[2024-01-24 13:57:27,232] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:27,234] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:27,234] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb683ab1-d580-469c-8ad9-66fbffece1f6/dqc_reference
[2024-01-24 13:57:28,571] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:28,572] [INFO] Task started: Prodigal
[2024-01-24 13:57:28,573] [INFO] Running command: gunzip -c /var/lib/cwl/stg793a358f-1b9c-43b5-aae6-73ef50e6b9e9/GCF_005281835.1_ASM528183v1_genomic.fna.gz | prodigal -d GCF_005281835.1_ASM528183v1_genomic.fna/cds.fna -a GCF_005281835.1_ASM528183v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:40,310] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:40,310] [INFO] Task started: HMMsearch
[2024-01-24 13:57:40,310] [INFO] Running command: hmmsearch --tblout GCF_005281835.1_ASM528183v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb683ab1-d580-469c-8ad9-66fbffece1f6/dqc_reference/reference_markers.hmm GCF_005281835.1_ASM528183v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:40,622] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:40,623] [INFO] Found 6/6 markers.
[2024-01-24 13:57:40,669] [INFO] Query marker FASTA was written to GCF_005281835.1_ASM528183v1_genomic.fna/markers.fasta
[2024-01-24 13:57:40,670] [INFO] Task started: Blastn
[2024-01-24 13:57:40,670] [INFO] Running command: blastn -query GCF_005281835.1_ASM528183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb683ab1-d580-469c-8ad9-66fbffece1f6/dqc_reference/reference_markers.fasta -out GCF_005281835.1_ASM528183v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:41,527] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:41,532] [INFO] Selected 16 target genomes.
[2024-01-24 13:57:41,533] [INFO] Target genome list was writen to GCF_005281835.1_ASM528183v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:41,545] [INFO] Task started: fastANI
[2024-01-24 13:57:41,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg793a358f-1b9c-43b5-aae6-73ef50e6b9e9/GCF_005281835.1_ASM528183v1_genomic.fna.gz --refList GCF_005281835.1_ASM528183v1_genomic.fna/target_genomes.txt --output GCF_005281835.1_ASM528183v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:57,672] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:57,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb683ab1-d580-469c-8ad9-66fbffece1f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:57,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb683ab1-d580-469c-8ad9-66fbffece1f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:57,686] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:57,686] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:57,686] [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 profundi	strain=TP187	GCA_005281835.1	1774960	1774960	type	True	100.0	1717	1718	95	conclusive
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	82.6021	695	1718	95	below_threshold
Vibrio chagasii	strain=CCUG 48643	GCA_008801295.1	170679	170679	suspected-type	True	82.5761	675	1718	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	82.5606	692	1718	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	82.3236	731	1718	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	82.3173	695	1718	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	82.2666	736	1718	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	82.248	715	1718	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	82.2323	693	1718	95	below_threshold
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	82.2097	698	1718	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	82.1379	732	1718	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	81.9073	692	1718	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	81.8606	685	1718	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	81.815	642	1718	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	81.8055	680	1718	95	below_threshold
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	81.7667	726	1718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:57,688] [INFO] DFAST Taxonomy check result was written to GCF_005281835.1_ASM528183v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:57,689] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:57,689] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:57,689] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb683ab1-d580-469c-8ad9-66fbffece1f6/dqc_reference/checkm_data
[2024-01-24 13:57:57,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:57,742] [INFO] Task started: CheckM
[2024-01-24 13:57:57,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005281835.1_ASM528183v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005281835.1_ASM528183v1_genomic.fna/checkm_input GCF_005281835.1_ASM528183v1_genomic.fna/checkm_result
[2024-01-24 13:58:39,789] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:39,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:39,810] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:39,810] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:39,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005281835.1_ASM528183v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:39,811] [INFO] Task started: Blastn
[2024-01-24 13:58:39,811] [INFO] Running command: blastn -query GCF_005281835.1_ASM528183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb683ab1-d580-469c-8ad9-66fbffece1f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_005281835.1_ASM528183v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:41,172] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:41,175] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:41,176] [INFO] Target genome list was writen to GCF_005281835.1_ASM528183v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:41,192] [INFO] Task started: fastANI
[2024-01-24 13:58:41,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg793a358f-1b9c-43b5-aae6-73ef50e6b9e9/GCF_005281835.1_ASM528183v1_genomic.fna.gz --refList GCF_005281835.1_ASM528183v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005281835.1_ASM528183v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:56,575] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:56,592] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:56,592] [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_005281835.1	s__Vibrio profundi	100.0	1717	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001635455.1	s__Vibrio sp001635455	82.7396	660	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954585.1	s__Vibrio chagasii_A	82.627	702	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.42	95.44	0.90	0.87	4	-
GCF_005281815.1	s__Vibrio chagasii	82.5768	689	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
GCF_013394185.1	s__Vibrio sp013394185	82.4903	711	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000316985.1	s__Vibrio sp000316985	82.267	674	1718	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	82.2462	714	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_002156525.1	s__Vibrio celticus	82.2239	672	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	-
GCA_000169995.1	s__Vibrio sp000169995	82.2008	663	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557875.1	s__Vibrio splendidus_F	82.1932	729	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_001558015.1	s__Vibrio splendidus	82.1854	695	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.85	95.03	0.88	0.83	97	-
GCF_000272105.2	s__Vibrio splendidus_I	82.0114	688	1718	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	81.9089	665	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_000695685.1	s__Vibrio fortis	81.8679	693	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:56,595] [INFO] GTDB search result was written to GCF_005281835.1_ASM528183v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:56,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:56,599] [INFO] DFAST_QC result json was written to GCF_005281835.1_ASM528183v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:56,599] [INFO] DFAST_QC completed!
[2024-01-24 13:58:56,599] [INFO] Total running time: 0h1m29s