[2023-03-16 17:05:30,958] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:05:30,958] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:05:30,958] [INFO] DQC Reference Directory: /var/lib/cwl/stgc65776eb-511a-4093-92fa-05f2d6c1e445/dqc_reference
[2023-03-16 17:05:33,252] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:05:33,252] [INFO] Task started: Prodigal
[2023-03-16 17:05:33,252] [INFO] Running command: cat /var/lib/cwl/stg7ddb7dbb-fc29-477b-8ead-bb6f653a25d3/OceanDNA-b34951.fa | prodigal -d OceanDNA-b34951/cds.fna -a OceanDNA-b34951/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:05:52,030] [INFO] Task succeeded: Prodigal
[2023-03-16 17:05:52,030] [INFO] Task started: HMMsearch
[2023-03-16 17:05:52,030] [INFO] Running command: hmmsearch --tblout OceanDNA-b34951/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc65776eb-511a-4093-92fa-05f2d6c1e445/dqc_reference/reference_markers.hmm OceanDNA-b34951/protein.faa > /dev/null
[2023-03-16 17:05:52,228] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:05:52,229] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7ddb7dbb-fc29-477b-8ead-bb6f653a25d3/OceanDNA-b34951.fa]
[2023-03-16 17:05:52,252] [INFO] Query marker FASTA was written to OceanDNA-b34951/markers.fasta
[2023-03-16 17:05:52,254] [INFO] Task started: Blastn
[2023-03-16 17:05:52,254] [INFO] Running command: blastn -query OceanDNA-b34951/markers.fasta -db /var/lib/cwl/stgc65776eb-511a-4093-92fa-05f2d6c1e445/dqc_reference/reference_markers.fasta -out OceanDNA-b34951/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:05:52,773] [INFO] Task succeeded: Blastn
[2023-03-16 17:05:52,775] [INFO] Selected 19 target genomes.
[2023-03-16 17:05:52,775] [INFO] Target genome list was writen to OceanDNA-b34951/target_genomes.txt
[2023-03-16 17:05:52,843] [INFO] Task started: fastANI
[2023-03-16 17:05:52,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ddb7dbb-fc29-477b-8ead-bb6f653a25d3/OceanDNA-b34951.fa --refList OceanDNA-b34951/target_genomes.txt --output OceanDNA-b34951/fastani_result.tsv --threads 1
[2023-03-16 17:06:08,557] [INFO] Task succeeded: fastANI
[2023-03-16 17:06:08,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc65776eb-511a-4093-92fa-05f2d6c1e445/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:06:08,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc65776eb-511a-4093-92fa-05f2d6c1e445/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:06:08,566] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:06:08,567] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:06:08,567] [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 citrea	strain=DSM 8771	GCA_000238375.4	43655	43655	type	True	89.2849	651	687	95	below_threshold
Pseudoalteromonas aurantia	strain=208	GCA_014858725.1	43654	43654	type	True	82.4152	442	687	95	below_threshold
Pseudoalteromonas byunsanensis	strain=JCM 12483	GCA_001854475.1	327939	327939	type	True	78.4508	173	687	95	below_threshold
Pseudoalteromonas caenipelagi	strain=JBTF-M23	GCA_013140855.1	2726988	2726988	type	True	78.3511	195	687	95	below_threshold
Pseudoalteromonas amylolytica	strain=JW1	GCA_001854605.1	1859457	1859457	type	True	78.3498	179	687	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	77.4787	107	687	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	77.3449	109	687	95	below_threshold
Pseudoalteromonas aliena	strain=SW19	GCA_014905615.1	247523	247523	type	True	77.0646	106	687	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	76.8596	116	687	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	76.8584	121	687	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	76.8201	120	687	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	76.8019	122	687	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	76.7867	118	687	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	76.7758	117	687	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:06:08,567] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34951/tc_result.tsv
[2023-03-16 17:06:08,567] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:06:08,567] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:06:08,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc65776eb-511a-4093-92fa-05f2d6c1e445/dqc_reference/checkm_data
[2023-03-16 17:06:08,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:06:08,783] [INFO] Task started: CheckM
[2023-03-16 17:06:08,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34951/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34951/checkm_input OceanDNA-b34951/checkm_result
[2023-03-16 17:06:44,658] [INFO] Task succeeded: CheckM
[2023-03-16 17:06:44,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:06:44,662] [INFO] ===== Completeness check finished =====
[2023-03-16 17:06:44,662] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:06:44,663] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34951/markers.fasta)
[2023-03-16 17:06:44,664] [INFO] Task started: Blastn
[2023-03-16 17:06:44,664] [INFO] Running command: blastn -query OceanDNA-b34951/markers.fasta -db /var/lib/cwl/stgc65776eb-511a-4093-92fa-05f2d6c1e445/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34951/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:06:45,479] [INFO] Task succeeded: Blastn
[2023-03-16 17:06:45,480] [INFO] Selected 9 target genomes.
[2023-03-16 17:06:45,480] [INFO] Target genome list was writen to OceanDNA-b34951/target_genomes_gtdb.txt
[2023-03-16 17:06:45,518] [INFO] Task started: fastANI
[2023-03-16 17:06:45,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ddb7dbb-fc29-477b-8ead-bb6f653a25d3/OceanDNA-b34951.fa --refList OceanDNA-b34951/target_genomes_gtdb.txt --output OceanDNA-b34951/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:06:52,967] [INFO] Task succeeded: fastANI
[2023-03-16 17:06:52,973] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:06:52,974] [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_003590335.1	s__Pseudoalteromonas sp003590335	97.5538	674	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.57	97.56	0.90	0.89	3	conclusive
GCF_005886875.1	s__Pseudoalteromonas aurantia_A	94.822	635	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.47	99.41	0.94	0.93	3	-
GCF_000238375.3	s__Pseudoalteromonas citrea	89.2849	651	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014858725.1	s__Pseudoalteromonas aurantia	82.4158	442	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.50	97.26	0.90	0.89	4	-
GCF_013140855.1	s__Pseudoalteromonas caenipelagi	78.3511	195	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014694405.1	s__Pseudoalteromonas sp014694405	78.125	189	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	76.8201	120	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
GCF_000238395.3	s__Pseudoalteromonas arctica	76.7663	119	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCA_018402495.1	s__Pseudoalteromonas sp018402495	76.6068	107	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:06:52,974] [INFO] GTDB search result was written to OceanDNA-b34951/result_gtdb.tsv
[2023-03-16 17:06:52,974] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:06:52,976] [INFO] DFAST_QC result json was written to OceanDNA-b34951/dqc_result.json
[2023-03-16 17:06:52,976] [INFO] DFAST_QC completed!
[2023-03-16 17:06:52,976] [INFO] Total running time: 0h1m22s