[2024-01-24 15:10:39,496] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:39,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:39,498] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fb9f905-c508-4e25-ba5a-723a8dfce00c/dqc_reference
[2024-01-24 15:10:40,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:40,843] [INFO] Task started: Prodigal
[2024-01-24 15:10:40,843] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7e46bbb-4d92-426b-9b81-a2d8837a40d1/GCF_002156525.1_ASM215652v1_genomic.fna.gz | prodigal -d GCF_002156525.1_ASM215652v1_genomic.fna/cds.fna -a GCF_002156525.1_ASM215652v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:53,077] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:53,077] [INFO] Task started: HMMsearch
[2024-01-24 15:10:53,077] [INFO] Running command: hmmsearch --tblout GCF_002156525.1_ASM215652v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fb9f905-c508-4e25-ba5a-723a8dfce00c/dqc_reference/reference_markers.hmm GCF_002156525.1_ASM215652v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:53,386] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:53,387] [INFO] Found 6/6 markers.
[2024-01-24 15:10:53,433] [INFO] Query marker FASTA was written to GCF_002156525.1_ASM215652v1_genomic.fna/markers.fasta
[2024-01-24 15:10:53,433] [INFO] Task started: Blastn
[2024-01-24 15:10:53,433] [INFO] Running command: blastn -query GCF_002156525.1_ASM215652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fb9f905-c508-4e25-ba5a-723a8dfce00c/dqc_reference/reference_markers.fasta -out GCF_002156525.1_ASM215652v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:54,246] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:54,253] [INFO] Selected 13 target genomes.
[2024-01-24 15:10:54,254] [INFO] Target genome list was writen to GCF_002156525.1_ASM215652v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:54,260] [INFO] Task started: fastANI
[2024-01-24 15:10:54,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7e46bbb-4d92-426b-9b81-a2d8837a40d1/GCF_002156525.1_ASM215652v1_genomic.fna.gz --refList GCF_002156525.1_ASM215652v1_genomic.fna/target_genomes.txt --output GCF_002156525.1_ASM215652v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:11,152] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:11,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fb9f905-c508-4e25-ba5a-723a8dfce00c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:11,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fb9f905-c508-4e25-ba5a-723a8dfce00c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:11,166] [INFO] Found 13 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 15:11:11,166] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:11:11,166] [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 celticus	strain=Rd 8.15	GCA_002156525.1	446372	446372	type	True	100.0	1661	1671	95	inconclusive
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	99.9939	1669	1671	95	inconclusive
Vibrio celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	99.9893	1665	1671	95	inconclusive
Vibrio coralliirubri	strain=Corallo1	GCA_002156455.1	1516159	1516159	type	True	95.2322	1337	1671	95	inconclusive
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	95.1878	1373	1671	95	inconclusive
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	92.6279	1352	1671	95	below_threshold
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	92.6174	1342	1671	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	90.4209	1279	1671	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	89.8223	1258	1671	95	below_threshold
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	89.7053	1199	1671	95	below_threshold
Vibrio kanaloae	strain=CCUG 56968	GCA_008801285.1	170673	170673	type	True	89.6826	1210	1671	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_900089765.1	1194427	1194427	type	True	88.3811	1215	1671	95	below_threshold
Vibrio toranzoniae	strain=Vb 10.8	GCA_001541335.1	1194427	1194427	type	True	88.3108	1205	1671	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:11,168] [INFO] DFAST Taxonomy check result was written to GCF_002156525.1_ASM215652v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:11,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:11,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:11,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fb9f905-c508-4e25-ba5a-723a8dfce00c/dqc_reference/checkm_data
[2024-01-24 15:11:11,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:11,230] [INFO] Task started: CheckM
[2024-01-24 15:11:11,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002156525.1_ASM215652v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002156525.1_ASM215652v1_genomic.fna/checkm_input GCF_002156525.1_ASM215652v1_genomic.fna/checkm_result
[2024-01-24 15:11:53,672] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:53,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:53,700] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:53,701] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:53,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002156525.1_ASM215652v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:53,701] [INFO] Task started: Blastn
[2024-01-24 15:11:53,702] [INFO] Running command: blastn -query GCF_002156525.1_ASM215652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fb9f905-c508-4e25-ba5a-723a8dfce00c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002156525.1_ASM215652v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:54,890] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:54,893] [INFO] Selected 12 target genomes.
[2024-01-24 15:11:54,893] [INFO] Target genome list was writen to GCF_002156525.1_ASM215652v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:54,902] [INFO] Task started: fastANI
[2024-01-24 15:11:54,902] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7e46bbb-4d92-426b-9b81-a2d8837a40d1/GCF_002156525.1_ASM215652v1_genomic.fna.gz --refList GCF_002156525.1_ASM215652v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002156525.1_ASM215652v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:09,489] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:09,510] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:09,511] [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_002156525.1	s__Vibrio celticus	100.0	1661	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	conclusive
GCF_002156455.1	s__Vibrio coralliirubri	95.2232	1337	1671	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	94.8168	1377	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_000272105.2	s__Vibrio splendidus_I	94.2616	1316	1671	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	92.9094	1348	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_001048535.1	s__Vibrio crassostreae	92.6057	1343	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_007858795.1	s__Vibrio sp007858795	92.0847	1341	1671	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	91.5935	1305	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_002156475.1	s__Vibrio gigantis	90.6349	1306	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_008801285.1	s__Vibrio kanaloae	89.6701	1211	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	-
GCF_014879975.1	s__Vibrio bathopelagicus	88.873	1299	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089765.1	s__Vibrio toranzoniae	88.3809	1215	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.37	97.69	0.93	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:09,512] [INFO] GTDB search result was written to GCF_002156525.1_ASM215652v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:09,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:09,517] [INFO] DFAST_QC result json was written to GCF_002156525.1_ASM215652v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:09,518] [INFO] DFAST_QC completed!
[2024-01-24 15:12:09,518] [INFO] Total running time: 0h1m30s