[2024-01-24 10:58:06,466] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg5aeb7095-3308-47e1-8b42-e0cd9b760ac0/dqc_reference
[2024-01-24 10:58:09,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,641] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,641] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd8e8a4f-baa5-4557-ae0e-bfe98d747abd/GCF_003002055.1_ASM300205v1_genomic.fna.gz | prodigal -d GCF_003002055.1_ASM300205v1_genomic.fna/cds.fna -a GCF_003002055.1_ASM300205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:23,923] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:23,923] [INFO] Task started: HMMsearch
[2024-01-24 10:58:23,923] [INFO] Running command: hmmsearch --tblout GCF_003002055.1_ASM300205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5aeb7095-3308-47e1-8b42-e0cd9b760ac0/dqc_reference/reference_markers.hmm GCF_003002055.1_ASM300205v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:24,300] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:24,302] [INFO] Found 6/6 markers.
[2024-01-24 10:58:24,362] [INFO] Query marker FASTA was written to GCF_003002055.1_ASM300205v1_genomic.fna/markers.fasta
[2024-01-24 10:58:24,363] [INFO] Task started: Blastn
[2024-01-24 10:58:24,363] [INFO] Running command: blastn -query GCF_003002055.1_ASM300205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5aeb7095-3308-47e1-8b42-e0cd9b760ac0/dqc_reference/reference_markers.fasta -out GCF_003002055.1_ASM300205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:25,703] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:25,706] [INFO] Selected 12 target genomes.
[2024-01-24 10:58:25,707] [INFO] Target genome list was writen to GCF_003002055.1_ASM300205v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:25,712] [INFO] Task started: fastANI
[2024-01-24 10:58:25,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd8e8a4f-baa5-4557-ae0e-bfe98d747abd/GCF_003002055.1_ASM300205v1_genomic.fna.gz --refList GCF_003002055.1_ASM300205v1_genomic.fna/target_genomes.txt --output GCF_003002055.1_ASM300205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:40,129] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:40,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5aeb7095-3308-47e1-8b42-e0cd9b760ac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:40,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5aeb7095-3308-47e1-8b42-e0cd9b760ac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:40,146] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:40,146] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:40,146] [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
Kineococcus rhizosphaerae	strain=DSM 19711	GCA_003002055.1	559628	559628	type	True	100.0	1838	1839	95	conclusive
Kineococcus aurantiacus	strain=DSM 7487	GCA_013409345.1	37633	37633	type	True	87.5943	1292	1839	95	below_threshold
Kineococcus radiotolerans	strain=SRS30216	GCA_000017305.1	131568	131568	type	True	83.9033	1069	1839	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	83.2287	839	1839	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	81.6338	701	1839	95	below_threshold
Kineococcus rubinsiae	strain=B12	GCA_011839805.1	2609562	2609562	type	True	81.0987	952	1839	95	below_threshold
Kineococcus siccus	strain=R8	GCA_009906795.1	2696567	2696567	type	True	80.8708	801	1839	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	76.8641	454	1839	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.8052	483	1839	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	76.6965	381	1839	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	76.3696	417	1839	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	76.351	421	1839	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:40,148] [INFO] DFAST Taxonomy check result was written to GCF_003002055.1_ASM300205v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:40,148] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:40,149] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:40,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5aeb7095-3308-47e1-8b42-e0cd9b760ac0/dqc_reference/checkm_data
[2024-01-24 10:58:40,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:40,202] [INFO] Task started: CheckM
[2024-01-24 10:58:40,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003002055.1_ASM300205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003002055.1_ASM300205v1_genomic.fna/checkm_input GCF_003002055.1_ASM300205v1_genomic.fna/checkm_result
[2024-01-24 11:00:00,328] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:00,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:00,354] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:00,355] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:00,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003002055.1_ASM300205v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:00,356] [INFO] Task started: Blastn
[2024-01-24 11:00:00,356] [INFO] Running command: blastn -query GCF_003002055.1_ASM300205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5aeb7095-3308-47e1-8b42-e0cd9b760ac0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003002055.1_ASM300205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:02,499] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:02,509] [INFO] Selected 6 target genomes.
[2024-01-24 11:00:02,511] [INFO] Target genome list was writen to GCF_003002055.1_ASM300205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:02,516] [INFO] Task started: fastANI
[2024-01-24 11:00:02,516] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd8e8a4f-baa5-4557-ae0e-bfe98d747abd/GCF_003002055.1_ASM300205v1_genomic.fna.gz --refList GCF_003002055.1_ASM300205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003002055.1_ASM300205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:12,232] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:12,240] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:12,241] [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_003002055.1	s__Kineococcus rhizosphaerae	100.0	1838	1839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013409345.1	s__Kineococcus aurantiacus	87.5858	1293	1839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017305.1	s__Kineococcus radiotolerans	83.9212	1067	1839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	98.46	98.46	0.90	0.90	2	-
GCF_009906315.1	s__Kineococcus vitellinus	83.1836	843	1839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011839805.1	s__Kineococcus rubinsiae	81.1144	950	1839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906795.1	s__Kineococcus siccus	80.8874	799	1839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:12,244] [INFO] GTDB search result was written to GCF_003002055.1_ASM300205v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:12,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:12,248] [INFO] DFAST_QC result json was written to GCF_003002055.1_ASM300205v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:12,248] [INFO] DFAST_QC completed!
[2024-01-24 11:00:12,248] [INFO] Total running time: 0h2m6s