[2024-01-25 17:49:05,884] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:05,885] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:05,885] [INFO] DQC Reference Directory: /var/lib/cwl/stg25418918-7348-4261-aa90-d97c3bd17eee/dqc_reference
[2024-01-25 17:49:07,033] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:07,033] [INFO] Task started: Prodigal
[2024-01-25 17:49:07,034] [INFO] Running command: gunzip -c /var/lib/cwl/stg344ae9af-d105-4798-a70c-1da8635e6d51/GCF_009756665.1_ASM975666v1_genomic.fna.gz | prodigal -d GCF_009756665.1_ASM975666v1_genomic.fna/cds.fna -a GCF_009756665.1_ASM975666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:25,417] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:25,417] [INFO] Task started: HMMsearch
[2024-01-25 17:49:25,417] [INFO] Running command: hmmsearch --tblout GCF_009756665.1_ASM975666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25418918-7348-4261-aa90-d97c3bd17eee/dqc_reference/reference_markers.hmm GCF_009756665.1_ASM975666v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:25,732] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:25,733] [INFO] Found 6/6 markers.
[2024-01-25 17:49:25,769] [INFO] Query marker FASTA was written to GCF_009756665.1_ASM975666v1_genomic.fna/markers.fasta
[2024-01-25 17:49:25,770] [INFO] Task started: Blastn
[2024-01-25 17:49:25,770] [INFO] Running command: blastn -query GCF_009756665.1_ASM975666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25418918-7348-4261-aa90-d97c3bd17eee/dqc_reference/reference_markers.fasta -out GCF_009756665.1_ASM975666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:26,533] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:26,536] [INFO] Selected 25 target genomes.
[2024-01-25 17:49:26,536] [INFO] Target genome list was writen to GCF_009756665.1_ASM975666v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:26,560] [INFO] Task started: fastANI
[2024-01-25 17:49:26,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg344ae9af-d105-4798-a70c-1da8635e6d51/GCF_009756665.1_ASM975666v1_genomic.fna.gz --refList GCF_009756665.1_ASM975666v1_genomic.fna/target_genomes.txt --output GCF_009756665.1_ASM975666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:46,832] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:46,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25418918-7348-4261-aa90-d97c3bd17eee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:46,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25418918-7348-4261-aa90-d97c3bd17eee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:46,840] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:49:46,840] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:46,840] [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
Permianibacter aggregans	strain=HW001	GCA_009756665.1	1510150	1510150	type	True	100.0	1420	1422	95	conclusive
Permianibacter aggregans	strain=DSM 103792	GCA_004363125.1	1510150	1510150	type	True	99.9688	1376	1422	95	conclusive
Permianibacter fluminis	strain=IMCC34836	GCA_013179735.1	2738515	2738515	type	True	77.6126	338	1422	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	77.3811	55	1422	95	below_threshold
Saccharospirillum mangrovi	strain=HK-33	GCA_003367315.1	2161747	2161747	type	True	76.6609	51	1422	95	below_threshold
Alcanivorax pacificus	strain=W11-5	GCA_000299335.2	1306787	1306787	type	True	76.3511	54	1422	95	below_threshold
Saccharospirillum mangrovi	strain=HK-33	GCA_003054775.1	2161747	2161747	type	True	76.3372	50	1422	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	76.1178	59	1422	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	76.1161	53	1422	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_001401315.1	251699	251699	pathovar	True	75.5313	54	1422	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:46,842] [INFO] DFAST Taxonomy check result was written to GCF_009756665.1_ASM975666v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:46,842] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:46,842] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:46,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25418918-7348-4261-aa90-d97c3bd17eee/dqc_reference/checkm_data
[2024-01-25 17:49:46,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:46,883] [INFO] Task started: CheckM
[2024-01-25 17:49:46,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009756665.1_ASM975666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009756665.1_ASM975666v1_genomic.fna/checkm_input GCF_009756665.1_ASM975666v1_genomic.fna/checkm_result
[2024-01-25 17:50:38,627] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:38,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:38,647] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:38,648] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:38,649] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009756665.1_ASM975666v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:38,649] [INFO] Task started: Blastn
[2024-01-25 17:50:38,649] [INFO] Running command: blastn -query GCF_009756665.1_ASM975666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25418918-7348-4261-aa90-d97c3bd17eee/dqc_reference/reference_markers_gtdb.fasta -out GCF_009756665.1_ASM975666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:39,965] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:39,968] [INFO] Selected 28 target genomes.
[2024-01-25 17:50:39,968] [INFO] Target genome list was writen to GCF_009756665.1_ASM975666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:39,989] [INFO] Task started: fastANI
[2024-01-25 17:50:39,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg344ae9af-d105-4798-a70c-1da8635e6d51/GCF_009756665.1_ASM975666v1_genomic.fna.gz --refList GCF_009756665.1_ASM975666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009756665.1_ASM975666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:04,110] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:04,117] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:04,118] [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_009756665.1	s__Permianibacter aggregans	100.0	1420	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__DSM-103792;g__Permianibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013179735.1	s__Permianibacter fluminis	77.61	339	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__DSM-103792;g__Permianibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367315.1	s__Saccharospirillum mangrovi	76.8671	52	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	76.4044	57	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_001598055.1	s__Cupriavidus nantongensis	76.3585	55	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.73	95.73	0.81	0.78	3	-
GCF_000299335.2	s__Alcanivorax_A pacificus	76.295	54	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002087235.1	s__Pseudomonas_E floridensis	76.0767	56	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803095.1	s__Pseudomonas_E sp002803095	75.786	61	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.6432	99.96	99.96	0.99	0.99	2	-
GCF_013522825.1	s__Pseudomonas_A stutzeri_AK	75.7501	54	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013284265.1	s__Rugamonas sp013284265	75.3167	55	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:04,119] [INFO] GTDB search result was written to GCF_009756665.1_ASM975666v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:04,119] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:04,122] [INFO] DFAST_QC result json was written to GCF_009756665.1_ASM975666v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:04,122] [INFO] DFAST_QC completed!
[2024-01-25 17:51:04,122] [INFO] Total running time: 0h1m58s