[2023-06-08 15:53:04,368] [INFO] DFAST_QC pipeline started.
[2023-06-08 15:53:04,374] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 15:53:04,374] [INFO] DQC Reference Directory: /var/lib/cwl/stgd63fee49-44a4-4f74-aaef-fff5a483d98f/dqc_reference
[2023-06-08 15:53:06,894] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 15:53:06,902] [INFO] Task started: Prodigal
[2023-06-08 15:53:06,902] [INFO] Running command: gunzip -c /var/lib/cwl/stg0916059a-9e9d-49fa-b1f2-164bcf48cc78/GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna.gz | prodigal -d GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/cds.fna -a GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 15:53:18,413] [INFO] Task succeeded: Prodigal
[2023-06-08 15:53:18,413] [INFO] Task started: HMMsearch
[2023-06-08 15:53:18,413] [INFO] Running command: hmmsearch --tblout GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd63fee49-44a4-4f74-aaef-fff5a483d98f/dqc_reference/reference_markers.hmm GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/protein.faa > /dev/null
[2023-06-08 15:53:18,711] [INFO] Task succeeded: HMMsearch
[2023-06-08 15:53:18,713] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0916059a-9e9d-49fa-b1f2-164bcf48cc78/GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna.gz]
[2023-06-08 15:53:18,769] [INFO] Query marker FASTA was written to GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/markers.fasta
[2023-06-08 15:53:18,769] [INFO] Task started: Blastn
[2023-06-08 15:53:18,769] [INFO] Running command: blastn -query GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd63fee49-44a4-4f74-aaef-fff5a483d98f/dqc_reference/reference_markers.fasta -out GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:53:19,405] [INFO] Task succeeded: Blastn
[2023-06-08 15:53:19,410] [INFO] Selected 22 target genomes.
[2023-06-08 15:53:19,411] [INFO] Target genome list was writen to GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/target_genomes.txt
[2023-06-08 15:53:19,415] [INFO] Task started: fastANI
[2023-06-08 15:53:19,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg0916059a-9e9d-49fa-b1f2-164bcf48cc78/GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna.gz --refList GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/target_genomes.txt --output GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 15:53:34,795] [INFO] Task succeeded: fastANI
[2023-06-08 15:53:34,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd63fee49-44a4-4f74-aaef-fff5a483d98f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 15:53:34,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd63fee49-44a4-4f74-aaef-fff5a483d98f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 15:53:34,806] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 15:53:34,806] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 15:53:34,806] [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
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	75.0545	63	1351	95	below_threshold
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	74.945	64	1351	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	74.88	51	1351	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	74.8218	53	1351	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	74.8142	52	1351	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	74.7922	67	1351	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_007993775.1	2292766	2292766	type	True	74.7922	67	1351	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	74.7826	65	1351	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.5988	91	1351	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 15:53:34,809] [INFO] DFAST Taxonomy check result was written to GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/tc_result.tsv
[2023-06-08 15:53:34,809] [INFO] ===== Taxonomy check completed =====
[2023-06-08 15:53:34,810] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 15:53:34,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd63fee49-44a4-4f74-aaef-fff5a483d98f/dqc_reference/checkm_data
[2023-06-08 15:53:34,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 15:53:34,861] [INFO] Task started: CheckM
[2023-06-08 15:53:34,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/checkm_input GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/checkm_result
[2023-06-08 15:54:09,508] [INFO] Task succeeded: CheckM
[2023-06-08 15:54:09,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 15:54:09,536] [INFO] ===== Completeness check finished =====
[2023-06-08 15:54:09,537] [INFO] ===== Start GTDB Search =====
[2023-06-08 15:54:09,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/markers.fasta)
[2023-06-08 15:54:09,538] [INFO] Task started: Blastn
[2023-06-08 15:54:09,538] [INFO] Running command: blastn -query GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd63fee49-44a4-4f74-aaef-fff5a483d98f/dqc_reference/reference_markers_gtdb.fasta -out GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:54:10,529] [INFO] Task succeeded: Blastn
[2023-06-08 15:54:10,534] [INFO] Selected 20 target genomes.
[2023-06-08 15:54:10,534] [INFO] Target genome list was writen to GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 15:54:10,542] [INFO] Task started: fastANI
[2023-06-08 15:54:10,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg0916059a-9e9d-49fa-b1f2-164bcf48cc78/GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna.gz --refList GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/target_genomes_gtdb.txt --output GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 15:54:25,038] [INFO] Task succeeded: fastANI
[2023-06-08 15:54:25,054] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 15:54:25,055] [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_011525905.1	s__JACTMI01 sp011525905	76.0785	160	1351	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584695.1	s__JACTMI01 sp014584695	75.9963	162	1351	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227875.1	s__M0029 sp006227875	75.9586	87	1351	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__M0029	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699405.1	s__JAAYLR01 sp016699405	75.9464	145	1351	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521815.1	s__JAAYLR01 sp012521815	75.9166	117	1351	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	99.12	98.38	0.89	0.78	5	-
GCA_002420005.1	s__UBA5704 sp002420005	75.8813	144	1351	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__UBA5704	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697015.1	s__J023 sp003697015	75.873	176	1351	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998715.1	s__JAGPDF01 sp017998715	75.7756	121	1351	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAGPDF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270995.1	s__WTGL01 sp012270995	75.7329	77	1351	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388555.1	s__QQVD01 sp003388555	75.6135	178	1351	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_009837085.1	s__WTGL01 sp009837085	75.612	84	1351	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.78	99.78	0.96	0.95	3	-
GCA_016793245.1	s__JADKAF01 sp016793245	74.8245	86	1351	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719295.1	s__JADKAF01 sp016719295	74.6989	96	1351	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 15:54:25,057] [INFO] GTDB search result was written to GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/result_gtdb.tsv
[2023-06-08 15:54:25,058] [INFO] ===== GTDB Search completed =====
[2023-06-08 15:54:25,063] [INFO] DFAST_QC result json was written to GCA_945787635.1_FO.M.Acidobacteriota.06.1_genomic.fna/dqc_result.json
[2023-06-08 15:54:25,064] [INFO] DFAST_QC completed!
[2023-06-08 15:54:25,064] [INFO] Total running time: 0h1m21s