[2024-01-24 11:44:05,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,456] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,457] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0967ed8-c4a5-47d7-bf1d-acda89ef195d/dqc_reference
[2024-01-24 11:44:08,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,841] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,841] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c7c1a00-6843-4aec-90e1-e68e5fcd2d56/GCF_026239995.1_ASM2623999v1_genomic.fna.gz | prodigal -d GCF_026239995.1_ASM2623999v1_genomic.fna/cds.fna -a GCF_026239995.1_ASM2623999v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:18,418] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:18,418] [INFO] Task started: HMMsearch
[2024-01-24 11:44:18,418] [INFO] Running command: hmmsearch --tblout GCF_026239995.1_ASM2623999v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0967ed8-c4a5-47d7-bf1d-acda89ef195d/dqc_reference/reference_markers.hmm GCF_026239995.1_ASM2623999v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:18,649] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:18,650] [INFO] Found 6/6 markers.
[2024-01-24 11:44:18,681] [INFO] Query marker FASTA was written to GCF_026239995.1_ASM2623999v1_genomic.fna/markers.fasta
[2024-01-24 11:44:18,682] [INFO] Task started: Blastn
[2024-01-24 11:44:18,682] [INFO] Running command: blastn -query GCF_026239995.1_ASM2623999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0967ed8-c4a5-47d7-bf1d-acda89ef195d/dqc_reference/reference_markers.fasta -out GCF_026239995.1_ASM2623999v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:19,447] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:19,451] [INFO] Selected 19 target genomes.
[2024-01-24 11:44:19,451] [INFO] Target genome list was writen to GCF_026239995.1_ASM2623999v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:19,469] [INFO] Task started: fastANI
[2024-01-24 11:44:19,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c7c1a00-6843-4aec-90e1-e68e5fcd2d56/GCF_026239995.1_ASM2623999v1_genomic.fna.gz --refList GCF_026239995.1_ASM2623999v1_genomic.fna/target_genomes.txt --output GCF_026239995.1_ASM2623999v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:30,019] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:30,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0967ed8-c4a5-47d7-bf1d-acda89ef195d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:30,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0967ed8-c4a5-47d7-bf1d-acda89ef195d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:30,044] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:30,044] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:30,044] [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
Acetobacter papayae	strain=JCM 25143	GCA_000613285.1	1076592	1076592	type	True	87.1313	742	1011	95	below_threshold
Acetobacter peroxydans	strain=LMG 1635	GCA_011516745.1	104098	104098	type	True	85.7613	728	1011	95	below_threshold
Acetobacter peroxydans	strain=NBRC 13755	GCA_006539345.1	104098	104098	type	True	85.7543	747	1011	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	80.0504	452	1011	95	below_threshold
Acetobacter okinawensis	strain=JCM 25146	GCA_000613865.1	1076594	1076594	type	True	79.7481	416	1011	95	below_threshold
Acetobacter lovaniensis	strain=LMG 1617	GCA_011516875.1	104100	104100	type	True	79.6556	444	1011	95	below_threshold
Acetobacter lovaniensis	strain=DSM 4491	GCA_014207635.1	104100	104100	type	True	79.6153	444	1011	95	below_threshold
Acetobacter lambici	strain=LMG 27439	GCA_011516885.1	1332824	1332824	type	True	79.5284	387	1011	95	below_threshold
Acetobacter pasteurianus subsp. pasteurianus	strain=NBRC 106471	GCA_003850805.1	481145	438	type	True	79.0202	296	1011	95	below_threshold
Acetobacter pasteurianus subsp. pasteurianus	strain=IFO 3191	GCA_000241625.2	481145	438	type	True	78.923	294	1011	95	below_threshold
Acetobacter syzygii	strain=9H-2	GCA_000964225.1	146476	146476	type	True	78.7595	323	1011	95	below_threshold
Acetobacter syzygii	strain=NBRC 16604	GCA_007989285.1	146476	146476	type	True	78.7324	326	1011	95	below_threshold
Komagataeibacter intermedius	strain=TF2	GCA_000964425.1	66229	66229	type	True	77.9498	199	1011	95	below_threshold
Komagataeibacter oboediens	strain=LMG 18849	GCA_003207815.1	65958	65958	type	True	77.7408	202	1011	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	77.6961	162	1011	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.6794	117	1011	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.3187	126	1011	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:30,046] [INFO] DFAST Taxonomy check result was written to GCF_026239995.1_ASM2623999v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:30,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:30,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:30,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0967ed8-c4a5-47d7-bf1d-acda89ef195d/dqc_reference/checkm_data
[2024-01-24 11:44:30,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:30,082] [INFO] Task started: CheckM
[2024-01-24 11:44:30,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026239995.1_ASM2623999v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026239995.1_ASM2623999v1_genomic.fna/checkm_input GCF_026239995.1_ASM2623999v1_genomic.fna/checkm_result
[2024-01-24 11:45:02,140] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:02,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:02,157] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:02,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:02,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026239995.1_ASM2623999v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:02,159] [INFO] Task started: Blastn
[2024-01-24 11:45:02,159] [INFO] Running command: blastn -query GCF_026239995.1_ASM2623999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0967ed8-c4a5-47d7-bf1d-acda89ef195d/dqc_reference/reference_markers_gtdb.fasta -out GCF_026239995.1_ASM2623999v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:03,506] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:03,510] [INFO] Selected 15 target genomes.
[2024-01-24 11:45:03,510] [INFO] Target genome list was writen to GCF_026239995.1_ASM2623999v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:03,522] [INFO] Task started: fastANI
[2024-01-24 11:45:03,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c7c1a00-6843-4aec-90e1-e68e5fcd2d56/GCF_026239995.1_ASM2623999v1_genomic.fna.gz --refList GCF_026239995.1_ASM2623999v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026239995.1_ASM2623999v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:12,748] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:12,767] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:12,767] [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_017377745.1	s__Acetobacter suratthaniensis	99.9701	989	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000613285.1	s__Acetobacter papayae	87.1372	742	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539345.1	s__Acetobacter peroxydans	85.7538	747	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_011516925.1	s__Acetobacter fabarum	80.1202	443	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.96	97.82	0.89	0.87	4	-
GCF_017377735.1	s__Acetobacter sp017377735	80.0676	452	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365315.1	s__Acetobacter sp008365315	80.0222	422	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613865.1	s__Acetobacter okinawensis	79.7481	416	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.60	97.58	0.84	0.82	3	-
GCF_014207635.1	s__Acetobacter lovaniensis	79.6153	444	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011516885.1	s__Acetobacter lambici	79.5269	386	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002153655.1	s__Acetobacter okinawensis_A	79.2562	373	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000723785.2	s__Acetobacter pasteurianus	79.1322	294	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.11	97.27	0.89	0.78	27	-
GCF_000964225.1	s__Acetobacter syzygii	78.7472	324	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.87	98.22	0.97	0.90	7	-
GCF_002738225.1	s__Acetobacter pomorum	78.7233	287	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.71	97.71	0.83	0.83	2	-
GCF_014174165.1	s__Gluconacetobacter dulcium	77.6961	162	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	-
GCF_014174395.1	s__Gluconacetobacter aggeris	77.5273	161	1011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:12,769] [INFO] GTDB search result was written to GCF_026239995.1_ASM2623999v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:12,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:12,773] [INFO] DFAST_QC result json was written to GCF_026239995.1_ASM2623999v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:12,773] [INFO] DFAST_QC completed!
[2024-01-24 11:45:12,773] [INFO] Total running time: 0h1m7s