[2024-01-24 11:12:24,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:24,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:24,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg804f6d34-88a0-454b-b1c9-a64bd1818be5/dqc_reference
[2024-01-24 11:12:27,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,093] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,094] [INFO] Running command: gunzip -c /var/lib/cwl/stgad2aea00-e93b-4d1b-a00a-fb549b5b81d9/GCF_014648415.1_ASM1464841v1_genomic.fna.gz | prodigal -d GCF_014648415.1_ASM1464841v1_genomic.fna/cds.fna -a GCF_014648415.1_ASM1464841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:47,388] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:47,388] [INFO] Task started: HMMsearch
[2024-01-24 11:12:47,388] [INFO] Running command: hmmsearch --tblout GCF_014648415.1_ASM1464841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg804f6d34-88a0-454b-b1c9-a64bd1818be5/dqc_reference/reference_markers.hmm GCF_014648415.1_ASM1464841v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:47,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:47,807] [INFO] Found 6/6 markers.
[2024-01-24 11:12:47,861] [INFO] Query marker FASTA was written to GCF_014648415.1_ASM1464841v1_genomic.fna/markers.fasta
[2024-01-24 11:12:47,861] [INFO] Task started: Blastn
[2024-01-24 11:12:47,861] [INFO] Running command: blastn -query GCF_014648415.1_ASM1464841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg804f6d34-88a0-454b-b1c9-a64bd1818be5/dqc_reference/reference_markers.fasta -out GCF_014648415.1_ASM1464841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:49,285] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:49,289] [INFO] Selected 21 target genomes.
[2024-01-24 11:12:49,289] [INFO] Target genome list was writen to GCF_014648415.1_ASM1464841v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:49,342] [INFO] Task started: fastANI
[2024-01-24 11:12:49,342] [INFO] Running command: fastANI --query /var/lib/cwl/stgad2aea00-e93b-4d1b-a00a-fb549b5b81d9/GCF_014648415.1_ASM1464841v1_genomic.fna.gz --refList GCF_014648415.1_ASM1464841v1_genomic.fna/target_genomes.txt --output GCF_014648415.1_ASM1464841v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:26,339] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:26,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg804f6d34-88a0-454b-b1c9-a64bd1818be5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:26,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg804f6d34-88a0-454b-b1c9-a64bd1818be5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:26,360] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:26,360] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:26,361] [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 fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	100.0	2338	2338	95	conclusive
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	81.3868	1130	2338	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	81.333	1160	2338	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	81.2415	1149	2338	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	81.1269	1146	2338	95	below_threshold
Actinokineospora pegani	strain=TRM 65233	GCA_009745975.1	2654637	2654637	type	True	81.1109	1143	2338	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	81.1017	1132	2338	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	81.0753	1125	2338	95	below_threshold
Actinokineospora alba	strain=DSM 45114	GCA_004362515.1	504798	504798	type	True	81.0661	1189	2338	95	below_threshold
Actinokineospora xionganensis	strain=HBU206404	GCA_014323725.1	2684470	2684470	type	True	81.0358	1129	2338	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	80.8667	1242	2338	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	80.8047	1147	2338	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	80.7644	1146	2338	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	79.1843	1138	2338	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	79.1451	1151	2338	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	79.0424	1099	2338	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	78.7832	909	2338	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	78.7459	908	2338	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	78.4803	985	2338	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.3436	871	2338	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	77.8011	691	2338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:26,362] [INFO] DFAST Taxonomy check result was written to GCF_014648415.1_ASM1464841v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:26,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:26,364] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:26,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg804f6d34-88a0-454b-b1c9-a64bd1818be5/dqc_reference/checkm_data
[2024-01-24 11:13:26,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:26,441] [INFO] Task started: CheckM
[2024-01-24 11:13:26,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648415.1_ASM1464841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648415.1_ASM1464841v1_genomic.fna/checkm_input GCF_014648415.1_ASM1464841v1_genomic.fna/checkm_result
[2024-01-24 11:14:36,756] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:36,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:36,784] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:36,784] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:36,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648415.1_ASM1464841v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:36,785] [INFO] Task started: Blastn
[2024-01-24 11:14:36,785] [INFO] Running command: blastn -query GCF_014648415.1_ASM1464841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg804f6d34-88a0-454b-b1c9-a64bd1818be5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648415.1_ASM1464841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:38,817] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:38,822] [INFO] Selected 20 target genomes.
[2024-01-24 11:14:38,823] [INFO] Target genome list was writen to GCF_014648415.1_ASM1464841v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:38,836] [INFO] Task started: fastANI
[2024-01-24 11:14:38,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgad2aea00-e93b-4d1b-a00a-fb549b5b81d9/GCF_014648415.1_ASM1464841v1_genomic.fna.gz --refList GCF_014648415.1_ASM1464841v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648415.1_ASM1464841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:15,523] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:15,544] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:15,545] [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_014648415.1	s__Actinokineospora fastidiosa	100.0	2338	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900101685.1	s__Actinokineospora iranica	81.3596	1135	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111175.1	s__Actinokineospora terrae	81.2616	1146	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_003182415.1	s__Actinokineospora mzabensis	81.1164	1224	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_009745975.1	s__Actinokineospora pegani	81.1156	1142	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907695.1	s__Actinokineospora baliensis	81.0831	1124	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362515.1	s__Actinokineospora alba	81.0579	1190	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002934265.1	s__Actinokineospora auranticolor	80.9321	1208	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940455.1	s__Actinokineospora bangkokensis	80.8875	1237	2338	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	80.7527	1147	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634995.1	s__Actinosynnema variisporeum	79.1716	1138	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280085.1	s__Actinosynnema sp001280085	79.1705	1186	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	79.1215	1158	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_009498035.1	s__Actinosynnema syringae	79.1115	1267	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_006716745.1	s__Actinosynnema saharense	79.1095	1175	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769385.1	s__Actinosynnema deserti	79.0539	1096	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	78.7693	904	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005405885.1	s__Gandjariella thermophila	78.5534	802	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Gandjariella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876755.1	s__Crossiella equi	78.407	1086	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900119165.1	s__Amycolatopsis australiensis	78.2175	1029	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:15,547] [INFO] GTDB search result was written to GCF_014648415.1_ASM1464841v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:15,547] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:15,552] [INFO] DFAST_QC result json was written to GCF_014648415.1_ASM1464841v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:15,552] [INFO] DFAST_QC completed!
[2024-01-24 11:15:15,552] [INFO] Total running time: 0h2m51s