[2023-03-19 02:34:18,438] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:34:18,438] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:34:18,438] [INFO] DQC Reference Directory: /var/lib/cwl/stgd77acd54-3b63-456f-8ea7-0e7f0906de9f/dqc_reference
[2023-03-19 02:34:19,578] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:34:19,578] [INFO] Task started: Prodigal
[2023-03-19 02:34:19,578] [INFO] Running command: cat /var/lib/cwl/stg0f1ce655-7e3e-4ec4-9dc9-0f97b10a3059/OceanDNA-b35232.fa | prodigal -d OceanDNA-b35232/cds.fna -a OceanDNA-b35232/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:34:35,190] [INFO] Task succeeded: Prodigal
[2023-03-19 02:34:35,190] [INFO] Task started: HMMsearch
[2023-03-19 02:34:35,190] [INFO] Running command: hmmsearch --tblout OceanDNA-b35232/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd77acd54-3b63-456f-8ea7-0e7f0906de9f/dqc_reference/reference_markers.hmm OceanDNA-b35232/protein.faa > /dev/null
[2023-03-19 02:34:35,389] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:34:35,390] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0f1ce655-7e3e-4ec4-9dc9-0f97b10a3059/OceanDNA-b35232.fa]
[2023-03-19 02:34:35,412] [INFO] Query marker FASTA was written to OceanDNA-b35232/markers.fasta
[2023-03-19 02:34:35,413] [INFO] Task started: Blastn
[2023-03-19 02:34:35,413] [INFO] Running command: blastn -query OceanDNA-b35232/markers.fasta -db /var/lib/cwl/stgd77acd54-3b63-456f-8ea7-0e7f0906de9f/dqc_reference/reference_markers.fasta -out OceanDNA-b35232/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:34:35,977] [INFO] Task succeeded: Blastn
[2023-03-19 02:34:35,978] [INFO] Selected 20 target genomes.
[2023-03-19 02:34:35,978] [INFO] Target genome list was writen to OceanDNA-b35232/target_genomes.txt
[2023-03-19 02:34:35,987] [INFO] Task started: fastANI
[2023-03-19 02:34:35,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f1ce655-7e3e-4ec4-9dc9-0f97b10a3059/OceanDNA-b35232.fa --refList OceanDNA-b35232/target_genomes.txt --output OceanDNA-b35232/fastani_result.tsv --threads 1
[2023-03-19 02:34:50,678] [INFO] Task succeeded: fastANI
[2023-03-19 02:34:50,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd77acd54-3b63-456f-8ea7-0e7f0906de9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:34:50,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd77acd54-3b63-456f-8ea7-0e7f0906de9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:34:50,690] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:34:50,690] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:34:50,690] [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
Shewanella colwelliana	strain=ATCC 39565	GCA_000518705.1	23	23	type	True	81.055	542	967	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_019655175.1	614070	614070	type	True	80.6518	495	967	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_003605125.1	614070	614070	type	True	80.5658	505	967	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	79.882	414	967	95	below_threshold
Shewanella loihica	strain=PV-4	GCA_000016065.1	359303	359303	type	True	79.5705	374	967	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	79.3904	374	967	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	79.1266	379	967	95	below_threshold
Shewanella piezotolerans	strain=WP3	GCA_000014885.1	404011	404011	type	True	78.2094	210	967	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	78.0878	246	967	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	78.0799	244	967	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	78.0576	225	967	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_019654995.1	190308	190308	type	True	78.0103	242	967	95	below_threshold
Shewanella kaireitica	strain=DSM 17170	GCA_023284045.1	212021	212021	type	True	77.9005	211	967	95	below_threshold
Shewanella halifaxensis	strain=HAW-EB4	GCA_000019185.1	271098	271098	type	True	77.8033	251	967	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	77.2913	169	967	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_014647215.1	1028752	1028752	type	True	77.2547	142	967	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	77.253	143	967	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	77.2051	158	967	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	77.1683	143	967	95	below_threshold
Shewanella surugensis	strain=DSM 17177	GCA_023284005.1	212020	212020	type	True	77.0934	114	967	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:34:50,690] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35232/tc_result.tsv
[2023-03-19 02:34:50,690] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:34:50,690] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:34:50,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd77acd54-3b63-456f-8ea7-0e7f0906de9f/dqc_reference/checkm_data
[2023-03-19 02:34:50,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:34:50,696] [INFO] Task started: CheckM
[2023-03-19 02:34:50,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35232/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35232/checkm_input OceanDNA-b35232/checkm_result
[2023-03-19 02:35:32,174] [INFO] Task succeeded: CheckM
[2023-03-19 02:35:32,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:35:32,191] [INFO] ===== Completeness check finished =====
[2023-03-19 02:35:32,191] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:35:32,191] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35232/markers.fasta)
[2023-03-19 02:35:32,192] [INFO] Task started: Blastn
[2023-03-19 02:35:32,192] [INFO] Running command: blastn -query OceanDNA-b35232/markers.fasta -db /var/lib/cwl/stgd77acd54-3b63-456f-8ea7-0e7f0906de9f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35232/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:35:33,014] [INFO] Task succeeded: Blastn
[2023-03-19 02:35:33,015] [INFO] Selected 19 target genomes.
[2023-03-19 02:35:33,015] [INFO] Target genome list was writen to OceanDNA-b35232/target_genomes_gtdb.txt
[2023-03-19 02:35:33,034] [INFO] Task started: fastANI
[2023-03-19 02:35:33,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f1ce655-7e3e-4ec4-9dc9-0f97b10a3059/OceanDNA-b35232.fa --refList OceanDNA-b35232/target_genomes_gtdb.txt --output OceanDNA-b35232/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:35:47,858] [INFO] Task succeeded: fastANI
[2023-03-19 02:35:47,869] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:35:47,869] [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_000518705.1	s__Shewanella colwelliana	81.0504	542	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.91	98.91	0.92	0.92	2	-
GCF_003605125.1	s__Shewanella algidipiscicola	80.5749	503	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
GCF_002215585.1	s__Shewanella marisflavi	79.9012	400	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.20	98.16	0.93	0.93	3	-
GCF_000016065.1	s__Shewanella loihica	79.5705	374	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_000832025.1	s__Shewanella sp000832025	79.4059	367	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831655.1	s__Shewanella insulae	79.3829	375	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014885.1	s__Shewanella piezotolerans	78.1925	211	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765635.1	s__Shewanella schlegeliana	78.1233	246	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757755.1	s__Shewanella sp016757755	78.0342	207	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518605.1	s__Shewanella fidelis	78.0077	215	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_015069875.1	s__Shewanella benthica	77.9909	158	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.81	96.81	0.66	0.66	2	-
GCF_000019185.1	s__Shewanella halifaxensis	77.8332	248	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018285.1	s__Shewanella pealeana	77.7881	239	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002966515.1	s__Shewanella sp002966515	77.6696	192	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCF_000217915.1	s__Shewanella sp000217915	77.435	169	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648035.1	s__Shewanella algicola	77.3036	145	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_002873615.1	s__Shewanella sp002873615	77.2859	136	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647215.1	s__Shewanella aestuarii	77.2547	142	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828585.1	s__Shewanella litoralis	77.2235	159	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:35:47,871] [INFO] GTDB search result was written to OceanDNA-b35232/result_gtdb.tsv
[2023-03-19 02:35:47,873] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:35:47,877] [INFO] DFAST_QC result json was written to OceanDNA-b35232/dqc_result.json
[2023-03-19 02:35:47,877] [INFO] DFAST_QC completed!
[2023-03-19 02:35:47,878] [INFO] Total running time: 0h1m29s