[2024-01-24 13:57:56,020] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,022] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,022] [INFO] DQC Reference Directory: /var/lib/cwl/stg445bc5d6-13ad-407f-b4ac-63f2759ca5bb/dqc_reference
[2024-01-24 13:57:57,325] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,326] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,326] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c6fcfa5-56f0-48f8-b90b-5a6df7837ad6/GCF_024346975.1_ASM2434697v1_genomic.fna.gz | prodigal -d GCF_024346975.1_ASM2434697v1_genomic.fna/cds.fna -a GCF_024346975.1_ASM2434697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:06,824] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:06,825] [INFO] Task started: HMMsearch
[2024-01-24 13:58:06,825] [INFO] Running command: hmmsearch --tblout GCF_024346975.1_ASM2434697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg445bc5d6-13ad-407f-b4ac-63f2759ca5bb/dqc_reference/reference_markers.hmm GCF_024346975.1_ASM2434697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:07,142] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:07,144] [INFO] Found 6/6 markers.
[2024-01-24 13:58:07,177] [INFO] Query marker FASTA was written to GCF_024346975.1_ASM2434697v1_genomic.fna/markers.fasta
[2024-01-24 13:58:07,178] [INFO] Task started: Blastn
[2024-01-24 13:58:07,178] [INFO] Running command: blastn -query GCF_024346975.1_ASM2434697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg445bc5d6-13ad-407f-b4ac-63f2759ca5bb/dqc_reference/reference_markers.fasta -out GCF_024346975.1_ASM2434697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:08,050] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:08,053] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:08,054] [INFO] Target genome list was writen to GCF_024346975.1_ASM2434697v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:08,057] [INFO] Task started: fastANI
[2024-01-24 13:58:08,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c6fcfa5-56f0-48f8-b90b-5a6df7837ad6/GCF_024346975.1_ASM2434697v1_genomic.fna.gz --refList GCF_024346975.1_ASM2434697v1_genomic.fna/target_genomes.txt --output GCF_024346975.1_ASM2434697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:17,339] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:17,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg445bc5d6-13ad-407f-b4ac-63f2759ca5bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:17,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg445bc5d6-13ad-407f-b4ac-63f2759ca5bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:17,349] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:17,349] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:17,349] [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 neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	100.0	1278	1279	95	conclusive
Vibrio halioticoli	strain=IAM 14596	GCA_003568965.1	71388	71388	type	True	93.9574	1114	1279	95	below_threshold
Vibrio halioticoli	strain=NBRC 102217	GCA_000496695.1	71388	71388	type	True	93.9115	1063	1279	95	below_threshold
Vibrio ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	89.0232	1012	1279	95	below_threshold
Vibrio ezurae	strain=NBRC 102218	GCA_000467185.1	252583	252583	type	True	88.9149	1008	1279	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	81.4168	619	1279	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	80.1223	238	1279	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	80.1151	247	1279	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.9811	254	1279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:17,351] [INFO] DFAST Taxonomy check result was written to GCF_024346975.1_ASM2434697v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:17,351] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:17,351] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:17,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg445bc5d6-13ad-407f-b4ac-63f2759ca5bb/dqc_reference/checkm_data
[2024-01-24 13:58:17,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:17,390] [INFO] Task started: CheckM
[2024-01-24 13:58:17,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024346975.1_ASM2434697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024346975.1_ASM2434697v1_genomic.fna/checkm_input GCF_024346975.1_ASM2434697v1_genomic.fna/checkm_result
[2024-01-24 13:58:51,977] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:51,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:52,001] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:52,001] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:52,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024346975.1_ASM2434697v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:52,002] [INFO] Task started: Blastn
[2024-01-24 13:58:52,003] [INFO] Running command: blastn -query GCF_024346975.1_ASM2434697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg445bc5d6-13ad-407f-b4ac-63f2759ca5bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_024346975.1_ASM2434697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:53,341] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:53,344] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:53,344] [INFO] Target genome list was writen to GCF_024346975.1_ASM2434697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:53,352] [INFO] Task started: fastANI
[2024-01-24 13:58:53,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c6fcfa5-56f0-48f8-b90b-5a6df7837ad6/GCF_024346975.1_ASM2434697v1_genomic.fna.gz --refList GCF_024346975.1_ASM2434697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024346975.1_ASM2434697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:03,955] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:03,970] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:03,970] [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_000496695.1	s__Vibrio halioticoli	93.9115	1063	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.31	0.94	0.87	3	-
GCF_000467185.1	s__Vibrio ezurae	88.9149	1008	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001676025.1	s__Vibrio sp001676025	81.7908	668	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001677275.1	s__Vibrio breoganii	81.5263	605	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.22	96.88	0.90	0.86	59	-
GCF_006538525.1	s__Vibrio inusitatus	81.3704	539	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538565.1	s__Vibrio comitans	81.3467	581	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569005.1	s__Vibrio superstes	81.2664	590	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000169995.1	s__Vibrio sp000169995	79.2011	225	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400365.1	s__Vibrio jasicida	78.7277	246	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:03,972] [INFO] GTDB search result was written to GCF_024346975.1_ASM2434697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:03,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:03,975] [INFO] DFAST_QC result json was written to GCF_024346975.1_ASM2434697v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:03,976] [INFO] DFAST_QC completed!
[2024-01-24 13:59:03,976] [INFO] Total running time: 0h1m8s