[2024-01-25 20:21:35,418] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:35,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:35,420] [INFO] DQC Reference Directory: /var/lib/cwl/stga5422c22-7218-45eb-a7ca-889cee21e809/dqc_reference
[2024-01-25 20:21:36,543] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:36,544] [INFO] Task started: Prodigal
[2024-01-25 20:21:36,545] [INFO] Running command: gunzip -c /var/lib/cwl/stg34de598e-02b6-451d-b634-83608ce53ea0/GCF_000565345.1_costicolaLMG11651_genomic.fna.gz | prodigal -d GCF_000565345.1_costicolaLMG11651_genomic.fna/cds.fna -a GCF_000565345.1_costicolaLMG11651_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:44,065] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:44,065] [INFO] Task started: HMMsearch
[2024-01-25 20:21:44,066] [INFO] Running command: hmmsearch --tblout GCF_000565345.1_costicolaLMG11651_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5422c22-7218-45eb-a7ca-889cee21e809/dqc_reference/reference_markers.hmm GCF_000565345.1_costicolaLMG11651_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:44,278] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:44,280] [INFO] Found 6/6 markers.
[2024-01-25 20:21:44,310] [INFO] Query marker FASTA was written to GCF_000565345.1_costicolaLMG11651_genomic.fna/markers.fasta
[2024-01-25 20:21:44,310] [INFO] Task started: Blastn
[2024-01-25 20:21:44,310] [INFO] Running command: blastn -query GCF_000565345.1_costicolaLMG11651_genomic.fna/markers.fasta -db /var/lib/cwl/stga5422c22-7218-45eb-a7ca-889cee21e809/dqc_reference/reference_markers.fasta -out GCF_000565345.1_costicolaLMG11651_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:45,007] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:45,011] [INFO] Selected 11 target genomes.
[2024-01-25 20:21:45,011] [INFO] Target genome list was writen to GCF_000565345.1_costicolaLMG11651_genomic.fna/target_genomes.txt
[2024-01-25 20:21:45,017] [INFO] Task started: fastANI
[2024-01-25 20:21:45,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg34de598e-02b6-451d-b634-83608ce53ea0/GCF_000565345.1_costicolaLMG11651_genomic.fna.gz --refList GCF_000565345.1_costicolaLMG11651_genomic.fna/target_genomes.txt --output GCF_000565345.1_costicolaLMG11651_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:53,001] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:53,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5422c22-7218-45eb-a7ca-889cee21e809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:53,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5422c22-7218-45eb-a7ca-889cee21e809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:53,008] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:21:53,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:53,009] [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 costicola subsp. alcaliphilus	strain=DSM 16359	GCA_001996185.1	272773	51367	type	True	98.3396	932	1031	95	conclusive
Salinivibrio socompensis	strain=S35	GCA_000513715.1	1510206	1510206	type	True	88.6754	824	1031	95	below_threshold
Salinivibrio kushneri	strain=AL184	GCA_005280275.1	1908198	1908198	type	True	84.4278	760	1031	95	below_threshold
Salinivibrio kushneri	strain=AL184	GCA_001995845.1	1908198	1908198	type	True	84.3905	756	1031	95	below_threshold
Salinivibrio sharmensis	strain=DSM 18182	GCA_001995985.1	390883	390883	type	True	84.0115	745	1031	95	below_threshold
Salinivibrio siamensis	strain=JCM 14472	GCA_001996005.1	414286	414286	type	True	83.8345	775	1031	95	below_threshold
Salinivibrio proteolyticus	strain=DSM 19052	GCA_001996165.1	334715	334715	type	True	82.7571	638	1031	95	below_threshold
Neiella holothuriorum	strain=126	GCA_019457915.1	2870530	2870530	type	True	76.8271	52	1031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:53,010] [INFO] DFAST Taxonomy check result was written to GCF_000565345.1_costicolaLMG11651_genomic.fna/tc_result.tsv
[2024-01-25 20:21:53,011] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:53,011] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:53,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5422c22-7218-45eb-a7ca-889cee21e809/dqc_reference/checkm_data
[2024-01-25 20:21:53,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:53,047] [INFO] Task started: CheckM
[2024-01-25 20:21:53,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000565345.1_costicolaLMG11651_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000565345.1_costicolaLMG11651_genomic.fna/checkm_input GCF_000565345.1_costicolaLMG11651_genomic.fna/checkm_result
[2024-01-25 20:22:21,043] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:21,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:21,083] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:21,083] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:21,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000565345.1_costicolaLMG11651_genomic.fna/markers.fasta)
[2024-01-25 20:22:21,084] [INFO] Task started: Blastn
[2024-01-25 20:22:21,084] [INFO] Running command: blastn -query GCF_000565345.1_costicolaLMG11651_genomic.fna/markers.fasta -db /var/lib/cwl/stga5422c22-7218-45eb-a7ca-889cee21e809/dqc_reference/reference_markers_gtdb.fasta -out GCF_000565345.1_costicolaLMG11651_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:22,122] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:22,126] [INFO] Selected 7 target genomes.
[2024-01-25 20:22:22,126] [INFO] Target genome list was writen to GCF_000565345.1_costicolaLMG11651_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:22,135] [INFO] Task started: fastANI
[2024-01-25 20:22:22,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg34de598e-02b6-451d-b634-83608ce53ea0/GCF_000565345.1_costicolaLMG11651_genomic.fna.gz --refList GCF_000565345.1_costicolaLMG11651_genomic.fna/target_genomes_gtdb.txt --output GCF_000565345.1_costicolaLMG11651_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:27,861] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:27,866] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:27,867] [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
GCA_000565345.1	s__Salinivibrio costicola	100.0	1020	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	98.14	97.51	0.90	0.87	10	conclusive
GCF_000513715.1	s__Salinivibrio socompensis	88.6873	825	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	98.85	98.82	0.88	0.87	3	-
GCF_900141775.1	s__Salinivibrio sp900141775	84.5105	816	1031	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	84.4374	759	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	98.18	97.28	0.92	0.89	16	-
GCF_001995985.1	s__Salinivibrio sharmensis	84.0073	745	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001996005.1	s__Salinivibrio siamensis	83.8345	775	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	97.67	97.44	0.92	0.89	15	-
GCF_001996165.1	s__Salinivibrio proteolyticus	82.7571	638	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	96.18	95.59	0.91	0.88	11	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:27,868] [INFO] GTDB search result was written to GCF_000565345.1_costicolaLMG11651_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:27,869] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:27,871] [INFO] DFAST_QC result json was written to GCF_000565345.1_costicolaLMG11651_genomic.fna/dqc_result.json
[2024-01-25 20:22:27,871] [INFO] DFAST_QC completed!
[2024-01-25 20:22:27,871] [INFO] Total running time: 0h0m52s