[2024-01-24 11:21:07,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,408] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg91e58ccb-28f2-4a57-9f64-7b22da1565cb/dqc_reference
[2024-01-24 11:21:11,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,964] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,965] [INFO] Running command: gunzip -c /var/lib/cwl/stg50b7f773-0bd3-4db7-919f-342564286978/GCF_004362515.1_ASM436251v1_genomic.fna.gz | prodigal -d GCF_004362515.1_ASM436251v1_genomic.fna/cds.fna -a GCF_004362515.1_ASM436251v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:37,561] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:37,561] [INFO] Task started: HMMsearch
[2024-01-24 11:21:37,561] [INFO] Running command: hmmsearch --tblout GCF_004362515.1_ASM436251v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91e58ccb-28f2-4a57-9f64-7b22da1565cb/dqc_reference/reference_markers.hmm GCF_004362515.1_ASM436251v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:37,901] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:37,902] [INFO] Found 6/6 markers.
[2024-01-24 11:21:37,958] [INFO] Query marker FASTA was written to GCF_004362515.1_ASM436251v1_genomic.fna/markers.fasta
[2024-01-24 11:21:37,959] [INFO] Task started: Blastn
[2024-01-24 11:21:37,959] [INFO] Running command: blastn -query GCF_004362515.1_ASM436251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91e58ccb-28f2-4a57-9f64-7b22da1565cb/dqc_reference/reference_markers.fasta -out GCF_004362515.1_ASM436251v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:39,248] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:39,252] [INFO] Selected 16 target genomes.
[2024-01-24 11:21:39,253] [INFO] Target genome list was writen to GCF_004362515.1_ASM436251v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:39,263] [INFO] Task started: fastANI
[2024-01-24 11:21:39,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b7f773-0bd3-4db7-919f-342564286978/GCF_004362515.1_ASM436251v1_genomic.fna.gz --refList GCF_004362515.1_ASM436251v1_genomic.fna/target_genomes.txt --output GCF_004362515.1_ASM436251v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:22:07,381] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:07,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91e58ccb-28f2-4a57-9f64-7b22da1565cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:22:07,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91e58ccb-28f2-4a57-9f64-7b22da1565cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:22:07,398] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:22:07,398] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:22:07,399] [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
Actinokineospora alba	strain=DSM 45114	GCA_004362515.1	504798	504798	type	True	100.0	2428	2429	95	conclusive
Actinokineospora xionganensis	strain=HBU206404	GCA_014323725.1	2684470	2684470	type	True	92.1768	1817	2429	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	82.0903	1152	2429	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	81.2458	1110	2429	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	81.1705	1104	2429	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	81.1568	1088	2429	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	81.1549	1124	2429	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	81.123	1175	2429	95	below_threshold
Actinokineospora pegani	strain=TRM 65233	GCA_009745975.1	2654637	2654637	type	True	81.0754	1055	2429	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	80.7449	1053	2429	95	below_threshold
Actinophytocola algeriensis	strain=DSM 46746	GCA_014874055.1	1768010	1768010	type	True	79.1039	1036	2429	95	below_threshold
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	78.774	1019	2429	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	78.6673	892	2429	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	78.5824	850	2429	95	below_threshold
Actinophytocola oryzae	strain=DSM 45499	GCA_004364325.1	502181	502181	type	True	78.4414	1016	2429	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	78.2883	772	2429	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:22:07,404] [INFO] DFAST Taxonomy check result was written to GCF_004362515.1_ASM436251v1_genomic.fna/tc_result.tsv
[2024-01-24 11:22:07,405] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:22:07,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:22:07,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91e58ccb-28f2-4a57-9f64-7b22da1565cb/dqc_reference/checkm_data
[2024-01-24 11:22:07,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:22:07,476] [INFO] Task started: CheckM
[2024-01-24 11:22:07,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362515.1_ASM436251v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362515.1_ASM436251v1_genomic.fna/checkm_input GCF_004362515.1_ASM436251v1_genomic.fna/checkm_result
[2024-01-24 11:23:55,620] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:55,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:55,642] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:55,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:55,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362515.1_ASM436251v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:55,643] [INFO] Task started: Blastn
[2024-01-24 11:23:55,644] [INFO] Running command: blastn -query GCF_004362515.1_ASM436251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91e58ccb-28f2-4a57-9f64-7b22da1565cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362515.1_ASM436251v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:57,611] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:57,615] [INFO] Selected 12 target genomes.
[2024-01-24 11:23:57,615] [INFO] Target genome list was writen to GCF_004362515.1_ASM436251v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:57,626] [INFO] Task started: fastANI
[2024-01-24 11:23:57,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b7f773-0bd3-4db7-919f-342564286978/GCF_004362515.1_ASM436251v1_genomic.fna.gz --refList GCF_004362515.1_ASM436251v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362515.1_ASM436251v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:19,421] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:19,444] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:19,444] [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_004362515.1	s__Actinokineospora alba	100.0	2427	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_014323725.1	s__Actinokineospora xionganensis	92.2056	1814	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900070365.1	s__Actinokineospora sp900070365	84.0255	1425	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101685.1	s__Actinokineospora iranica	82.0899	1151	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182415.1	s__Actinokineospora mzabensis	81.2949	1163	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_016907695.1	s__Actinokineospora baliensis	81.1796	1105	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	81.0805	1183	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009745975.1	s__Actinokineospora pegani	81.0781	1054	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	80.9904	1149	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	80.7344	1055	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002815.1	s__Umezawaea tangerina	78.751	1031	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Umezawaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876755.1	s__Crossiella equi	78.3602	931	2429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:19,446] [INFO] GTDB search result was written to GCF_004362515.1_ASM436251v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:19,447] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:19,451] [INFO] DFAST_QC result json was written to GCF_004362515.1_ASM436251v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:19,451] [INFO] DFAST_QC completed!
[2024-01-24 11:24:19,451] [INFO] Total running time: 0h3m12s