[2024-01-24 13:18:33,348] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,353] [INFO] DQC Reference Directory: /var/lib/cwl/stg70759ebb-670a-4196-a4ae-5581f61ec940/dqc_reference
[2024-01-24 13:18:34,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,833] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,833] [INFO] Running command: gunzip -c /var/lib/cwl/stgccfd90b2-1182-4f70-83bf-f334ef433a5d/GCF_014873915.1_ASM1487391v1_genomic.fna.gz | prodigal -d GCF_014873915.1_ASM1487391v1_genomic.fna/cds.fna -a GCF_014873915.1_ASM1487391v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:02,964] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:02,964] [INFO] Task started: HMMsearch
[2024-01-24 13:19:02,964] [INFO] Running command: hmmsearch --tblout GCF_014873915.1_ASM1487391v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70759ebb-670a-4196-a4ae-5581f61ec940/dqc_reference/reference_markers.hmm GCF_014873915.1_ASM1487391v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:03,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:03,391] [INFO] Found 6/6 markers.
[2024-01-24 13:19:03,467] [INFO] Query marker FASTA was written to GCF_014873915.1_ASM1487391v1_genomic.fna/markers.fasta
[2024-01-24 13:19:03,468] [INFO] Task started: Blastn
[2024-01-24 13:19:03,468] [INFO] Running command: blastn -query GCF_014873915.1_ASM1487391v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70759ebb-670a-4196-a4ae-5581f61ec940/dqc_reference/reference_markers.fasta -out GCF_014873915.1_ASM1487391v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:04,838] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:04,841] [INFO] Selected 20 target genomes.
[2024-01-24 13:19:04,841] [INFO] Target genome list was writen to GCF_014873915.1_ASM1487391v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:04,848] [INFO] Task started: fastANI
[2024-01-24 13:19:04,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgccfd90b2-1182-4f70-83bf-f334ef433a5d/GCF_014873915.1_ASM1487391v1_genomic.fna.gz --refList GCF_014873915.1_ASM1487391v1_genomic.fna/target_genomes.txt --output GCF_014873915.1_ASM1487391v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:47,978] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:47,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70759ebb-670a-4196-a4ae-5581f61ec940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:47,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70759ebb-670a-4196-a4ae-5581f61ec940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:47,998] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:47,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:47,998] [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 roodepoortensis	strain=DSM 46661	GCA_014873915.1	700274	700274	type	True	100.0	3028	3034	95	conclusive
Amycolatopsis lurida	strain=DSM 43134	GCA_900105055.1	31959	31959	type	True	94.3466	2500	3034	95	below_threshold
Amycolatopsis lurida	strain=NRRL 2430	GCA_000749465.3	31959	31959	type	True	94.3441	2471	3034	95	below_threshold
Amycolatopsis keratiniphila subsp. nogabecina	strain=FH 1893	GCA_001953855.1	208442	129921	type	True	92.6999	2506	3034	95	below_threshold
Amycolatopsis keratiniphila subsp. keratiniphila	strain=DSM 44409	GCA_001620365.2	227715	129921	type	True	92.6004	2425	3034	95	below_threshold
Amycolatopsis japonica	strain=MG417-CF17	GCA_000732925.1	208439	208439	type	True	92.4862	2484	3034	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	91.11	2296	3034	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	91.0514	2344	3034	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	90.7334	2177	3034	95	below_threshold
Amycolatopsis orientalis	strain=KCTC 9412	GCA_000478275.1	31958	31958	type	True	90.1271	2256	3034	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.6604	1692	3034	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.0735	1114	3034	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.1907	1027	3034	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	79.1314	1040	3034	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	79.0988	1034	3034	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.7993	1060	3034	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.099	844	3034	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	77.9258	986	3034	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	77.8448	1038	3034	95	below_threshold
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	77.4552	1014	3034	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:48,000] [INFO] DFAST Taxonomy check result was written to GCF_014873915.1_ASM1487391v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:48,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:48,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:48,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70759ebb-670a-4196-a4ae-5581f61ec940/dqc_reference/checkm_data
[2024-01-24 13:19:48,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:48,080] [INFO] Task started: CheckM
[2024-01-24 13:19:48,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014873915.1_ASM1487391v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014873915.1_ASM1487391v1_genomic.fna/checkm_input GCF_014873915.1_ASM1487391v1_genomic.fna/checkm_result
[2024-01-24 13:21:14,613] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:14,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:14,643] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:14,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:14,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014873915.1_ASM1487391v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:14,644] [INFO] Task started: Blastn
[2024-01-24 13:21:14,645] [INFO] Running command: blastn -query GCF_014873915.1_ASM1487391v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70759ebb-670a-4196-a4ae-5581f61ec940/dqc_reference/reference_markers_gtdb.fasta -out GCF_014873915.1_ASM1487391v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:16,646] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:16,650] [INFO] Selected 14 target genomes.
[2024-01-24 13:21:16,650] [INFO] Target genome list was writen to GCF_014873915.1_ASM1487391v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:16,682] [INFO] Task started: fastANI
[2024-01-24 13:21:16,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgccfd90b2-1182-4f70-83bf-f334ef433a5d/GCF_014873915.1_ASM1487391v1_genomic.fna.gz --refList GCF_014873915.1_ASM1487391v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014873915.1_ASM1487391v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:49,236] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:49,248] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:49,248] [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_014873915.1	s__Amycolatopsis roodepoortensis	100.0	3033	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.45	96.45	0.88	0.88	2	conclusive
GCF_900105055.1	s__Amycolatopsis lurida	94.3495	2498	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.56	95.13	0.93	0.86	3	-
GCF_001620365.2	s__Amycolatopsis keratiniphila	92.5994	2425	3034	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	92.4566	2487	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.30	96.67	0.90	0.88	4	-
GCF_000342005.1	s__Amycolatopsis decaplanina	92.4112	2248	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003947415.1	s__Amycolatopsis sp003947415	92.0977	2450	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.38	96.38	0.89	0.88	3	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	91.1832	2330	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001995215.1	s__Amycolatopsis azurea	91.0665	2343	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002234405.1	s__Amycolatopsis thailandensis	90.7482	2175	3034	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	90.147	2253	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.64	96.64	0.89	0.89	2	-
GCF_900115565.1	s__Yuhushiella arida	79.0656	1042	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003634995.1	s__Actinosynnema variisporeum	77.9261	986	3034	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	77.8373	1050	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_001921215.1	s__Actinophytocola xinjiangensis	77.4178	1029	3034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:49,250] [INFO] GTDB search result was written to GCF_014873915.1_ASM1487391v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:49,251] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:49,256] [INFO] DFAST_QC result json was written to GCF_014873915.1_ASM1487391v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:49,256] [INFO] DFAST_QC completed!
[2024-01-24 13:21:49,257] [INFO] Total running time: 0h3m16s