[2023-03-18 04:16:54,162] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:54,162] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:54,163] [INFO] DQC Reference Directory: /var/lib/cwl/stg4518fb45-8234-49d2-8db3-a7e635741b4d/dqc_reference
[2023-03-18 04:16:55,826] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:55,826] [INFO] Task started: Prodigal
[2023-03-18 04:16:55,826] [INFO] Running command: cat /var/lib/cwl/stgfc986037-428b-4c5d-b11f-245f79dc356a/OceanDNA-b35104.fa | prodigal -d OceanDNA-b35104/cds.fna -a OceanDNA-b35104/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:02,345] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:02,346] [INFO] Task started: HMMsearch
[2023-03-18 04:17:02,346] [INFO] Running command: hmmsearch --tblout OceanDNA-b35104/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4518fb45-8234-49d2-8db3-a7e635741b4d/dqc_reference/reference_markers.hmm OceanDNA-b35104/protein.faa > /dev/null
[2023-03-18 04:17:02,523] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:02,524] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfc986037-428b-4c5d-b11f-245f79dc356a/OceanDNA-b35104.fa]
[2023-03-18 04:17:02,543] [INFO] Query marker FASTA was written to OceanDNA-b35104/markers.fasta
[2023-03-18 04:17:02,543] [INFO] Task started: Blastn
[2023-03-18 04:17:02,543] [INFO] Running command: blastn -query OceanDNA-b35104/markers.fasta -db /var/lib/cwl/stg4518fb45-8234-49d2-8db3-a7e635741b4d/dqc_reference/reference_markers.fasta -out OceanDNA-b35104/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:03,073] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:03,074] [INFO] Selected 14 target genomes.
[2023-03-18 04:17:03,074] [INFO] Target genome list was writen to OceanDNA-b35104/target_genomes.txt
[2023-03-18 04:17:03,110] [INFO] Task started: fastANI
[2023-03-18 04:17:03,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc986037-428b-4c5d-b11f-245f79dc356a/OceanDNA-b35104.fa --refList OceanDNA-b35104/target_genomes.txt --output OceanDNA-b35104/fastani_result.tsv --threads 1
[2023-03-18 04:17:11,588] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:11,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4518fb45-8234-49d2-8db3-a7e635741b4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:11,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4518fb45-8234-49d2-8db3-a7e635741b4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:11,597] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 04:17:11,597] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 04:17:11,598] [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
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	97.9912	184	188	95	conclusive
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	90.7955	187	188	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	90.7522	187	188	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	90.5875	184	188	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	90.5847	183	188	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	80.2651	132	188	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	80.1833	137	188	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	80.0651	138	188	95	below_threshold
Pseudoalteromonas aliena	strain=SW19	GCA_014905615.1	247523	247523	type	True	79.9829	130	188	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	79.2044	104	188	95	below_threshold
Pseudoalteromonas prydzensis	strain=ACAM 620	GCA_014925355.1	182141	182141	type	True	79.08	99	188	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	79.0726	98	188	95	below_threshold
Pseudoalteromonas ostreae	strain=hOe-66	GCA_018069805.1	2774154	2774154	type	True	78.939	96	188	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	78.3471	77	188	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:17:11,598] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35104/tc_result.tsv
[2023-03-18 04:17:11,598] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:11,598] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:11,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4518fb45-8234-49d2-8db3-a7e635741b4d/dqc_reference/checkm_data
[2023-03-18 04:17:11,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:11,603] [INFO] Task started: CheckM
[2023-03-18 04:17:11,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35104/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35104/checkm_input OceanDNA-b35104/checkm_result
[2023-03-18 04:17:34,172] [INFO] Task succeeded: CheckM
[2023-03-18 04:17:34,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:17:34,375] [INFO] ===== Completeness check finished =====
[2023-03-18 04:17:34,375] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:17:34,376] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35104/markers.fasta)
[2023-03-18 04:17:34,377] [INFO] Task started: Blastn
[2023-03-18 04:17:34,377] [INFO] Running command: blastn -query OceanDNA-b35104/markers.fasta -db /var/lib/cwl/stg4518fb45-8234-49d2-8db3-a7e635741b4d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35104/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:35,063] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:35,065] [INFO] Selected 18 target genomes.
[2023-03-18 04:17:35,065] [INFO] Target genome list was writen to OceanDNA-b35104/target_genomes_gtdb.txt
[2023-03-18 04:17:35,383] [INFO] Task started: fastANI
[2023-03-18 04:17:35,384] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc986037-428b-4c5d-b11f-245f79dc356a/OceanDNA-b35104.fa --refList OceanDNA-b35104/target_genomes_gtdb.txt --output OceanDNA-b35104/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:17:46,874] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:46,885] [INFO] Found 18 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 04:17:46,885] [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_000238275.3	s__Pseudoalteromonas undina	97.9912	184	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	inconclusive
GCF_004328665.1	s__Pseudoalteromonas sp001974855	95.4771	173	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	inconclusive
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	90.7955	187	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
GCA_018402495.1	s__Pseudoalteromonas sp018402495	88.4376	173	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	80.7069	126	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	80.5562	133	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	80.536	131	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	80.396	128	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	80.3858	134	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_000238395.3	s__Pseudoalteromonas arctica	80.2651	132	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCA_000814675.1	s__Pseudoalteromonas distincta	80.1833	137	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	80.0651	138	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_014905615.1	s__Pseudoalteromonas aliena	79.9829	130	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.51	97.10	0.91	0.88	7	-
GCF_902498845.1	s__Pseudoalteromonas rhizosphaerae	79.2044	104	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.81	97.24	0.86	0.81	17	-
GCF_018069805.1	s__Pseudoalteromonas sp018069805	78.939	96	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469215.1	s__Pseudoalteromonas sp001469215	78.883	86	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723455.1	s__Pseudoalteromonas sp002723455	78.8603	81	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.50	98.50	0.93	0.93	2	-
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	78.4722	100	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:17:46,885] [INFO] GTDB search result was written to OceanDNA-b35104/result_gtdb.tsv
[2023-03-18 04:17:46,885] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:17:46,887] [INFO] DFAST_QC result json was written to OceanDNA-b35104/dqc_result.json
[2023-03-18 04:17:46,887] [INFO] DFAST_QC completed!
[2023-03-18 04:17:46,887] [INFO] Total running time: 0h0m53s