[2024-01-24 13:49:16,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:16,217] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:16,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg2df71d4a-ec5e-4817-b075-44fab1cacb50/dqc_reference
[2024-01-24 13:49:17,486] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:17,487] [INFO] Task started: Prodigal
[2024-01-24 13:49:17,487] [INFO] Running command: gunzip -c /var/lib/cwl/stgca295f6c-7c83-4137-aa7b-12547a489264/GCF_024346875.1_ASM2434687v1_genomic.fna.gz | prodigal -d GCF_024346875.1_ASM2434687v1_genomic.fna/cds.fna -a GCF_024346875.1_ASM2434687v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:25,852] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:25,853] [INFO] Task started: HMMsearch
[2024-01-24 13:49:25,853] [INFO] Running command: hmmsearch --tblout GCF_024346875.1_ASM2434687v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2df71d4a-ec5e-4817-b075-44fab1cacb50/dqc_reference/reference_markers.hmm GCF_024346875.1_ASM2434687v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:26,154] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:26,155] [INFO] Found 6/6 markers.
[2024-01-24 13:49:26,184] [INFO] Query marker FASTA was written to GCF_024346875.1_ASM2434687v1_genomic.fna/markers.fasta
[2024-01-24 13:49:26,184] [INFO] Task started: Blastn
[2024-01-24 13:49:26,184] [INFO] Running command: blastn -query GCF_024346875.1_ASM2434687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2df71d4a-ec5e-4817-b075-44fab1cacb50/dqc_reference/reference_markers.fasta -out GCF_024346875.1_ASM2434687v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:27,013] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:27,017] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:27,017] [INFO] Target genome list was writen to GCF_024346875.1_ASM2434687v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:27,022] [INFO] Task started: fastANI
[2024-01-24 13:49:27,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgca295f6c-7c83-4137-aa7b-12547a489264/GCF_024346875.1_ASM2434687v1_genomic.fna.gz --refList GCF_024346875.1_ASM2434687v1_genomic.fna/target_genomes.txt --output GCF_024346875.1_ASM2434687v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:39,225] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:39,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2df71d4a-ec5e-4817-b075-44fab1cacb50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:39,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2df71d4a-ec5e-4817-b075-44fab1cacb50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:39,239] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:39,239] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:39,239] [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 gallicus	strain=CIP 107863	GCA_024346875.1	190897	190897	type	True	100.0	1170	1171	95	conclusive
Vibrio inusitatus	strain=LMG 23434	GCA_024346935.1	413402	413402	type	True	81.0192	353	1171	95	below_threshold
Vibrio comitans	strain=LMG 23416	GCA_024346835.1	413401	413401	type	True	80.965	366	1171	95	below_threshold
Vibrio superstes	strain=G3-29	GCA_003569005.1	198815	198815	type	True	80.9489	354	1171	95	below_threshold
Vibrio superstes	strain=NBRC 103154	GCA_007990955.1	198815	198815	type	True	80.831	341	1171	95	below_threshold
Vibrio ishigakensis	strain=JCM 19231	GCA_024347675.1	1481914	1481914	type	True	80.5667	475	1171	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	80.5146	312	1171	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	80.4626	343	1171	95	below_threshold
Vibrio comitans	strain=NBRC 102076	GCA_006538565.1	413401	413401	type	True	80.3715	344	1171	95	below_threshold
Vibrio inusitatus	strain=NBRC 102082	GCA_006538525.1	413402	413402	type	True	80.2697	328	1171	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.8552	184	1171	95	below_threshold
Vibrio ezurae	strain=NBRC 102218	GCA_000467185.1	252583	252583	type	True	79.6423	301	1171	95	below_threshold
Vibrio ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	79.6287	317	1171	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	78.9128	169	1171	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	78.8778	173	1171	95	below_threshold
Aliivibrio fischeri	strain=ATCC 7744	GCA_016464335.1	668	668	suspected-type	True	78.6149	169	1171	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:39,241] [INFO] DFAST Taxonomy check result was written to GCF_024346875.1_ASM2434687v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:39,242] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:39,242] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:39,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2df71d4a-ec5e-4817-b075-44fab1cacb50/dqc_reference/checkm_data
[2024-01-24 13:49:39,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:39,280] [INFO] Task started: CheckM
[2024-01-24 13:49:39,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024346875.1_ASM2434687v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024346875.1_ASM2434687v1_genomic.fna/checkm_input GCF_024346875.1_ASM2434687v1_genomic.fna/checkm_result
[2024-01-24 13:50:09,765] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:09,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:09,783] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:09,783] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:09,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024346875.1_ASM2434687v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:09,784] [INFO] Task started: Blastn
[2024-01-24 13:50:09,784] [INFO] Running command: blastn -query GCF_024346875.1_ASM2434687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2df71d4a-ec5e-4817-b075-44fab1cacb50/dqc_reference/reference_markers_gtdb.fasta -out GCF_024346875.1_ASM2434687v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:11,029] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:11,034] [INFO] Selected 21 target genomes.
[2024-01-24 13:50:11,034] [INFO] Target genome list was writen to GCF_024346875.1_ASM2434687v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:11,050] [INFO] Task started: fastANI
[2024-01-24 13:50:11,050] [INFO] Running command: fastANI --query /var/lib/cwl/stgca295f6c-7c83-4137-aa7b-12547a489264/GCF_024346875.1_ASM2434687v1_genomic.fna.gz --refList GCF_024346875.1_ASM2434687v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024346875.1_ASM2434687v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:26,478] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:26,499] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:26,499] [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_001677275.1	s__Vibrio breoganii	81.8712	367	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.22	96.88	0.90	0.86	59	-
GCF_003569005.1	s__Vibrio superstes	80.9167	353	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006538565.1	s__Vibrio comitans	80.3715	344	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538525.1	s__Vibrio inusitatus	80.253	329	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000830415.1	s__Vibrio ishigakensis	80.0661	430	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.42	95.17	0.89	0.89	4	-
GCF_000496695.1	s__Vibrio halioticoli	79.805	306	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.31	0.94	0.87	3	-
GCF_002218045.2	s__Vibrio rumoiensis	79.7618	165	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938205.1	s__Vibrio panuliri	79.6752	182	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_001676025.1	s__Vibrio sp001676025	79.6243	336	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000467185.1	s__Vibrio ezurae	79.617	303	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000189275.1	s__Vibrio sinaloensis_B	79.1092	170	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811315.1	s__Vibrio atypicus	79.0959	191	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_000222605.1	s__Vibrio ichthyoenteri	79.0322	164	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004551525.1	s__Vibrio ouci	79.0004	199	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014694375.1	s__Vibrio sp014694375	79.0001	121	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014050145.1	s__Vibrio marinisediminis	78.9324	167	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350325.1	s__Vibrio rhodolitus	78.8667	171	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCA_001874155.1	s__Vibrio sp001874155	78.7264	142	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009727955.1	s__Aliivibrio fischeri_A	78.6023	168	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.1568	98.75	97.87	0.96	0.92	6	-
GCF_016464335.1	s__Aliivibrio fischeri	78.5895	169	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.1568	96.45	95.48	0.88	0.84	60	-
GCF_015223435.1	s__Vibrio hibernica	78.3967	123	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:26,501] [INFO] GTDB search result was written to GCF_024346875.1_ASM2434687v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:26,501] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:26,505] [INFO] DFAST_QC result json was written to GCF_024346875.1_ASM2434687v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:26,505] [INFO] DFAST_QC completed!
[2024-01-24 13:50:26,505] [INFO] Total running time: 0h1m10s