[2024-01-25 20:17:50,680] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:50,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:50,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg75bc4f3b-beb9-4392-b2d2-ce1be32650d1/dqc_reference
[2024-01-25 20:17:51,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:51,890] [INFO] Task started: Prodigal
[2024-01-25 20:17:51,890] [INFO] Running command: gunzip -c /var/lib/cwl/stgc81fe176-b6d9-42b8-a727-2ba7f11005be/GCF_000482705.1_ASM48270v1_genomic.fna.gz | prodigal -d GCF_000482705.1_ASM48270v1_genomic.fna/cds.fna -a GCF_000482705.1_ASM48270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:03,843] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:03,843] [INFO] Task started: HMMsearch
[2024-01-25 20:18:03,843] [INFO] Running command: hmmsearch --tblout GCF_000482705.1_ASM48270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75bc4f3b-beb9-4392-b2d2-ce1be32650d1/dqc_reference/reference_markers.hmm GCF_000482705.1_ASM48270v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:04,155] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:04,156] [INFO] Found 6/6 markers.
[2024-01-25 20:18:04,196] [INFO] Query marker FASTA was written to GCF_000482705.1_ASM48270v1_genomic.fna/markers.fasta
[2024-01-25 20:18:04,196] [INFO] Task started: Blastn
[2024-01-25 20:18:04,196] [INFO] Running command: blastn -query GCF_000482705.1_ASM48270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75bc4f3b-beb9-4392-b2d2-ce1be32650d1/dqc_reference/reference_markers.fasta -out GCF_000482705.1_ASM48270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:05,364] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:05,366] [INFO] Selected 11 target genomes.
[2024-01-25 20:18:05,367] [INFO] Target genome list was writen to GCF_000482705.1_ASM48270v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:05,379] [INFO] Task started: fastANI
[2024-01-25 20:18:05,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgc81fe176-b6d9-42b8-a727-2ba7f11005be/GCF_000482705.1_ASM48270v1_genomic.fna.gz --refList GCF_000482705.1_ASM48270v1_genomic.fna/target_genomes.txt --output GCF_000482705.1_ASM48270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:21,139] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:21,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75bc4f3b-beb9-4392-b2d2-ce1be32650d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:21,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75bc4f3b-beb9-4392-b2d2-ce1be32650d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:21,147] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:21,147] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:21,148] [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
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	100.0	1656	1660	95	conclusive
Glycomyces tenuis	strain=DSM 44171	GCA_000427885.1	58116	58116	type	True	89.5071	1283	1660	95	below_threshold
Glycomyces tenuis	strain=NRRL B-16895	GCA_000715885.1	58116	58116	type	True	89.4072	1304	1660	95	below_threshold
Glycomyces xiaoerkulensis	strain=TRM 41368	GCA_002798405.1	2038139	2038139	type	True	83.8113	972	1660	95	below_threshold
Glycomyces salinus	strain=YIM 93776	GCA_016428645.1	980294	980294	type	True	83.7957	1061	1660	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	83.3971	1068	1660	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	83.3946	1072	1660	95	below_threshold
Glycomyces buryatensis	strain=18	GCA_004912275.1	2570927	2570927	type	True	83.3394	1066	1660	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	83.2772	994	1660	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	83.2604	1069	1660	95	below_threshold
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	83.0063	1093	1660	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:21,150] [INFO] DFAST Taxonomy check result was written to GCF_000482705.1_ASM48270v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:21,151] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:21,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:21,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75bc4f3b-beb9-4392-b2d2-ce1be32650d1/dqc_reference/checkm_data
[2024-01-25 20:18:21,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:21,203] [INFO] Task started: CheckM
[2024-01-25 20:18:21,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000482705.1_ASM48270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000482705.1_ASM48270v1_genomic.fna/checkm_input GCF_000482705.1_ASM48270v1_genomic.fna/checkm_result
[2024-01-25 20:19:12,935] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:12,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:12,954] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:12,955] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:12,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000482705.1_ASM48270v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:12,955] [INFO] Task started: Blastn
[2024-01-25 20:19:12,955] [INFO] Running command: blastn -query GCF_000482705.1_ASM48270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75bc4f3b-beb9-4392-b2d2-ce1be32650d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000482705.1_ASM48270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:14,770] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:14,773] [INFO] Selected 11 target genomes.
[2024-01-25 20:19:14,773] [INFO] Target genome list was writen to GCF_000482705.1_ASM48270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:14,795] [INFO] Task started: fastANI
[2024-01-25 20:19:14,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgc81fe176-b6d9-42b8-a727-2ba7f11005be/GCF_000482705.1_ASM48270v1_genomic.fna.gz --refList GCF_000482705.1_ASM48270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000482705.1_ASM48270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:30,010] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:30,018] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:30,018] [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_000482705.1	s__Glycomyces arizonensis	100.0	1656	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000427885.1	s__Glycomyces tenuis	89.5189	1282	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798405.1	s__Glycomyces xiaoerkulensis	83.8139	972	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428645.1	s__Glycomyces sp016428645	83.771	1064	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719515.1	s__Glycomyces sp000719515	83.6062	1037	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900101745.1	s__Glycomyces harbinensis	83.5519	1117	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003933745.1	s__Glycomyces terrestris	83.4197	1068	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009451885.1	s__Glycomyces albidus	83.402	1068	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912275.1	s__Glycomyces buryatensis	83.3518	1064	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912155.1	s__Glycomyces paridis	83.3164	1063	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002955.1	s__Glycomyces artemisiae	83.0476	1088	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	97.80	97.80	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:30,019] [INFO] GTDB search result was written to GCF_000482705.1_ASM48270v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:30,020] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:30,023] [INFO] DFAST_QC result json was written to GCF_000482705.1_ASM48270v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:30,023] [INFO] DFAST_QC completed!
[2024-01-25 20:19:30,023] [INFO] Total running time: 0h1m39s