[2024-01-24 13:32:33,791] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:33,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:33,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg900c2e0b-ae95-47bb-a6e1-ee07bc518cf3/dqc_reference
[2024-01-24 13:32:35,246] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:35,247] [INFO] Task started: Prodigal
[2024-01-24 13:32:35,247] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a1c1bcc-f2aa-4a33-9ec8-3cdff2e09d61/GCF_001996005.1_ASM199600v1_genomic.fna.gz | prodigal -d GCF_001996005.1_ASM199600v1_genomic.fna/cds.fna -a GCF_001996005.1_ASM199600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:45,691] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:45,691] [INFO] Task started: HMMsearch
[2024-01-24 13:32:45,691] [INFO] Running command: hmmsearch --tblout GCF_001996005.1_ASM199600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg900c2e0b-ae95-47bb-a6e1-ee07bc518cf3/dqc_reference/reference_markers.hmm GCF_001996005.1_ASM199600v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:46,073] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:46,075] [INFO] Found 6/6 markers.
[2024-01-24 13:32:46,119] [INFO] Query marker FASTA was written to GCF_001996005.1_ASM199600v1_genomic.fna/markers.fasta
[2024-01-24 13:32:46,120] [INFO] Task started: Blastn
[2024-01-24 13:32:46,120] [INFO] Running command: blastn -query GCF_001996005.1_ASM199600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg900c2e0b-ae95-47bb-a6e1-ee07bc518cf3/dqc_reference/reference_markers.fasta -out GCF_001996005.1_ASM199600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:47,005] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:47,008] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:47,008] [INFO] Target genome list was writen to GCF_001996005.1_ASM199600v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:47,013] [INFO] Task started: fastANI
[2024-01-24 13:32:47,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a1c1bcc-f2aa-4a33-9ec8-3cdff2e09d61/GCF_001996005.1_ASM199600v1_genomic.fna.gz --refList GCF_001996005.1_ASM199600v1_genomic.fna/target_genomes.txt --output GCF_001996005.1_ASM199600v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:56,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:56,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg900c2e0b-ae95-47bb-a6e1-ee07bc518cf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:56,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg900c2e0b-ae95-47bb-a6e1-ee07bc518cf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:56,574] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:56,574] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:56,574] [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
Salinivibrio siamensis	strain=JCM 14472	GCA_001996005.1	414286	414286	type	True	100.0	1109	1114	95	conclusive
Salinivibrio sharmensis	strain=DSM 18182	GCA_001995985.1	390883	390883	type	True	92.3779	949	1114	95	below_threshold
Salinivibrio kushneri	strain=AL184	GCA_005280275.1	1908198	1908198	type	True	92.2045	985	1114	95	below_threshold
Salinivibrio kushneri	strain=AL184	GCA_001995845.1	1908198	1908198	type	True	92.1934	966	1114	95	below_threshold
Salinivibrio proteolyticus	strain=DSM 19052	GCA_001996165.1	334715	334715	type	True	84.6712	762	1114	95	below_threshold
Salinivibrio costicola subsp. alcaliphilus	strain=DSM 16359	GCA_001996185.1	272773	51367	type	True	84.0305	789	1114	95	below_threshold
Salinivibrio socompensis	strain=S35	GCA_000513715.1	1510206	1510206	type	True	83.3145	729	1114	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	77.7927	70	1114	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	77.6631	116	1114	95	below_threshold
Vibrio zhugei	strain=KCTC 62784	GCA_024347155.1	2479546	2479546	type	True	77.6335	84	1114	95	below_threshold
Vibrio albus	strain=E4404	GCA_003144035.1	2200953	2200953	type	True	77.4316	68	1114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:56,581] [INFO] DFAST Taxonomy check result was written to GCF_001996005.1_ASM199600v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:56,587] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:56,587] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:56,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg900c2e0b-ae95-47bb-a6e1-ee07bc518cf3/dqc_reference/checkm_data
[2024-01-24 13:32:56,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:56,636] [INFO] Task started: CheckM
[2024-01-24 13:32:56,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001996005.1_ASM199600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001996005.1_ASM199600v1_genomic.fna/checkm_input GCF_001996005.1_ASM199600v1_genomic.fna/checkm_result
[2024-01-24 13:33:33,424] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:33,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:33,444] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:33,445] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:33,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001996005.1_ASM199600v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:33,445] [INFO] Task started: Blastn
[2024-01-24 13:33:33,445] [INFO] Running command: blastn -query GCF_001996005.1_ASM199600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg900c2e0b-ae95-47bb-a6e1-ee07bc518cf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001996005.1_ASM199600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:34,799] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:34,803] [INFO] Selected 7 target genomes.
[2024-01-24 13:33:34,803] [INFO] Target genome list was writen to GCF_001996005.1_ASM199600v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:34,810] [INFO] Task started: fastANI
[2024-01-24 13:33:34,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a1c1bcc-f2aa-4a33-9ec8-3cdff2e09d61/GCF_001996005.1_ASM199600v1_genomic.fna.gz --refList GCF_001996005.1_ASM199600v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001996005.1_ASM199600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:40,919] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:40,927] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:40,927] [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_001996005.1	s__Salinivibrio siamensis	100.0	1109	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	97.67	97.44	0.92	0.89	15	conclusive
GCF_001995985.1	s__Salinivibrio sharmensis	92.365	950	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280275.1	s__Salinivibrio kushneri	92.2045	985	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	98.18	97.28	0.92	0.89	16	-
GCF_900141775.1	s__Salinivibrio sp900141775	86.6656	907	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001996165.1	s__Salinivibrio proteolyticus	84.6444	764	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	96.18	95.59	0.91	0.88	11	-
GCA_000565345.1	s__Salinivibrio costicola	84.0636	746	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	98.14	97.51	0.90	0.87	10	-
GCF_000513715.1	s__Salinivibrio socompensis	83.3145	729	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	98.85	98.82	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:40,929] [INFO] GTDB search result was written to GCF_001996005.1_ASM199600v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:40,930] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:40,934] [INFO] DFAST_QC result json was written to GCF_001996005.1_ASM199600v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:40,935] [INFO] DFAST_QC completed!
[2024-01-24 13:33:40,935] [INFO] Total running time: 0h1m7s