[2024-01-24 13:22:02,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,216] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c83abae-c4be-4a27-b90e-baad14f4ef4d/dqc_reference
[2024-01-24 13:22:03,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,599] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,599] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9002cea-1393-479f-a873-c81cb0387bb8/GCF_900239935.1_PCAR91_V1_genomic.fna.gz | prodigal -d GCF_900239935.1_PCAR91_V1_genomic.fna/cds.fna -a GCF_900239935.1_PCAR91_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:12,987] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:12,987] [INFO] Task started: HMMsearch
[2024-01-24 13:22:12,988] [INFO] Running command: hmmsearch --tblout GCF_900239935.1_PCAR91_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c83abae-c4be-4a27-b90e-baad14f4ef4d/dqc_reference/reference_markers.hmm GCF_900239935.1_PCAR91_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:13,299] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:13,300] [INFO] Found 6/6 markers.
[2024-01-24 13:22:13,343] [INFO] Query marker FASTA was written to GCF_900239935.1_PCAR91_V1_genomic.fna/markers.fasta
[2024-01-24 13:22:13,343] [INFO] Task started: Blastn
[2024-01-24 13:22:13,343] [INFO] Running command: blastn -query GCF_900239935.1_PCAR91_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c83abae-c4be-4a27-b90e-baad14f4ef4d/dqc_reference/reference_markers.fasta -out GCF_900239935.1_PCAR91_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:14,084] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:14,087] [INFO] Selected 11 target genomes.
[2024-01-24 13:22:14,087] [INFO] Target genome list was writen to GCF_900239935.1_PCAR91_V1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:14,091] [INFO] Task started: fastANI
[2024-01-24 13:22:14,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9002cea-1393-479f-a873-c81cb0387bb8/GCF_900239935.1_PCAR91_V1_genomic.fna.gz --refList GCF_900239935.1_PCAR91_V1_genomic.fna/target_genomes.txt --output GCF_900239935.1_PCAR91_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:26,508] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:26,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c83abae-c4be-4a27-b90e-baad14f4ef4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:26,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c83abae-c4be-4a27-b90e-baad14f4ef4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:26,518] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:22:26,518] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:26,519] [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 carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	100.0	1525	1526	95	conclusive
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	99.9641	1498	1526	95	conclusive
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	99.9135	1423	1526	95	conclusive
Pseudoalteromonas espejiana	strain=ATCC 29659	GCA_002221525.1	28107	28107	type	True	88.0239	1137	1526	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	87.8904	1110	1526	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	85.6537	1141	1526	95	below_threshold
Pseudoalteromonas marina	strain=DSM 17587	GCA_000238335.4	267375	267375	type	True	84.3203	976	1526	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.2855	642	1526	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	77.1322	75	1526	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	76.775	67	1526	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:26,520] [INFO] DFAST Taxonomy check result was written to GCF_900239935.1_PCAR91_V1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:26,520] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:26,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:26,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c83abae-c4be-4a27-b90e-baad14f4ef4d/dqc_reference/checkm_data
[2024-01-24 13:22:26,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:26,570] [INFO] Task started: CheckM
[2024-01-24 13:22:26,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900239935.1_PCAR91_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900239935.1_PCAR91_V1_genomic.fna/checkm_input GCF_900239935.1_PCAR91_V1_genomic.fna/checkm_result
[2024-01-24 13:23:00,020] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:00,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:00,036] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:00,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:00,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900239935.1_PCAR91_V1_genomic.fna/markers.fasta)
[2024-01-24 13:23:00,037] [INFO] Task started: Blastn
[2024-01-24 13:23:00,037] [INFO] Running command: blastn -query GCF_900239935.1_PCAR91_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c83abae-c4be-4a27-b90e-baad14f4ef4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900239935.1_PCAR91_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:01,230] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:01,234] [INFO] Selected 11 target genomes.
[2024-01-24 13:23:01,234] [INFO] Target genome list was writen to GCF_900239935.1_PCAR91_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:01,246] [INFO] Task started: fastANI
[2024-01-24 13:23:01,247] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9002cea-1393-479f-a873-c81cb0387bb8/GCF_900239935.1_PCAR91_V1_genomic.fna.gz --refList GCF_900239935.1_PCAR91_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_900239935.1_PCAR91_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:14,499] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:14,510] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:14,511] [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_900239935.1	s__Pseudoalteromonas carrageenovora	100.0	1525	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	conclusive
GCF_018100985.1	s__Pseudoalteromonas sp018100985	92.2907	1215	1526	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	88.0215	1141	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	85.9763	1087	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	85.825	1134	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000814675.1	s__Pseudoalteromonas distincta	85.6478	1142	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	85.0793	1098	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000238335.3	s__Pseudoalteromonas marina	84.3005	978	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	97.57	0.91	0.88	12	-
GCF_001468485.1	s__Pseudoalteromonas sp001468485	84.2523	963	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.31	96.95	0.95	0.92	8	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	84.021	1036	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	81.8487	820	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:14,512] [INFO] GTDB search result was written to GCF_900239935.1_PCAR91_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:14,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:14,517] [INFO] DFAST_QC result json was written to GCF_900239935.1_PCAR91_V1_genomic.fna/dqc_result.json
[2024-01-24 13:23:14,518] [INFO] DFAST_QC completed!
[2024-01-24 13:23:14,518] [INFO] Total running time: 0h1m12s