[2024-01-24 13:10:03,975] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:03,977] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:03,977] [INFO] DQC Reference Directory: /var/lib/cwl/stgef245e04-f744-4c36-a09c-2fd54b8e35c9/dqc_reference
[2024-01-24 13:10:05,259] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,260] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,260] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe05e9f9-f103-4588-8003-5e52029165e0/GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna.gz | prodigal -d GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/cds.fna -a GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:18,836] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:18,837] [INFO] Task started: HMMsearch
[2024-01-24 13:10:18,837] [INFO] Running command: hmmsearch --tblout GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef245e04-f744-4c36-a09c-2fd54b8e35c9/dqc_reference/reference_markers.hmm GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:19,196] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:19,198] [INFO] Found 6/6 markers.
[2024-01-24 13:10:19,245] [INFO] Query marker FASTA was written to GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/markers.fasta
[2024-01-24 13:10:19,246] [INFO] Task started: Blastn
[2024-01-24 13:10:19,246] [INFO] Running command: blastn -query GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/markers.fasta -db /var/lib/cwl/stgef245e04-f744-4c36-a09c-2fd54b8e35c9/dqc_reference/reference_markers.fasta -out GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:20,065] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:20,069] [INFO] Selected 14 target genomes.
[2024-01-24 13:10:20,070] [INFO] Target genome list was writen to GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/target_genomes.txt
[2024-01-24 13:10:20,074] [INFO] Task started: fastANI
[2024-01-24 13:10:20,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe05e9f9-f103-4588-8003-5e52029165e0/GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna.gz --refList GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/target_genomes.txt --output GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:37,165] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:37,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef245e04-f744-4c36-a09c-2fd54b8e35c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:37,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef245e04-f744-4c36-a09c-2fd54b8e35c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:37,179] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:37,180] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:37,180] [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
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	100.0	1826	1832	95	conclusive
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	99.9961	1824	1832	95	conclusive
Vibrio celticus	strain=Rd 8.15	GCA_002156525.1	446372	446372	type	True	92.6104	1360	1832	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	92.6061	1364	1832	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	92.3836	1411	1832	95	below_threshold
Vibrio coralliirubri	strain=Corallo1	GCA_002156455.1	1516159	1516159	type	True	92.2182	1392	1832	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	92.0749	1455	1832	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	91.3473	1436	1832	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	89.6268	1327	1832	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	89.2104	1327	1832	95	below_threshold
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	88.7543	1261	1832	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	88.5688	1346	1832	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	87.9279	1261	1832	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	87.8988	1278	1832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:37,182] [INFO] DFAST Taxonomy check result was written to GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/tc_result.tsv
[2024-01-24 13:10:37,183] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:37,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:37,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef245e04-f744-4c36-a09c-2fd54b8e35c9/dqc_reference/checkm_data
[2024-01-24 13:10:37,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:37,250] [INFO] Task started: CheckM
[2024-01-24 13:10:37,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/checkm_input GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/checkm_result
[2024-01-24 13:11:22,501] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:22,502] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:22,523] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:22,524] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:22,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/markers.fasta)
[2024-01-24 13:11:22,525] [INFO] Task started: Blastn
[2024-01-24 13:11:22,525] [INFO] Running command: blastn -query GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/markers.fasta -db /var/lib/cwl/stgef245e04-f744-4c36-a09c-2fd54b8e35c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:23,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:23,701] [INFO] Selected 13 target genomes.
[2024-01-24 13:11:23,701] [INFO] Target genome list was writen to GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:23,708] [INFO] Task started: fastANI
[2024-01-24 13:11:23,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe05e9f9-f103-4588-8003-5e52029165e0/GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna.gz --refList GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/target_genomes_gtdb.txt --output GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:39,530] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:39,546] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:39,546] [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_001048535.1	s__Vibrio crassostreae	100.0	1825	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	conclusive
GCF_002156525.1	s__Vibrio celticus	92.6206	1359	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	-
GCF_000272105.2	s__Vibrio splendidus_I	92.4109	1404	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858795.1	s__Vibrio sp007858795	92.3656	1449	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557875.1	s__Vibrio splendidus_F	92.3459	1449	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_002156455.1	s__Vibrio coralliirubri	92.2182	1392	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	96.55	95.77	0.88	0.83	22	-
GCF_000272045.2	s__Vibrio crassostreae_C	92.1557	1398	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_013394185.1	s__Vibrio sp013394185	91.4087	1412	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000316985.1	s__Vibrio sp000316985	91.2205	1299	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002875705.1	s__Vibrio sp002875705	91.0963	1370	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_014879975.1	s__Vibrio bathopelagicus	88.9567	1397	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801285.1	s__Vibrio kanaloae	88.8209	1258	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	-
GCF_005281815.1	s__Vibrio chagasii	87.9472	1259	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:39,560] [INFO] GTDB search result was written to GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:39,561] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:39,564] [INFO] DFAST_QC result json was written to GCF_001048535.1_VLGP7_PRJEB5883_genomic.fna/dqc_result.json
[2024-01-24 13:11:39,564] [INFO] DFAST_QC completed!
[2024-01-24 13:11:39,565] [INFO] Total running time: 0h1m36s