[2024-01-24 13:40:28,563] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,565] [INFO] DQC Reference Directory: /var/lib/cwl/stg2738a0e9-ce21-4781-b55a-6856e0d5b5c3/dqc_reference
[2024-01-24 13:40:31,142] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,144] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,144] [INFO] Running command: gunzip -c /var/lib/cwl/stg1878f541-804b-4114-ba60-e74d8dd3cc51/GCF_005280275.1_ASM528027v1_genomic.fna.gz | prodigal -d GCF_005280275.1_ASM528027v1_genomic.fna/cds.fna -a GCF_005280275.1_ASM528027v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:42,875] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:42,875] [INFO] Task started: HMMsearch
[2024-01-24 13:40:42,875] [INFO] Running command: hmmsearch --tblout GCF_005280275.1_ASM528027v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2738a0e9-ce21-4781-b55a-6856e0d5b5c3/dqc_reference/reference_markers.hmm GCF_005280275.1_ASM528027v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:43,180] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:43,181] [INFO] Found 6/6 markers.
[2024-01-24 13:40:43,225] [INFO] Query marker FASTA was written to GCF_005280275.1_ASM528027v1_genomic.fna/markers.fasta
[2024-01-24 13:40:43,225] [INFO] Task started: Blastn
[2024-01-24 13:40:43,225] [INFO] Running command: blastn -query GCF_005280275.1_ASM528027v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2738a0e9-ce21-4781-b55a-6856e0d5b5c3/dqc_reference/reference_markers.fasta -out GCF_005280275.1_ASM528027v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:44,325] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:44,330] [INFO] Selected 10 target genomes.
[2024-01-24 13:40:44,331] [INFO] Target genome list was writen to GCF_005280275.1_ASM528027v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:44,332] [INFO] Task started: fastANI
[2024-01-24 13:40:44,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg1878f541-804b-4114-ba60-e74d8dd3cc51/GCF_005280275.1_ASM528027v1_genomic.fna.gz --refList GCF_005280275.1_ASM528027v1_genomic.fna/target_genomes.txt --output GCF_005280275.1_ASM528027v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:52,857] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:52,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2738a0e9-ce21-4781-b55a-6856e0d5b5c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:52,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2738a0e9-ce21-4781-b55a-6856e0d5b5c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:52,871] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:52,871] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:52,871] [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 kushneri	strain=AL184	GCA_005280275.1	1908198	1908198	type	True	100.0	1144	1146	95	conclusive
Salinivibrio kushneri	strain=AL184	GCA_001995845.1	1908198	1908198	type	True	99.9398	1106	1146	95	conclusive
Salinivibrio siamensis	strain=JCM 14472	GCA_001996005.1	414286	414286	type	True	92.1694	989	1146	95	below_threshold
Salinivibrio sharmensis	strain=DSM 18182	GCA_001995985.1	390883	390883	type	True	91.9987	979	1146	95	below_threshold
Salinivibrio costicola subsp. alcaliphilus	strain=DSM 16359	GCA_001996185.1	272773	51367	type	True	84.2223	803	1146	95	below_threshold
Salinivibrio proteolyticus	strain=DSM 19052	GCA_001996165.1	334715	334715	type	True	84.1951	764	1146	95	below_threshold
Salinivibrio socompensis	strain=S35	GCA_000513715.1	1510206	1510206	type	True	83.147	738	1146	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	79.7111	73	1146	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	79.3773	89	1146	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	77.5975	117	1146	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:52,873] [INFO] DFAST Taxonomy check result was written to GCF_005280275.1_ASM528027v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:52,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:52,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:52,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2738a0e9-ce21-4781-b55a-6856e0d5b5c3/dqc_reference/checkm_data
[2024-01-24 13:40:52,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:52,911] [INFO] Task started: CheckM
[2024-01-24 13:40:52,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005280275.1_ASM528027v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005280275.1_ASM528027v1_genomic.fna/checkm_input GCF_005280275.1_ASM528027v1_genomic.fna/checkm_result
[2024-01-24 13:41:32,372] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:32,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:32,405] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:32,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:32,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005280275.1_ASM528027v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:32,406] [INFO] Task started: Blastn
[2024-01-24 13:41:32,407] [INFO] Running command: blastn -query GCF_005280275.1_ASM528027v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2738a0e9-ce21-4781-b55a-6856e0d5b5c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_005280275.1_ASM528027v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:33,656] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:33,661] [INFO] Selected 7 target genomes.
[2024-01-24 13:41:33,661] [INFO] Target genome list was writen to GCF_005280275.1_ASM528027v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:33,663] [INFO] Task started: fastANI
[2024-01-24 13:41:33,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg1878f541-804b-4114-ba60-e74d8dd3cc51/GCF_005280275.1_ASM528027v1_genomic.fna.gz --refList GCF_005280275.1_ASM528027v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005280275.1_ASM528027v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:39,963] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:39,971] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:39,972] [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_005280275.1	s__Salinivibrio kushneri	100.0	1144	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	98.18	97.28	0.92	0.89	16	conclusive
GCF_001996005.1	s__Salinivibrio siamensis	92.1694	989	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	97.67	97.44	0.92	0.89	15	-
GCF_001995985.1	s__Salinivibrio sharmensis	91.9987	979	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141775.1	s__Salinivibrio sp900141775	85.8736	877	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000565345.1	s__Salinivibrio costicola	84.3062	762	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	98.14	97.51	0.90	0.87	10	-
GCF_001996165.1	s__Salinivibrio proteolyticus	84.197	765	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Salinivibrio	95.0	96.18	95.59	0.91	0.88	11	-
GCF_000513715.1	s__Salinivibrio socompensis	83.147	738	1146	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 13:41:39,974] [INFO] GTDB search result was written to GCF_005280275.1_ASM528027v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:39,974] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:39,979] [INFO] DFAST_QC result json was written to GCF_005280275.1_ASM528027v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:39,979] [INFO] DFAST_QC completed!
[2024-01-24 13:41:39,979] [INFO] Total running time: 0h1m11s