[2024-01-25 19:49:20,985] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:20,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:20,986] [INFO] DQC Reference Directory: /var/lib/cwl/stgae7d84b3-09ee-4978-8132-39434b7b3f98/dqc_reference
[2024-01-25 19:49:22,172] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:22,173] [INFO] Task started: Prodigal
[2024-01-25 19:49:22,173] [INFO] Running command: gunzip -c /var/lib/cwl/stg0773b8a8-8f62-45db-b8be-e97b55f3b0a1/GCF_016464335.1_ASM1646433v1_genomic.fna.gz | prodigal -d GCF_016464335.1_ASM1646433v1_genomic.fna/cds.fna -a GCF_016464335.1_ASM1646433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:29,311] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:29,311] [INFO] Task started: HMMsearch
[2024-01-25 19:49:29,312] [INFO] Running command: hmmsearch --tblout GCF_016464335.1_ASM1646433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae7d84b3-09ee-4978-8132-39434b7b3f98/dqc_reference/reference_markers.hmm GCF_016464335.1_ASM1646433v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:29,577] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:29,578] [INFO] Found 6/6 markers.
[2024-01-25 19:49:29,614] [INFO] Query marker FASTA was written to GCF_016464335.1_ASM1646433v1_genomic.fna/markers.fasta
[2024-01-25 19:49:29,615] [INFO] Task started: Blastn
[2024-01-25 19:49:29,615] [INFO] Running command: blastn -query GCF_016464335.1_ASM1646433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae7d84b3-09ee-4978-8132-39434b7b3f98/dqc_reference/reference_markers.fasta -out GCF_016464335.1_ASM1646433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:30,375] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:30,378] [INFO] Selected 13 target genomes.
[2024-01-25 19:49:30,378] [INFO] Target genome list was writen to GCF_016464335.1_ASM1646433v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:30,385] [INFO] Task started: fastANI
[2024-01-25 19:49:30,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg0773b8a8-8f62-45db-b8be-e97b55f3b0a1/GCF_016464335.1_ASM1646433v1_genomic.fna.gz --refList GCF_016464335.1_ASM1646433v1_genomic.fna/target_genomes.txt --output GCF_016464335.1_ASM1646433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:41,380] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:41,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae7d84b3-09ee-4978-8132-39434b7b3f98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:41,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae7d84b3-09ee-4978-8132-39434b7b3f98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:41,392] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:49:41,392] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:41,392] [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
Aliivibrio fischeri	strain=ATCC 7744	GCA_016464335.1	668	668	suspected-type	True	100.0	1362	1366	95	conclusive
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	99.9981	1363	1366	95	conclusive
Aliivibrio finisterrensis	strain=LMG 23869	GCA_008933155.1	511998	511998	suspected-type	True	84.6185	843	1366	95	below_threshold
Aliivibrio sifiae	strain=NBRC 105001	GCA_002954715.1	566293	566293	type	True	83.245	945	1366	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.32	281	1366	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.85	275	1366	95	below_threshold
Vibrio ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	78.6482	187	1366	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	78.493	156	1366	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.452	215	1366	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.4319	217	1366	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	78.2341	245	1366	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	77.966	189	1366	95	below_threshold
Vibrio hibernica	strain=B1.19	GCA_015223435.1	2587465	2587465	type	True	77.9516	182	1366	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:41,394] [INFO] DFAST Taxonomy check result was written to GCF_016464335.1_ASM1646433v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:41,394] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:41,394] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:41,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae7d84b3-09ee-4978-8132-39434b7b3f98/dqc_reference/checkm_data
[2024-01-25 19:49:41,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:41,441] [INFO] Task started: CheckM
[2024-01-25 19:49:41,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016464335.1_ASM1646433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016464335.1_ASM1646433v1_genomic.fna/checkm_input GCF_016464335.1_ASM1646433v1_genomic.fna/checkm_result
[2024-01-25 19:50:08,048] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:08,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:08,078] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:08,079] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:08,080] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016464335.1_ASM1646433v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:08,080] [INFO] Task started: Blastn
[2024-01-25 19:50:08,080] [INFO] Running command: blastn -query GCF_016464335.1_ASM1646433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae7d84b3-09ee-4978-8132-39434b7b3f98/dqc_reference/reference_markers_gtdb.fasta -out GCF_016464335.1_ASM1646433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:09,269] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:09,272] [INFO] Selected 9 target genomes.
[2024-01-25 19:50:09,272] [INFO] Target genome list was writen to GCF_016464335.1_ASM1646433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:09,291] [INFO] Task started: fastANI
[2024-01-25 19:50:09,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg0773b8a8-8f62-45db-b8be-e97b55f3b0a1/GCF_016464335.1_ASM1646433v1_genomic.fna.gz --refList GCF_016464335.1_ASM1646433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016464335.1_ASM1646433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:18,897] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:18,904] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:18,904] [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_016464335.1	s__Aliivibrio fischeri	100.0	1362	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.1568	96.45	95.48	0.88	0.84	60	conclusive
GCF_009727955.1	s__Aliivibrio fischeri_A	95.1542	1169	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.1568	98.75	97.87	0.96	0.92	6	-
GCF_008933155.1	s__Aliivibrio finisterrensis	84.6075	845	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	95.53	95.03	0.81	0.80	11	-
GCF_900312675.1	s__Aliivibrio sp900312675	83.4194	926	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000953695.1	s__Aliivibrio wodanis	83.2416	824	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954715.1	s__Aliivibrio sifiae	83.2265	949	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	98.51	98.40	0.92	0.91	7	-
GCF_002954705.1	s__Aliivibrio sifiae_A	83.2033	945	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001690985.1	s__Aliivibrio sp001690985	82.7396	860	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	99.59	99.19	0.97	0.95	3	-
GCF_000196495.1	s__Aliivibrio salmonicida_A	82.0526	796	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	97.90	97.13	0.84	0.80	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:18,906] [INFO] GTDB search result was written to GCF_016464335.1_ASM1646433v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:18,906] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:18,910] [INFO] DFAST_QC result json was written to GCF_016464335.1_ASM1646433v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:18,910] [INFO] DFAST_QC completed!
[2024-01-25 19:50:18,911] [INFO] Total running time: 0h0m58s