[2024-01-24 14:06:07,175] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,177] [INFO] DQC Reference Directory: /var/lib/cwl/stga9d8e469-24a8-4cc2-a465-fc0a7b2fb8fa/dqc_reference
[2024-01-24 14:06:08,501] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,502] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d36e3aa-3c79-4e23-9333-18a814ab0754/GCF_000429265.1_ASM42926v1_genomic.fna.gz | prodigal -d GCF_000429265.1_ASM42926v1_genomic.fna/cds.fna -a GCF_000429265.1_ASM42926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:18,496] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:18,496] [INFO] Task started: HMMsearch
[2024-01-24 14:06:18,497] [INFO] Running command: hmmsearch --tblout GCF_000429265.1_ASM42926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9d8e469-24a8-4cc2-a465-fc0a7b2fb8fa/dqc_reference/reference_markers.hmm GCF_000429265.1_ASM42926v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:18,819] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:18,820] [INFO] Found 6/6 markers.
[2024-01-24 14:06:18,852] [INFO] Query marker FASTA was written to GCF_000429265.1_ASM42926v1_genomic.fna/markers.fasta
[2024-01-24 14:06:18,853] [INFO] Task started: Blastn
[2024-01-24 14:06:18,853] [INFO] Running command: blastn -query GCF_000429265.1_ASM42926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9d8e469-24a8-4cc2-a465-fc0a7b2fb8fa/dqc_reference/reference_markers.fasta -out GCF_000429265.1_ASM42926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:20,056] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:20,059] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:20,060] [INFO] Target genome list was writen to GCF_000429265.1_ASM42926v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:20,065] [INFO] Task started: fastANI
[2024-01-24 14:06:20,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d36e3aa-3c79-4e23-9333-18a814ab0754/GCF_000429265.1_ASM42926v1_genomic.fna.gz --refList GCF_000429265.1_ASM42926v1_genomic.fna/target_genomes.txt --output GCF_000429265.1_ASM42926v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:30,815] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:30,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9d8e469-24a8-4cc2-a465-fc0a7b2fb8fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:30,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9d8e469-24a8-4cc2-a465-fc0a7b2fb8fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:30,828] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:30,828] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:30,829] [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
Actinomyces gerencseriae	strain=DSM 6844	GCA_000429265.1	52769	52769	type	True	100.0	1127	1127	95	conclusive
Actinomyces israelii	strain=DSM 43320	GCA_000711965.1	1659	1659	type	True	86.477	819	1127	95	below_threshold
Actinomyces massiliensis	strain=4401292	GCA_000269805.1	461393	461393	type	True	85.1132	793	1127	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	83.0468	641	1127	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	81.9249	573	1127	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	81.7754	569	1127	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	80.9324	546	1127	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	80.8607	494	1127	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	80.8238	504	1127	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	80.6619	426	1127	95	below_threshold
Actinomyces respiraculi	strain=ZJ750	GCA_014595995.2	2744574	2744574	type	True	80.4786	509	1127	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	76.7436	183	1127	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.3521	219	1127	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.2008	257	1127	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:30,830] [INFO] DFAST Taxonomy check result was written to GCF_000429265.1_ASM42926v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:30,831] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:30,831] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:30,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9d8e469-24a8-4cc2-a465-fc0a7b2fb8fa/dqc_reference/checkm_data
[2024-01-24 14:06:30,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:30,873] [INFO] Task started: CheckM
[2024-01-24 14:06:30,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429265.1_ASM42926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429265.1_ASM42926v1_genomic.fna/checkm_input GCF_000429265.1_ASM42926v1_genomic.fna/checkm_result
[2024-01-24 14:07:18,815] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:18,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:18,833] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:18,834] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:18,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429265.1_ASM42926v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:18,835] [INFO] Task started: Blastn
[2024-01-24 14:07:18,835] [INFO] Running command: blastn -query GCF_000429265.1_ASM42926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9d8e469-24a8-4cc2-a465-fc0a7b2fb8fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429265.1_ASM42926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:20,430] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:20,435] [INFO] Selected 10 target genomes.
[2024-01-24 14:07:20,435] [INFO] Target genome list was writen to GCF_000429265.1_ASM42926v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:20,445] [INFO] Task started: fastANI
[2024-01-24 14:07:20,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d36e3aa-3c79-4e23-9333-18a814ab0754/GCF_000429265.1_ASM42926v1_genomic.fna.gz --refList GCF_000429265.1_ASM42926v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429265.1_ASM42926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:28,278] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:28,292] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:28,293] [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_000429265.1	s__Actinomyces gerencseriae	100.0	1127	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.51	98.51	0.94	0.94	2	conclusive
GCA_000711965.1	s__Actinomyces israelii	86.477	819	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.26	99.26	0.94	0.94	2	-
GCF_000269805.1	s__Actinomyces massiliensis	85.1256	790	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.53	98.51	0.94	0.94	3	-
GCF_000220835.1	s__Actinomyces sp000220835	83.4197	704	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.31	99.28	0.97	0.96	3	-
GCF_000429225.1	s__Actinomyces dentalis	83.0604	640	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	98.22	0.92	0.92	2	-
GCF_001278845.1	s__Actinomyces sp001278845	82.697	631	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752065.1	s__Actinomyces sp011752065	81.8728	579	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001929375.1	s__Actinomyces oris_B	81.6681	539	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCF_001553565.1	s__Actinomyces radicidentis	80.9354	546	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595995.2	s__Actinomyces sp011751985	80.4202	514	1127	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.79	99.58	0.98	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:28,294] [INFO] GTDB search result was written to GCF_000429265.1_ASM42926v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:28,295] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:28,299] [INFO] DFAST_QC result json was written to GCF_000429265.1_ASM42926v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:28,299] [INFO] DFAST_QC completed!
[2024-01-24 14:07:28,299] [INFO] Total running time: 0h1m21s