[2023-03-16 03:47:32,867] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,867] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,867] [INFO] DQC Reference Directory: /var/lib/cwl/stg767e9942-eeb7-4ca1-997e-0475fb87f64e/dqc_reference
[2023-03-16 03:47:34,536] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,536] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,537] [INFO] Running command: cat /var/lib/cwl/stg0bb6ab4f-29cf-4dd7-b6df-8af49e397124/OceanDNA-b35005.fa | prodigal -d OceanDNA-b35005/cds.fna -a OceanDNA-b35005/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:58,084] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:58,084] [INFO] Task started: HMMsearch
[2023-03-16 03:47:58,084] [INFO] Running command: hmmsearch --tblout OceanDNA-b35005/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg767e9942-eeb7-4ca1-997e-0475fb87f64e/dqc_reference/reference_markers.hmm OceanDNA-b35005/protein.faa > /dev/null
[2023-03-16 03:47:58,388] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:58,388] [INFO] Found 6/6 markers.
[2023-03-16 03:47:58,414] [INFO] Query marker FASTA was written to OceanDNA-b35005/markers.fasta
[2023-03-16 03:47:58,414] [INFO] Task started: Blastn
[2023-03-16 03:47:58,414] [INFO] Running command: blastn -query OceanDNA-b35005/markers.fasta -db /var/lib/cwl/stg767e9942-eeb7-4ca1-997e-0475fb87f64e/dqc_reference/reference_markers.fasta -out OceanDNA-b35005/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:59,072] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:59,073] [INFO] Selected 14 target genomes.
[2023-03-16 03:47:59,074] [INFO] Target genome list was writen to OceanDNA-b35005/target_genomes.txt
[2023-03-16 03:47:59,080] [INFO] Task started: fastANI
[2023-03-16 03:47:59,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bb6ab4f-29cf-4dd7-b6df-8af49e397124/OceanDNA-b35005.fa --refList OceanDNA-b35005/target_genomes.txt --output OceanDNA-b35005/fastani_result.tsv --threads 1
[2023-03-16 03:48:14,144] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:14,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg767e9942-eeb7-4ca1-997e-0475fb87f64e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:14,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg767e9942-eeb7-4ca1-997e-0475fb87f64e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:14,153] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 03:48:14,153] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 03:48:14,153] [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 distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	97.089	1294	1476	95	conclusive
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	93.7146	1246	1476	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	91.0673	1103	1476	95	below_threshold
Pseudoalteromonas aliena	strain=SW19	GCA_014905615.1	247523	247523	type	True	86.9852	1015	1476	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	85.7566	1147	1476	95	below_threshold
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	85.6511	1163	1476	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	85.5766	1136	1476	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	83.4563	982	1476	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=NCTC10691	GCA_900455185.1	28109	28109	type	True	82.9953	872	1476	95	below_threshold
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	82.7843	817	1476	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.7668	662	1476	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	78.4064	214	1476	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	76.7524	53	1476	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	76.4269	93	1476	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:14,154] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35005/tc_result.tsv
[2023-03-16 03:48:14,154] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:14,154] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:14,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg767e9942-eeb7-4ca1-997e-0475fb87f64e/dqc_reference/checkm_data
[2023-03-16 03:48:14,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:14,194] [INFO] Task started: CheckM
[2023-03-16 03:48:14,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35005/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35005/checkm_input OceanDNA-b35005/checkm_result
[2023-03-16 03:49:11,283] [INFO] Task succeeded: CheckM
[2023-03-16 03:49:11,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:49:11,286] [INFO] ===== Completeness check finished =====
[2023-03-16 03:49:11,286] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:49:11,286] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35005/markers.fasta)
[2023-03-16 03:49:11,287] [INFO] Task started: Blastn
[2023-03-16 03:49:11,287] [INFO] Running command: blastn -query OceanDNA-b35005/markers.fasta -db /var/lib/cwl/stg767e9942-eeb7-4ca1-997e-0475fb87f64e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35005/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:49:12,321] [INFO] Task succeeded: Blastn
[2023-03-16 03:49:12,322] [INFO] Selected 8 target genomes.
[2023-03-16 03:49:12,322] [INFO] Target genome list was writen to OceanDNA-b35005/target_genomes_gtdb.txt
[2023-03-16 03:49:12,329] [INFO] Task started: fastANI
[2023-03-16 03:49:12,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bb6ab4f-29cf-4dd7-b6df-8af49e397124/OceanDNA-b35005.fa --refList OceanDNA-b35005/target_genomes_gtdb.txt --output OceanDNA-b35005/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:49:22,831] [INFO] Task succeeded: fastANI
[2023-03-16 03:49:22,837] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:49:22,837] [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
GCA_000814675.1	s__Pseudoalteromonas distincta	97.1031	1293	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	conclusive
GCF_008370255.1	s__Pseudoalteromonas sp008370255	94.4454	1207	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238395.3	s__Pseudoalteromonas arctica	93.7146	1246	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	93.4791	1289	1476	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	91.9163	1161	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	91.0771	1102	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_000239855.1	s__Pseudoalteromonas sp000239855	91.0696	1072	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905615.1	s__Pseudoalteromonas aliena	86.9658	1016	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.51	97.10	0.91	0.88	7	-
--------------------------------------------------------------------------------
[2023-03-16 03:49:22,837] [INFO] GTDB search result was written to OceanDNA-b35005/result_gtdb.tsv
[2023-03-16 03:49:22,837] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:49:22,839] [INFO] DFAST_QC result json was written to OceanDNA-b35005/dqc_result.json
[2023-03-16 03:49:22,839] [INFO] DFAST_QC completed!
[2023-03-16 03:49:22,839] [INFO] Total running time: 0h1m50s