[2023-03-15 23:07:02,632] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,632] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cd9fb2b-4348-4794-9e58-babfde676b7b/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,966] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,967] [INFO] Running command: cat /var/lib/cwl/stg5827a50a-cdb1-496d-a032-45f44fa4341f/OceanDNA-b10441.fa | prodigal -d OceanDNA-b10441/cds.fna -a OceanDNA-b10441/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:13,074] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:13,075] [INFO] Task started: HMMsearch
[2023-03-15 23:07:13,075] [INFO] Running command: hmmsearch --tblout OceanDNA-b10441/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cd9fb2b-4348-4794-9e58-babfde676b7b/dqc_reference/reference_markers.hmm OceanDNA-b10441/protein.faa > /dev/null
[2023-03-15 23:07:13,245] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:13,246] [INFO] Found 6/6 markers.
[2023-03-15 23:07:13,262] [INFO] Query marker FASTA was written to OceanDNA-b10441/markers.fasta
[2023-03-15 23:07:13,263] [INFO] Task started: Blastn
[2023-03-15 23:07:13,264] [INFO] Running command: blastn -query OceanDNA-b10441/markers.fasta -db /var/lib/cwl/stg7cd9fb2b-4348-4794-9e58-babfde676b7b/dqc_reference/reference_markers.fasta -out OceanDNA-b10441/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:13,834] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:13,835] [INFO] Selected 23 target genomes.
[2023-03-15 23:07:13,835] [INFO] Target genome list was writen to OceanDNA-b10441/target_genomes.txt
[2023-03-15 23:07:13,891] [INFO] Task started: fastANI
[2023-03-15 23:07:13,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg5827a50a-cdb1-496d-a032-45f44fa4341f/OceanDNA-b10441.fa --refList OceanDNA-b10441/target_genomes.txt --output OceanDNA-b10441/fastani_result.tsv --threads 1
[2023-03-15 23:07:25,030] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:25,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cd9fb2b-4348-4794-9e58-babfde676b7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:25,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cd9fb2b-4348-4794-9e58-babfde676b7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:25,043] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:07:25,043] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:07:25,044] [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 aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	77.1763	110	426	95	below_threshold
Tenacibaculum gallaicum	strain=DSM 18841	GCA_003387615.1	561505	561505	type	True	77.1589	105	426	95	below_threshold
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	77.1358	106	426	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	77.1083	110	426	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	77.0809	95	426	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	77.0777	109	426	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_003867075.1	104268	104268	type	True	77.0772	108	426	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	77.0722	109	426	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	77.0285	92	426	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	76.8331	94	426	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	76.8068	114	426	95	below_threshold
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	76.6789	82	426	95	below_threshold
Tenacibaculum agarivorans	strain=HZ1	GCA_001936575.1	1908389	1908389	type	True	76.6439	85	426	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	76.6061	59	426	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	76.5665	74	426	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	76.4278	74	426	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	76.2854	72	426	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.0843	66	426	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	76.0609	67	426	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	76.0609	67	426	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	75.9405	72	426	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	75.871	62	426	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:07:25,044] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10441/tc_result.tsv
[2023-03-15 23:07:25,044] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:25,044] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:25,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cd9fb2b-4348-4794-9e58-babfde676b7b/dqc_reference/checkm_data
[2023-03-15 23:07:25,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:25,048] [INFO] Task started: CheckM
[2023-03-15 23:07:25,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10441/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10441/checkm_input OceanDNA-b10441/checkm_result
[2023-03-15 23:07:53,314] [INFO] Task succeeded: CheckM
[2023-03-15 23:07:53,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:07:53,374] [INFO] ===== Completeness check finished =====
[2023-03-15 23:07:53,375] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:07:53,375] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10441/markers.fasta)
[2023-03-15 23:07:53,376] [INFO] Task started: Blastn
[2023-03-15 23:07:53,376] [INFO] Running command: blastn -query OceanDNA-b10441/markers.fasta -db /var/lib/cwl/stg7cd9fb2b-4348-4794-9e58-babfde676b7b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10441/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:54,217] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:54,218] [INFO] Selected 22 target genomes.
[2023-03-15 23:07:54,218] [INFO] Target genome list was writen to OceanDNA-b10441/target_genomes_gtdb.txt
[2023-03-15 23:07:54,234] [INFO] Task started: fastANI
[2023-03-15 23:07:54,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg5827a50a-cdb1-496d-a032-45f44fa4341f/OceanDNA-b10441.fa --refList OceanDNA-b10441/target_genomes_gtdb.txt --output OceanDNA-b10441/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:08:06,538] [INFO] Task succeeded: fastANI
[2023-03-15 23:08:06,550] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:08:06,550] [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_900105455.1	s__Tenacibaculum sp900105455	78.7104	201	426	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	77.5693	92	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	-
GCF_008806755.1	s__Tenacibaculum aiptasiae	77.1763	110	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387615.1	s__Tenacibaculum gallaicum	77.1589	105	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610735.1	s__Tenacibaculum lutimaris	77.1358	106	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCF_004363005.1	s__Tenacibaculum caenipelagi	77.0809	95	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003867015.1	s__Tenacibaculum singaporense	77.0777	109	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
GCF_003867075.1	s__Tenacibaculum mesophilum	77.0772	108	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
GCF_900105985.1	s__Tenacibaculum sp900105985	77.0584	139	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_014062345.1	s__Tenacibaculum pelagium	77.0285	92	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002120225.1	s__Tenacibaculum holothuriorum	76.8071	95	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	76.8068	114	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_900198195.1	s__Tenacibaculum jejuense	76.6789	82	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693415.1	s__Tenacibaculum soleae	76.6558	99	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	76.6061	59	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152945.2	s__Polaribacter sp000152945	76.5214	55	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	76.3606	68	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345825.1	s__Tenacibaculum skagerrakense	76.2854	72	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	76.2444	76	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	76.1482	65	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_018861005.1	s__Polaribacter vadi_A	75.8947	80	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:08:06,555] [INFO] GTDB search result was written to OceanDNA-b10441/result_gtdb.tsv
[2023-03-15 23:08:06,561] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:08:06,566] [INFO] DFAST_QC result json was written to OceanDNA-b10441/dqc_result.json
[2023-03-15 23:08:06,566] [INFO] DFAST_QC completed!
[2023-03-15 23:08:06,566] [INFO] Total running time: 0h1m4s