[2024-01-25 19:07:35,714] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:35,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:35,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg33cabbbc-aa62-44e4-996b-9caaa2176f55/dqc_reference
[2024-01-25 19:07:36,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:36,874] [INFO] Task started: Prodigal
[2024-01-25 19:07:36,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg99cba6b1-cb9a-431a-9a65-675160b81163/GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/cds.fna -a GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:03,908] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:03,908] [INFO] Task started: HMMsearch
[2024-01-25 19:08:03,908] [INFO] Running command: hmmsearch --tblout GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33cabbbc-aa62-44e4-996b-9caaa2176f55/dqc_reference/reference_markers.hmm GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:04,336] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:04,337] [INFO] Found 6/6 markers.
[2024-01-25 19:08:04,409] [INFO] Query marker FASTA was written to GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:08:04,409] [INFO] Task started: Blastn
[2024-01-25 19:08:04,409] [INFO] Running command: blastn -query GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg33cabbbc-aa62-44e4-996b-9caaa2176f55/dqc_reference/reference_markers.fasta -out GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:05,765] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:05,775] [INFO] Selected 27 target genomes.
[2024-01-25 19:08:05,775] [INFO] Target genome list was writen to GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:08:05,793] [INFO] Task started: fastANI
[2024-01-25 19:08:05,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg99cba6b1-cb9a-431a-9a65-675160b81163/GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna.gz --refList GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:01,400] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:01,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33cabbbc-aa62-44e4-996b-9caaa2176f55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:01,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33cabbbc-aa62-44e4-996b-9caaa2176f55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:01,415] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:01,416] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:01,416] [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 xylanica	strain=CPCC 202699	GCA_900107045.1	589385	589385	type	True	100.0	3124	3124	95	conclusive
Amycolatopsis pittospori	strain=PIP199	GCA_013870525.1	2749434	2749434	type	True	81.3786	1441	3124	95	below_threshold
Amycolatopsis keratiniphila subsp. keratiniphila	strain=DSM 44409	GCA_001620365.2	227715	129921	type	True	81.2885	1523	3124	95	below_threshold
Amycolatopsis keratiniphila subsp. nogabecina	strain=FH 1893	GCA_001953855.1	208442	129921	type	True	81.2847	1521	3124	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	81.2549	1418	3124	95	below_threshold
Amycolatopsis orientalis	strain=KCTC 9412	GCA_000478275.1	31958	31958	type	True	81.2424	1511	3124	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	81.1793	1501	3124	95	below_threshold
Amycolatopsis alba	strain=DSM 44262	GCA_000384215.1	76020	76020	type	True	81.1629	1537	3124	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	81.1563	1676	3124	95	below_threshold
Amycolatopsis alba	strain=DSM 44262	GCA_002234385.1	76020	76020	type	True	81.1523	1431	3124	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	81.1019	1448	3124	95	below_threshold
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	81.0676	1673	3124	95	below_threshold
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	81.0612	1547	3124	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	81.0494	1437	3124	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	80.9634	1660	3124	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	80.9221	1637	3124	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	80.9097	1594	3124	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	80.7948	1492	3124	95	below_threshold
Amycolatopsis dendrobii	strain=DR6-1	GCA_014145675.1	2760662	2760662	type	True	80.2202	1305	3124	95	below_threshold
Amycolatopsis acidiphila	strain=JCM 30562	GCA_007713745.1	715473	715473	type	True	79.8989	1109	3124	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.8711	1111	3124	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	79.8552	1162	3124	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	79.6045	1154	3124	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	79.4953	1084	3124	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.2684	1041	3124	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.8776	1019	3124	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.2823	899	3124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:01,418] [INFO] DFAST Taxonomy check result was written to GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:09:01,418] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:01,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:01,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33cabbbc-aa62-44e4-996b-9caaa2176f55/dqc_reference/checkm_data
[2024-01-25 19:09:01,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:01,503] [INFO] Task started: CheckM
[2024-01-25 19:09:01,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/checkm_input GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:10:32,842] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:32,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:32,868] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:32,868] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:32,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:10:32,869] [INFO] Task started: Blastn
[2024-01-25 19:10:32,869] [INFO] Running command: blastn -query GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg33cabbbc-aa62-44e4-996b-9caaa2176f55/dqc_reference/reference_markers_gtdb.fasta -out GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:34,915] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:34,918] [INFO] Selected 25 target genomes.
[2024-01-25 19:10:34,918] [INFO] Target genome list was writen to GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:34,967] [INFO] Task started: fastANI
[2024-01-25 19:10:34,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg99cba6b1-cb9a-431a-9a65-675160b81163/GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna.gz --refList GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:31,718] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:31,733] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:31,733] [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_900107045.1	s__Amycolatopsis xylanica	100.0	3124	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001620365.2	s__Amycolatopsis keratiniphila	81.3012	1519	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.78	96.67	0.89	0.86	5	-
GCF_000732925.1	s__Amycolatopsis japonica	81.2873	1549	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.30	96.67	0.90	0.88	4	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	81.2695	1539	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234405.1	s__Amycolatopsis thailandensis	81.2637	1417	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478275.1	s__Amycolatopsis orientalis	81.2547	1510	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.64	96.64	0.89	0.89	2	-
GCF_000342005.1	s__Amycolatopsis decaplanina	81.2079	1456	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384215.1	s__Amycolatopsis alba	81.1671	1535	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003937945.1	s__Amycolatopsis eburnea	81.148	1678	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155975.1	s__Amycolatopsis kentuckyensis	81.0879	1453	3124	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	81.0741	1672	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002234595.1	s__Amycolatopsis vastitatis	81.0635	1547	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953865.1	s__Amycolatopsis coloradensis	81.0233	1409	3124	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	80.9754	1561	3124	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	80.9713	1567	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013364075.1	s__Amycolatopsis sp013364075	80.9662	1637	3124	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	80.9522	1583	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	0.99	7	-
GCF_017308975.1	s__Amycolatopsis sp017308975	80.9454	1596	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110575.1	s__Amycolatopsis saalfeldensis	80.7634	1500	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145675.1	s__Amycolatopsis sp014145675	80.2111	1306	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016889705.1	s__Amycolatopsis sp016889705	80.0102	1298	3124	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	79.857	1118	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014191255.1	s__Amycolatopsis bartoniae	79.7172	1125	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	0.99	0.99	3	-
GCF_900114035.1	s__Amycolatopsis sacchari	79.6404	1146	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410405.1	s__Amycolatopsis endophytica	79.502	1082	3124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:31,735] [INFO] GTDB search result was written to GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:31,735] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:31,742] [INFO] DFAST_QC result json was written to GCF_900107045.1_IMG-taxon_2675903050_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:11:31,742] [INFO] DFAST_QC completed!
[2024-01-25 19:11:31,742] [INFO] Total running time: 0h3m56s