[2024-01-25 17:49:20,707] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:20,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:20,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b14be52-b969-4bbd-8179-b34bb5eb2dbd/dqc_reference
[2024-01-25 17:49:21,848] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:21,849] [INFO] Task started: Prodigal
[2024-01-25 17:49:21,849] [INFO] Running command: gunzip -c /var/lib/cwl/stg528c8f63-c48e-4527-9a1c-549da4a99db4/GCF_024347475.1_ASM2434747v1_genomic.fna.gz | prodigal -d GCF_024347475.1_ASM2434747v1_genomic.fna/cds.fna -a GCF_024347475.1_ASM2434747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:33,204] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:33,204] [INFO] Task started: HMMsearch
[2024-01-25 17:49:33,204] [INFO] Running command: hmmsearch --tblout GCF_024347475.1_ASM2434747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b14be52-b969-4bbd-8179-b34bb5eb2dbd/dqc_reference/reference_markers.hmm GCF_024347475.1_ASM2434747v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:33,494] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:33,495] [INFO] Found 6/6 markers.
[2024-01-25 17:49:33,542] [INFO] Query marker FASTA was written to GCF_024347475.1_ASM2434747v1_genomic.fna/markers.fasta
[2024-01-25 17:49:33,542] [INFO] Task started: Blastn
[2024-01-25 17:49:33,542] [INFO] Running command: blastn -query GCF_024347475.1_ASM2434747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b14be52-b969-4bbd-8179-b34bb5eb2dbd/dqc_reference/reference_markers.fasta -out GCF_024347475.1_ASM2434747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:34,320] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:34,324] [INFO] Selected 11 target genomes.
[2024-01-25 17:49:34,324] [INFO] Target genome list was writen to GCF_024347475.1_ASM2434747v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:34,328] [INFO] Task started: fastANI
[2024-01-25 17:49:34,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg528c8f63-c48e-4527-9a1c-549da4a99db4/GCF_024347475.1_ASM2434747v1_genomic.fna.gz --refList GCF_024347475.1_ASM2434747v1_genomic.fna/target_genomes.txt --output GCF_024347475.1_ASM2434747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:46,809] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:46,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b14be52-b969-4bbd-8179-b34bb5eb2dbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:46,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b14be52-b969-4bbd-8179-b34bb5eb2dbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:46,819] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:49:46,819] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:46,819] [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 fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	100.0	1749	1759	95	conclusive
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	88.2984	1281	1759	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	83.7292	908	1759	95	below_threshold
Vibrio chagasii	strain=CCUG 48643	GCA_008801295.1	170679	170679	suspected-type	True	83.4738	861	1759	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	83.3837	868	1759	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	83.3576	951	1759	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	83.169	976	1759	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	82.8823	947	1759	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	82.7154	865	1759	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	82.5501	870	1759	95	below_threshold
Vibrio maerlii	strain=G62	GCA_003415655.1	2231648	2231648	type	True	80.9496	455	1759	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:46,821] [INFO] DFAST Taxonomy check result was written to GCF_024347475.1_ASM2434747v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:46,821] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:46,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:46,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b14be52-b969-4bbd-8179-b34bb5eb2dbd/dqc_reference/checkm_data
[2024-01-25 17:49:46,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:46,872] [INFO] Task started: CheckM
[2024-01-25 17:49:46,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347475.1_ASM2434747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347475.1_ASM2434747v1_genomic.fna/checkm_input GCF_024347475.1_ASM2434747v1_genomic.fna/checkm_result
[2024-01-25 17:50:24,019] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:24,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:24,086] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:24,086] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:24,087] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347475.1_ASM2434747v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:24,087] [INFO] Task started: Blastn
[2024-01-25 17:50:24,087] [INFO] Running command: blastn -query GCF_024347475.1_ASM2434747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b14be52-b969-4bbd-8179-b34bb5eb2dbd/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347475.1_ASM2434747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:25,306] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:25,309] [INFO] Selected 15 target genomes.
[2024-01-25 17:50:25,309] [INFO] Target genome list was writen to GCF_024347475.1_ASM2434747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:25,335] [INFO] Task started: fastANI
[2024-01-25 17:50:25,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg528c8f63-c48e-4527-9a1c-549da4a99db4/GCF_024347475.1_ASM2434747v1_genomic.fna.gz --refList GCF_024347475.1_ASM2434747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347475.1_ASM2434747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:42,063] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:42,073] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:50:42,073] [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_000695685.1	s__Vibrio fortis	89.2943	1457	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	-
GCF_002954585.1	s__Vibrio chagasii_A	83.694	883	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.42	95.44	0.90	0.87	4	-
GCF_001635455.1	s__Vibrio sp001635455	83.436	797	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281815.1	s__Vibrio chagasii	83.3935	867	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
GCA_000169995.1	s__Vibrio sp000169995	83.3732	880	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394185.1	s__Vibrio sp013394185	83.3214	958	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000272045.2	s__Vibrio crassostreae_C	83.1088	929	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_002875705.1	s__Vibrio sp002875705	83.0179	902	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_000316985.1	s__Vibrio sp000316985	82.9796	881	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156475.1	s__Vibrio gigantis	82.892	946	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_001557875.1	s__Vibrio splendidus_F	82.8138	925	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_000272105.2	s__Vibrio splendidus_I	82.7285	900	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006333845.1	s__Vibrio tasmaniensis	82.3052	845	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_004764665.1	s__Vibrio echinoideorum	82.2094	937	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.83	0.88	0.82	5	-
GCF_003415655.1	s__Vibrio maerlii	80.9473	455	1759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:42,075] [INFO] GTDB search result was written to GCF_024347475.1_ASM2434747v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:42,075] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:42,078] [INFO] DFAST_QC result json was written to GCF_024347475.1_ASM2434747v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:42,079] [INFO] DFAST_QC completed!
[2024-01-25 17:50:42,079] [INFO] Total running time: 0h1m21s