[2023-03-18 03:27:00,923] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,945] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,945] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbda17b2-eba9-4d11-9518-845096e97b88/dqc_reference
[2023-03-18 03:27:02,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,637] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,637] [INFO] Running command: cat /var/lib/cwl/stg820310b1-09d9-45d8-8b74-4ad19abefccb/OceanDNA-b35038.fa | prodigal -d OceanDNA-b35038/cds.fna -a OceanDNA-b35038/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:23,989] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:23,990] [INFO] Task started: HMMsearch
[2023-03-18 03:27:23,990] [INFO] Running command: hmmsearch --tblout OceanDNA-b35038/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbda17b2-eba9-4d11-9518-845096e97b88/dqc_reference/reference_markers.hmm OceanDNA-b35038/protein.faa > /dev/null
[2023-03-18 03:27:24,215] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:24,216] [INFO] Found 6/6 markers.
[2023-03-18 03:27:24,240] [INFO] Query marker FASTA was written to OceanDNA-b35038/markers.fasta
[2023-03-18 03:27:24,240] [INFO] Task started: Blastn
[2023-03-18 03:27:24,240] [INFO] Running command: blastn -query OceanDNA-b35038/markers.fasta -db /var/lib/cwl/stgdbda17b2-eba9-4d11-9518-845096e97b88/dqc_reference/reference_markers.fasta -out OceanDNA-b35038/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:24,904] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:24,904] [INFO] Selected 15 target genomes.
[2023-03-18 03:27:24,905] [INFO] Target genome list was writen to OceanDNA-b35038/target_genomes.txt
[2023-03-18 03:27:24,914] [INFO] Task started: fastANI
[2023-03-18 03:27:24,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg820310b1-09d9-45d8-8b74-4ad19abefccb/OceanDNA-b35038.fa --refList OceanDNA-b35038/target_genomes.txt --output OceanDNA-b35038/fastani_result.tsv --threads 1
[2023-03-18 03:27:37,385] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:37,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbda17b2-eba9-4d11-9518-845096e97b88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:37,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbda17b2-eba9-4d11-9518-845096e97b88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:37,394] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 03:27:37,394] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 03:27:37,394] [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 marina	strain=DSM 17587	GCA_000238335.4	267375	267375	type	True	97.8381	1265	1338	95	conclusive
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	84.2876	970	1338	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	84.2156	938	1338	95	below_threshold
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	84.2141	982	1338	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	83.2814	893	1338	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	82.8879	970	1338	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	82.6847	887	1338	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	81.5942	734	1338	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	81.3458	764	1338	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	81.3232	731	1338	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	81.2952	754	1338	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	76.3593	71	1338	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	76.3563	54	1338	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:27:37,394] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35038/tc_result.tsv
[2023-03-18 03:27:37,394] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:37,394] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:37,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbda17b2-eba9-4d11-9518-845096e97b88/dqc_reference/checkm_data
[2023-03-18 03:27:37,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:37,400] [INFO] Task started: CheckM
[2023-03-18 03:27:37,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35038/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35038/checkm_input OceanDNA-b35038/checkm_result
[2023-03-18 03:28:30,995] [INFO] Task succeeded: CheckM
[2023-03-18 03:28:30,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:28:30,998] [INFO] ===== Completeness check finished =====
[2023-03-18 03:28:30,998] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:28:30,998] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35038/markers.fasta)
[2023-03-18 03:28:30,998] [INFO] Task started: Blastn
[2023-03-18 03:28:30,998] [INFO] Running command: blastn -query OceanDNA-b35038/markers.fasta -db /var/lib/cwl/stgdbda17b2-eba9-4d11-9518-845096e97b88/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35038/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:32,011] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:32,011] [INFO] Selected 14 target genomes.
[2023-03-18 03:28:32,011] [INFO] Target genome list was writen to OceanDNA-b35038/target_genomes_gtdb.txt
[2023-03-18 03:28:32,023] [INFO] Task started: fastANI
[2023-03-18 03:28:32,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg820310b1-09d9-45d8-8b74-4ad19abefccb/OceanDNA-b35038.fa --refList OceanDNA-b35038/target_genomes_gtdb.txt --output OceanDNA-b35038/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:28:44,766] [INFO] Task succeeded: fastANI
[2023-03-18 03:28:44,775] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:28:44,775] [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_000238335.3	s__Pseudoalteromonas marina	97.8381	1265	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	97.57	0.91	0.88	12	conclusive
GCF_001468485.1	s__Pseudoalteromonas sp001468485	91.5076	1177	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.31	96.95	0.95	0.92	8	-
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	84.2181	982	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	83.5208	865	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	83.2244	932	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	82.7027	967	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	82.6864	887	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	82.637	909	1338	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	82.6176	902	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000238395.3	s__Pseudoalteromonas arctica	82.5427	929	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_004328665.1	s__Pseudoalteromonas sp001974855	81.6033	697	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
GCF_000238275.3	s__Pseudoalteromonas undina	81.5967	733	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	81.3462	763	1338	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	80.9045	708	1338	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 03:28:44,775] [INFO] GTDB search result was written to OceanDNA-b35038/result_gtdb.tsv
[2023-03-18 03:28:44,776] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:28:44,777] [INFO] DFAST_QC result json was written to OceanDNA-b35038/dqc_result.json
[2023-03-18 03:28:44,777] [INFO] DFAST_QC completed!
[2023-03-18 03:28:44,777] [INFO] Total running time: 0h1m44s