[2023-03-16 17:47:09,001] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:47:09,001] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:47:09,001] [INFO] DQC Reference Directory: /var/lib/cwl/stge65558bd-3d0a-41b9-94ee-b77a0afe6479/dqc_reference
[2023-03-16 17:47:10,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:47:10,102] [INFO] Task started: Prodigal
[2023-03-16 17:47:10,102] [INFO] Running command: cat /var/lib/cwl/stgae828ac6-a599-4aba-a79f-6c211c8a8cb3/OceanDNA-b6666.fa | prodigal -d OceanDNA-b6666/cds.fna -a OceanDNA-b6666/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:47:48,534] [INFO] Task succeeded: Prodigal
[2023-03-16 17:47:48,534] [INFO] Task started: HMMsearch
[2023-03-16 17:47:48,534] [INFO] Running command: hmmsearch --tblout OceanDNA-b6666/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge65558bd-3d0a-41b9-94ee-b77a0afe6479/dqc_reference/reference_markers.hmm OceanDNA-b6666/protein.faa > /dev/null
[2023-03-16 17:47:48,763] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:47:48,763] [INFO] Found 6/6 markers.
[2023-03-16 17:47:48,898] [INFO] Query marker FASTA was written to OceanDNA-b6666/markers.fasta
[2023-03-16 17:47:48,899] [INFO] Task started: Blastn
[2023-03-16 17:47:48,899] [INFO] Running command: blastn -query OceanDNA-b6666/markers.fasta -db /var/lib/cwl/stge65558bd-3d0a-41b9-94ee-b77a0afe6479/dqc_reference/reference_markers.fasta -out OceanDNA-b6666/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:47:49,514] [INFO] Task succeeded: Blastn
[2023-03-16 17:47:49,515] [INFO] Selected 21 target genomes.
[2023-03-16 17:47:49,515] [INFO] Target genome list was writen to OceanDNA-b6666/target_genomes.txt
[2023-03-16 17:47:49,526] [INFO] Task started: fastANI
[2023-03-16 17:47:49,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgae828ac6-a599-4aba-a79f-6c211c8a8cb3/OceanDNA-b6666.fa --refList OceanDNA-b6666/target_genomes.txt --output OceanDNA-b6666/fastani_result.tsv --threads 1
[2023-03-16 17:48:04,832] [INFO] Task succeeded: fastANI
[2023-03-16 17:48:04,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge65558bd-3d0a-41b9-94ee-b77a0afe6479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:48:04,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge65558bd-3d0a-41b9-94ee-b77a0afe6479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:48:04,854] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:48:04,854] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:48:04,854] [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
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	79.277	566	1417	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	79.014	542	1417	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	78.8936	518	1417	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	77.1143	269	1417	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.9788	299	1417	95	below_threshold
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	76.9777	263	1417	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.9489	258	1417	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	76.8578	229	1417	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.6629	176	1417	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	76.5828	251	1417	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.2478	131	1417	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.1557	93	1417	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	76.1148	127	1417	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.1005	139	1417	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.0903	91	1417	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	76.0235	123	1417	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	76.0201	119	1417	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	76.0114	120	1417	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	75.8935	99	1417	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	75.567	90	1417	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	75.3263	66	1417	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:48:04,854] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6666/tc_result.tsv
[2023-03-16 17:48:04,871] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:48:04,871] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:48:04,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge65558bd-3d0a-41b9-94ee-b77a0afe6479/dqc_reference/checkm_data
[2023-03-16 17:48:04,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:48:04,886] [INFO] Task started: CheckM
[2023-03-16 17:48:04,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6666/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6666/checkm_input OceanDNA-b6666/checkm_result
[2023-03-16 17:49:21,830] [INFO] Task succeeded: CheckM
[2023-03-16 17:49:21,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:49:21,834] [INFO] ===== Completeness check finished =====
[2023-03-16 17:49:21,835] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:49:21,835] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6666/markers.fasta)
[2023-03-16 17:49:21,836] [INFO] Task started: Blastn
[2023-03-16 17:49:21,836] [INFO] Running command: blastn -query OceanDNA-b6666/markers.fasta -db /var/lib/cwl/stge65558bd-3d0a-41b9-94ee-b77a0afe6479/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6666/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:49:22,679] [INFO] Task succeeded: Blastn
[2023-03-16 17:49:22,681] [INFO] Selected 14 target genomes.
[2023-03-16 17:49:22,681] [INFO] Target genome list was writen to OceanDNA-b6666/target_genomes_gtdb.txt
[2023-03-16 17:49:22,724] [INFO] Task started: fastANI
[2023-03-16 17:49:22,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgae828ac6-a599-4aba-a79f-6c211c8a8cb3/OceanDNA-b6666.fa --refList OceanDNA-b6666/target_genomes_gtdb.txt --output OceanDNA-b6666/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:49:31,828] [INFO] Task succeeded: fastANI
[2023-03-16 17:49:31,837] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:49:31,838] [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_019021925.1	s__Cellulophaga sp019021925	79.3636	538	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	79.2669	567	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	79.017	541	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_900102165.1	s__Cellulophaga baltica	78.894	519	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_009797025.1	s__Cellulophaga sp009797025	78.811	556	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861125.1	s__Cellulophaga baltica_A	78.6502	479	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799565.1	s__Cellulophaga sp000799565	78.5128	463	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119145.1	s__Cellulophaga fucicola	77.0948	270	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	76.557	228	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009741275.1	s__Winogradskyella endarachnes	76.2418	130	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	75.9548	133	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195315.1	s__Lutibacter sp004195315	75.8082	72	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479615.1	s__Eudoraea sp905479615	75.771	84	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733285.1	s__Lutibacter sp002733285	75.6504	71	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	97.79	97.79	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-16 17:49:31,838] [INFO] GTDB search result was written to OceanDNA-b6666/result_gtdb.tsv
[2023-03-16 17:49:31,838] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:49:31,840] [INFO] DFAST_QC result json was written to OceanDNA-b6666/dqc_result.json
[2023-03-16 17:49:31,840] [INFO] DFAST_QC completed!
[2023-03-16 17:49:31,840] [INFO] Total running time: 0h2m23s