[2024-01-24 13:58:41,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:41,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:41,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d32cb86-a96c-4bab-a23d-730beac855f5/dqc_reference
[2024-01-24 13:58:43,400] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:43,401] [INFO] Task started: Prodigal
[2024-01-24 13:58:43,401] [INFO] Running command: gunzip -c /var/lib/cwl/stgd80ec9a9-da8c-4b41-bdf2-72e7af647210/GCF_006364355.1_ASM636435v1_genomic.fna.gz | prodigal -d GCF_006364355.1_ASM636435v1_genomic.fna/cds.fna -a GCF_006364355.1_ASM636435v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:00,154] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:00,154] [INFO] Task started: HMMsearch
[2024-01-24 13:59:00,154] [INFO] Running command: hmmsearch --tblout GCF_006364355.1_ASM636435v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d32cb86-a96c-4bab-a23d-730beac855f5/dqc_reference/reference_markers.hmm GCF_006364355.1_ASM636435v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:00,457] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:00,459] [INFO] Found 6/6 markers.
[2024-01-24 13:59:00,503] [INFO] Query marker FASTA was written to GCF_006364355.1_ASM636435v1_genomic.fna/markers.fasta
[2024-01-24 13:59:00,504] [INFO] Task started: Blastn
[2024-01-24 13:59:00,504] [INFO] Running command: blastn -query GCF_006364355.1_ASM636435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d32cb86-a96c-4bab-a23d-730beac855f5/dqc_reference/reference_markers.fasta -out GCF_006364355.1_ASM636435v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:01,366] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:01,369] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:01,369] [INFO] Target genome list was writen to GCF_006364355.1_ASM636435v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:01,373] [INFO] Task started: fastANI
[2024-01-24 13:59:01,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgd80ec9a9-da8c-4b41-bdf2-72e7af647210/GCF_006364355.1_ASM636435v1_genomic.fna.gz --refList GCF_006364355.1_ASM636435v1_genomic.fna/target_genomes.txt --output GCF_006364355.1_ASM636435v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:11,297] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:11,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d32cb86-a96c-4bab-a23d-730beac855f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:11,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d32cb86-a96c-4bab-a23d-730beac855f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:11,314] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:59:11,314] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:11,314] [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 furnissii	strain=FDAARGOS_777	GCA_006364355.1	29494	29494	type	True	100.0	1663	1663	95	conclusive
Vibrio furnissii	strain=NCTC13120	GCA_900460225.1	29494	29494	type	True	99.9997	1659	1663	95	conclusive
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	99.9988	1661	1663	95	conclusive
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	99.9891	1637	1663	95	conclusive
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	87.5354	1323	1663	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	80.0236	536	1663	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.4796	432	1663	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.3766	353	1663	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	79.1481	372	1663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:11,316] [INFO] DFAST Taxonomy check result was written to GCF_006364355.1_ASM636435v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:11,317] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:11,317] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:11,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d32cb86-a96c-4bab-a23d-730beac855f5/dqc_reference/checkm_data
[2024-01-24 13:59:11,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:11,371] [INFO] Task started: CheckM
[2024-01-24 13:59:11,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006364355.1_ASM636435v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006364355.1_ASM636435v1_genomic.fna/checkm_input GCF_006364355.1_ASM636435v1_genomic.fna/checkm_result
[2024-01-24 13:59:59,869] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:59,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:59,891] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:59,891] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:59,891] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006364355.1_ASM636435v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:59,892] [INFO] Task started: Blastn
[2024-01-24 13:59:59,892] [INFO] Running command: blastn -query GCF_006364355.1_ASM636435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d32cb86-a96c-4bab-a23d-730beac855f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_006364355.1_ASM636435v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:01,224] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:01,228] [INFO] Selected 17 target genomes.
[2024-01-24 14:00:01,228] [INFO] Target genome list was writen to GCF_006364355.1_ASM636435v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:01,255] [INFO] Task started: fastANI
[2024-01-24 14:00:01,255] [INFO] Running command: fastANI --query /var/lib/cwl/stgd80ec9a9-da8c-4b41-bdf2-72e7af647210/GCF_006364355.1_ASM636435v1_genomic.fna.gz --refList GCF_006364355.1_ASM636435v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006364355.1_ASM636435v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:18,410] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:18,425] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:18,425] [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_000176175.1	s__Vibrio furnissii	99.9891	1637	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	conclusive
GCF_900460245.1	s__Vibrio fluvialis	87.6119	1314	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_019226825.1	s__Vibrio sp004804295	81.2359	819	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.23	99.23	0.93	0.93	2	-
GCF_009763805.1	s__Vibrio cidicii	80.2156	451	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.20	97.77	0.90	0.87	8	-
GCF_000764325.1	s__Vibrio navarrensis	79.9096	479	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.19	97.06	0.93	0.87	22	-
GCF_019048845.1	s__Vibrio sp000176715	79.8748	523	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.20	96.20	0.92	0.92	2	-
GCF_001471585.2	s__Vibrio cholerae	79.7745	545	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.72	95.09	0.90	0.82	1544	-
GCF_000467125.1	s__Vibrio proteolyticus	79.7505	474	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.93	98.89	0.93	0.91	5	-
GCF_011064285.1	s__Vibrio ziniensis	79.7179	483	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015767675.1	s__Vibrio sp000960595	79.672	491	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.38	0.94	0.90	8	-
GCF_009665255.1	s__Vibrio metoecus_B	79.628	524	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.11	98.11	0.94	0.94	2	-
GCF_900167345.1	s__Vibrio cincinnatiensis	79.531	407	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	99.06	0.97	0.94	6	-
GCF_900460535.1	s__Vibrio parahaemolyticus	79.4903	449	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCF_009938205.1	s__Vibrio panuliri	79.3352	351	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_000696385.1	s__Vibrio metoecus	79.3088	519	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.79	97.58	0.93	0.89	26	-
GCF_002749895.1	s__Vibrio fujianensis	79.2944	354	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.21	99.14	0.95	0.93	8	-
GCF_000417905.1	s__Vibrio natriegens	78.9106	411	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:18,427] [INFO] GTDB search result was written to GCF_006364355.1_ASM636435v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:18,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:18,432] [INFO] DFAST_QC result json was written to GCF_006364355.1_ASM636435v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:18,432] [INFO] DFAST_QC completed!
[2024-01-24 14:00:18,432] [INFO] Total running time: 0h1m36s