-4e3958f4eccb/OceanDNA-b10444.fa --refList OceanDNA-b10444/target_genomes_gtdb.txt --output OceanDNA-b10444/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:35:58,298] [INFO] Task succeeded: fastANI
[2023-03-18 04:35:58,306] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:35:58,306] [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_004345825.1	s__Tenacibaculum skagerrakense	96.6283	490	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002813915.1	s__Tenacibaculum sp002813915	81.3379	378	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900198195.1	s__Tenacibaculum jejuense	79.2126	294	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001936575.1	s__Tenacibaculum agarivorans	78.8141	273	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337695.1	s__Tenacibaculum sp004337695	78.6989	256	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664185.1	s__Tenacibaculum discolor	78.2369	187	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	-
GCF_002120225.1	s__Tenacibaculum holothuriorum	78.2312	199	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806755.1	s__Tenacibaculum aiptasiae	78.0937	192	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003867075.1	s__Tenacibaculum mesophilum	77.9423	165	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
GCF_008124875.1	s__Tenacibaculum adriaticum	77.9252	196	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861005.1	s__Polaribacter vadi_A	77.2756	138	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	77.2418	154	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCA_000981625.1	s__Polaribacter sp000981625	76.9861	92	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:35:58,309] [INFO] GTDB search result was written to OceanDNA-b10444/result_gtdb.tsv
[2023-03-18 04:35:58,312] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:35:58,317] [INFO] DFAST_QC result json was written to OceanDNA-b10444/dqc_result.json
[2023-03-18 04:35:58,317] [INFO] DFAST_QC completed!
[2023-03-18 04:35:58,317] [INFO] Total running time: 0h1m7s