[2024-01-25 20:11:20,553] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:11:20,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:11:20,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg87b1ca6b-ce8d-4af0-8e72-eeeb71504a2c/dqc_reference
[2024-01-25 20:11:21,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:11:21,671] [INFO] Task started: Prodigal
[2024-01-25 20:11:21,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg05db4dcf-029d-4641-99c1-26bc92a5db07/GCF_024703995.1_ASM2470399v1_genomic.fna.gz | prodigal -d GCF_024703995.1_ASM2470399v1_genomic.fna/cds.fna -a GCF_024703995.1_ASM2470399v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:11:47,664] [INFO] Task succeeded: Prodigal
[2024-01-25 20:11:47,665] [INFO] Task started: HMMsearch
[2024-01-25 20:11:47,665] [INFO] Running command: hmmsearch --tblout GCF_024703995.1_ASM2470399v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87b1ca6b-ce8d-4af0-8e72-eeeb71504a2c/dqc_reference/reference_markers.hmm GCF_024703995.1_ASM2470399v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:11:48,023] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:11:48,024] [INFO] Found 6/6 markers.
[2024-01-25 20:11:48,109] [INFO] Query marker FASTA was written to GCF_024703995.1_ASM2470399v1_genomic.fna/markers.fasta
[2024-01-25 20:11:48,110] [INFO] Task started: Blastn
[2024-01-25 20:11:48,110] [INFO] Running command: blastn -query GCF_024703995.1_ASM2470399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87b1ca6b-ce8d-4af0-8e72-eeeb71504a2c/dqc_reference/reference_markers.fasta -out GCF_024703995.1_ASM2470399v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:11:49,386] [INFO] Task succeeded: Blastn
[2024-01-25 20:11:49,388] [INFO] Selected 18 target genomes.
[2024-01-25 20:11:49,389] [INFO] Target genome list was writen to GCF_024703995.1_ASM2470399v1_genomic.fna/target_genomes.txt
[2024-01-25 20:11:49,454] [INFO] Task started: fastANI
[2024-01-25 20:11:49,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg05db4dcf-029d-4641-99c1-26bc92a5db07/GCF_024703995.1_ASM2470399v1_genomic.fna.gz --refList GCF_024703995.1_ASM2470399v1_genomic.fna/target_genomes.txt --output GCF_024703995.1_ASM2470399v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:37,113] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:37,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87b1ca6b-ce8d-4af0-8e72-eeeb71504a2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:37,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87b1ca6b-ce8d-4af0-8e72-eeeb71504a2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:37,126] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:12:37,126] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:12:37,126] [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
Amycolatopsis pretoriensis	strain=NRRL B-24133	GCA_002156025.1	218821	218821	type	True	90.1402	2366	3442	95	below_threshold
Amycolatopsis pretoriensis	strain=DSM 44654	GCA_900107925.1	218821	218821	type	True	90.1207	2609	3442	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	89.8963	2632	3442	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	89.2543	2557	3442	95	below_threshold
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	89.1364	2584	3442	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	89.0023	2271	3442	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	88.5808	2052	3442	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	88.5786	2438	3442	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	88.3379	2380	3442	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	88.2984	2073	3442	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	88.284	2389	3442	95	below_threshold
Amycolatopsis balhimycina	strain=DSM 44591	GCA_000384295.1	208443	208443	type	True	88.2533	2304	3442	95	below_threshold
Amycolatopsis rifamycinica	strain=DSM 46095	GCA_000695625.1	287986	287986	type	True	88.2291	2294	3442	95	below_threshold
Amycolatopsis jejuensis	strain=NRRL B-24427	GCA_000717335.1	330084	330084	type	True	80.7345	1542	3442	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	80.0365	1373	3442	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	78.5869	894	3442	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	77.9179	1156	3442	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	77.8386	1132	3442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:37,128] [INFO] DFAST Taxonomy check result was written to GCF_024703995.1_ASM2470399v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:37,128] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:37,128] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:37,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87b1ca6b-ce8d-4af0-8e72-eeeb71504a2c/dqc_reference/checkm_data
[2024-01-25 20:12:37,129] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:37,221] [INFO] Task started: CheckM
[2024-01-25 20:12:37,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024703995.1_ASM2470399v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024703995.1_ASM2470399v1_genomic.fna/checkm_input GCF_024703995.1_ASM2470399v1_genomic.fna/checkm_result
[2024-01-25 20:15:02,659] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:02,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:02,687] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:02,687] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:02,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024703995.1_ASM2470399v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:02,689] [INFO] Task started: Blastn
[2024-01-25 20:15:02,689] [INFO] Running command: blastn -query GCF_024703995.1_ASM2470399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87b1ca6b-ce8d-4af0-8e72-eeeb71504a2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_024703995.1_ASM2470399v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:04,740] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:04,747] [INFO] Selected 18 target genomes.
[2024-01-25 20:15:04,747] [INFO] Target genome list was writen to GCF_024703995.1_ASM2470399v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:04,766] [INFO] Task started: fastANI
[2024-01-25 20:15:04,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg05db4dcf-029d-4641-99c1-26bc92a5db07/GCF_024703995.1_ASM2470399v1_genomic.fna.gz --refList GCF_024703995.1_ASM2470399v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024703995.1_ASM2470399v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:56,805] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:56,816] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:15:56,817] [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_900107925.1	s__Amycolatopsis pretoriensis	90.1111	2611	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_902497555.1	s__Amycolatopsis sp902497555	89.9205	2628	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003937945.1	s__Amycolatopsis eburnea	89.2517	2557	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873755.1	s__Amycolatopsis lexingtonensis	89.1578	2581	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900119165.1	s__Amycolatopsis australiensis	88.7548	2343	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716785.1	s__Amycolatopsis vancoresmycina	88.5751	2439	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002234595.1	s__Amycolatopsis vastitatis	88.4842	2309	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002904335.1	s__Amycolatopsis sp002904335	88.4449	2423	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654205.1	s__Amycolatopsis bullii	88.4274	2338	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220945.1	s__Amycolatopsis mediterranei	88.3469	2378	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	0.99	7	-
GCF_002155975.1	s__Amycolatopsis kentuckyensis	88.2894	2075	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384295.1	s__Amycolatopsis balhimycina	88.271	2301	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900105945.1	s__Amycolatopsis tolypomycina	88.2368	2396	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695625.1	s__Amycolatopsis rifamycinica	88.1902	2301	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522235.1	s__Amycolatopsis nivea	81.5182	1684	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.97	97.28	0.91	0.88	6	-
GCF_900115345.1	s__Amycolatopsis rubida	81.4432	1675	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.28	99.27	0.88	0.87	4	-
GCF_000717335.1	s__Amycolatopsis jejuensis	80.7628	1534	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713745.1	s__Amycolatopsis acidiphila	80.0738	1328	3442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:56,818] [INFO] GTDB search result was written to GCF_024703995.1_ASM2470399v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:56,818] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:56,822] [INFO] DFAST_QC result json was written to GCF_024703995.1_ASM2470399v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:56,822] [INFO] DFAST_QC completed!
[2024-01-25 20:15:56,822] [INFO] Total running time: 0h4m36s