[2023-03-14 11:33:35,046] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:35,046] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:35,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg66cca7e6-3294-4b2c-9ffd-9443f8de6fa5/dqc_reference
[2023-03-14 11:33:36,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,195] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,195] [INFO] Running command: cat /var/lib/cwl/stg072406c7-f850-4d24-a811-78ebbda88633/OceanDNA-b35065.fa | prodigal -d OceanDNA-b35065/cds.fna -a OceanDNA-b35065/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:56,028] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:56,028] [INFO] Task started: HMMsearch
[2023-03-14 11:33:56,028] [INFO] Running command: hmmsearch --tblout OceanDNA-b35065/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66cca7e6-3294-4b2c-9ffd-9443f8de6fa5/dqc_reference/reference_markers.hmm OceanDNA-b35065/protein.faa > /dev/null
[2023-03-14 11:33:56,284] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:56,284] [INFO] Found 6/6 markers.
[2023-03-14 11:33:56,309] [INFO] Query marker FASTA was written to OceanDNA-b35065/markers.fasta
[2023-03-14 11:33:56,309] [INFO] Task started: Blastn
[2023-03-14 11:33:56,310] [INFO] Running command: blastn -query OceanDNA-b35065/markers.fasta -db /var/lib/cwl/stg66cca7e6-3294-4b2c-9ffd-9443f8de6fa5/dqc_reference/reference_markers.fasta -out OceanDNA-b35065/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:56,988] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:56,989] [INFO] Selected 12 target genomes.
[2023-03-14 11:33:56,989] [INFO] Target genome list was writen to OceanDNA-b35065/target_genomes.txt
[2023-03-14 11:33:56,997] [INFO] Task started: fastANI
[2023-03-14 11:33:56,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg072406c7-f850-4d24-a811-78ebbda88633/OceanDNA-b35065.fa --refList OceanDNA-b35065/target_genomes.txt --output OceanDNA-b35065/fastani_result.tsv --threads 1
[2023-03-14 11:34:08,490] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:08,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66cca7e6-3294-4b2c-9ffd-9443f8de6fa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:08,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66cca7e6-3294-4b2c-9ffd-9443f8de6fa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:08,498] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2023-03-14 11:34:08,499] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-14 11:34:08,499] [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 nigrifaciens	strain=NBRC 103036	GCA_007991255.1	28109	28109	type	True	98.7964	1095	1254	95	inconclusive
Pseudoalteromonas nigrifaciens	strain=NCTC10691	GCA_900455185.1	28109	28109	type	True	98.7586	1144	1254	95	inconclusive
Pseudoalteromonas nigrifaciens	strain=KMM 661	GCA_002221505.1	28109	28109	type	True	98.7227	1146	1254	95	inconclusive
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	96.3931	1126	1254	95	inconclusive
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	83.1027	837	1254	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	82.8939	828	1254	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	82.6617	799	1254	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	81.5379	773	1254	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.0694	601	1254	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	76.7117	60	1254	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	76.5801	54	1254	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	75.8365	65	1254	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:34:08,499] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35065/tc_result.tsv
[2023-03-14 11:34:08,499] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:08,499] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:08,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66cca7e6-3294-4b2c-9ffd-9443f8de6fa5/dqc_reference/checkm_data
[2023-03-14 11:34:08,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:08,505] [INFO] Task started: CheckM
[2023-03-14 11:34:08,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35065/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35065/checkm_input OceanDNA-b35065/checkm_result
[2023-03-14 11:34:58,166] [INFO] Task succeeded: CheckM
[2023-03-14 11:34:58,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:34:58,168] [INFO] ===== Completeness check finished =====
[2023-03-14 11:34:58,169] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:34:58,169] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35065/markers.fasta)
[2023-03-14 11:34:58,169] [INFO] Task started: Blastn
[2023-03-14 11:34:58,169] [INFO] Running command: blastn -query OceanDNA-b35065/markers.fasta -db /var/lib/cwl/stg66cca7e6-3294-4b2c-9ffd-9443f8de6fa5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35065/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:59,191] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:59,192] [INFO] Selected 10 target genomes.
[2023-03-14 11:34:59,192] [INFO] Target genome list was writen to OceanDNA-b35065/target_genomes_gtdb.txt
[2023-03-14 11:34:59,201] [INFO] Task started: fastANI
[2023-03-14 11:34:59,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg072406c7-f850-4d24-a811-78ebbda88633/OceanDNA-b35065.fa --refList OceanDNA-b35065/target_genomes_gtdb.txt --output OceanDNA-b35065/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:35:09,381] [INFO] Task succeeded: fastANI
[2023-03-14 11:35:09,388] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-14 11:35:09,388] [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_002221505.1	s__Pseudoalteromonas nigrifaciens	98.7227	1146	1254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	98.65	98.00	0.90	0.81	15	inconclusive
GCF_001465295.1	s__Pseudoalteromonas translucida	96.3844	1127	1254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000238395.3	s__Pseudoalteromonas arctica	83.1187	834	1254	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	82.9076	827	1254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	82.8453	813	1254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	82.791	838	1254	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	82.6545	808	1254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	82.6524	800	1254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_000498095.1	s__Pseudoalteromonas sp000498095	82.5889	785	1254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.86	97.76	0.88	0.87	3	-
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	79.8361	555	1254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:35:09,388] [INFO] GTDB search result was written to OceanDNA-b35065/result_gtdb.tsv
[2023-03-14 11:35:09,388] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:35:09,390] [INFO] DFAST_QC result json was written to OceanDNA-b35065/dqc_result.json
[2023-03-14 11:35:09,390] [INFO] DFAST_QC completed!
[2023-03-14 11:35:09,390] [INFO] Total running time: 0h1m34s