[2024-01-24 15:02:07,440] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,444] [INFO] DQC Reference Directory: /var/lib/cwl/stg62888d87-d18e-4c5b-9517-2c23892d9c57/dqc_reference
[2024-01-24 15:02:09,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,614] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg0aa35e89-7788-4124-a84c-69cdd9005455/GCF_001921205.1_ASM192120v1_genomic.fna.gz | prodigal -d GCF_001921205.1_ASM192120v1_genomic.fna/cds.fna -a GCF_001921205.1_ASM192120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:36,894] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:36,894] [INFO] Task started: HMMsearch
[2024-01-24 15:02:36,894] [INFO] Running command: hmmsearch --tblout GCF_001921205.1_ASM192120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62888d87-d18e-4c5b-9517-2c23892d9c57/dqc_reference/reference_markers.hmm GCF_001921205.1_ASM192120v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:37,217] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:37,218] [INFO] Found 6/6 markers.
[2024-01-24 15:02:37,284] [INFO] Query marker FASTA was written to GCF_001921205.1_ASM192120v1_genomic.fna/markers.fasta
[2024-01-24 15:02:37,284] [INFO] Task started: Blastn
[2024-01-24 15:02:37,284] [INFO] Running command: blastn -query GCF_001921205.1_ASM192120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62888d87-d18e-4c5b-9517-2c23892d9c57/dqc_reference/reference_markers.fasta -out GCF_001921205.1_ASM192120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:38,632] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:38,636] [INFO] Selected 19 target genomes.
[2024-01-24 15:02:38,637] [INFO] Target genome list was writen to GCF_001921205.1_ASM192120v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:38,655] [INFO] Task started: fastANI
[2024-01-24 15:02:38,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aa35e89-7788-4124-a84c-69cdd9005455/GCF_001921205.1_ASM192120v1_genomic.fna.gz --refList GCF_001921205.1_ASM192120v1_genomic.fna/target_genomes.txt --output GCF_001921205.1_ASM192120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:14,350] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:14,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62888d87-d18e-4c5b-9517-2c23892d9c57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:14,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62888d87-d18e-4c5b-9517-2c23892d9c57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:14,368] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:14,368] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:14,368] [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
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	100.0	2678	2689	95	conclusive
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	81.9791	1549	2689	95	below_threshold
Actinophytocola algeriensis	strain=CECT 8960	GCA_014203735.1	1768010	1768010	type	True	80.4829	1493	2689	95	below_threshold
Actinophytocola algeriensis	strain=DSM 46746	GCA_014874055.1	1768010	1768010	type	True	80.4491	1502	2689	95	below_threshold
Actinophytocola oryzae	strain=DSM 45499	GCA_004364325.1	502181	502181	type	True	80.0067	1451	2689	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	78.8877	888	2689	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.7824	947	2689	95	below_threshold
Actinokineospora inagensis	strain=DSM 44258	GCA_000482865.1	103730	103730	type	True	78.7673	821	2689	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.7257	882	2689	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	78.6866	919	2689	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	78.5977	967	2689	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	78.2979	954	2689	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	78.1276	952	2689	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	78.0579	818	2689	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	77.9624	826	2689	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	77.8822	847	2689	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	77.8647	785	2689	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	77.8545	841	2689	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.7155	1086	2689	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:14,370] [INFO] DFAST Taxonomy check result was written to GCF_001921205.1_ASM192120v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:14,370] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:14,371] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:14,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62888d87-d18e-4c5b-9517-2c23892d9c57/dqc_reference/checkm_data
[2024-01-24 15:03:14,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:14,454] [INFO] Task started: CheckM
[2024-01-24 15:03:14,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001921205.1_ASM192120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001921205.1_ASM192120v1_genomic.fna/checkm_input GCF_001921205.1_ASM192120v1_genomic.fna/checkm_result
[2024-01-24 15:04:47,940] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:47,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:47,961] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:47,961] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:47,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001921205.1_ASM192120v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:47,962] [INFO] Task started: Blastn
[2024-01-24 15:04:47,962] [INFO] Running command: blastn -query GCF_001921205.1_ASM192120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62888d87-d18e-4c5b-9517-2c23892d9c57/dqc_reference/reference_markers_gtdb.fasta -out GCF_001921205.1_ASM192120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:49,965] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:49,969] [INFO] Selected 15 target genomes.
[2024-01-24 15:04:49,969] [INFO] Target genome list was writen to GCF_001921205.1_ASM192120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:49,979] [INFO] Task started: fastANI
[2024-01-24 15:04:49,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aa35e89-7788-4124-a84c-69cdd9005455/GCF_001921205.1_ASM192120v1_genomic.fna.gz --refList GCF_001921205.1_ASM192120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001921205.1_ASM192120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:17,400] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:17,412] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:17,412] [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_001921205.1	s__Actinophytocola xanthii	100.0	2678	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009379765.1	s__Actinophytocola sp009379765	82.08	1365	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921215.1	s__Actinophytocola xinjiangensis	82.0131	1541	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203735.1	s__Actinophytocola algeriensis	80.5138	1484	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004364325.1	s__Actinophytocola oryzae	80.0278	1446	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216555.1	s__Herbihabitans rhizosphaerae	78.9465	863	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Herbihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907695.1	s__Actinokineospora baliensis	78.8874	887	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482865.1	s__Actinokineospora inagensis	78.7631	823	2689	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	78.665	925	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362825.1	s__Labedaea rhizosphaerae	78.6498	1004	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Labedaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	78.576	973	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214935.1	s__Amycolatopsis suaedae	78.2915	971	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	78.1891	953	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	78.1156	955	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	77.9807	819	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:17,414] [INFO] GTDB search result was written to GCF_001921205.1_ASM192120v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:17,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:17,418] [INFO] DFAST_QC result json was written to GCF_001921205.1_ASM192120v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:17,419] [INFO] DFAST_QC completed!
[2024-01-24 15:05:17,419] [INFO] Total running time: 0h3m10s