[2024-01-24 14:05:53,408] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,410] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,411] [INFO] DQC Reference Directory: /var/lib/cwl/stg852cf29d-2ac2-4730-a475-6cb7507d0b8c/dqc_reference
[2024-01-24 14:05:54,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:54,814] [INFO] Task started: Prodigal
[2024-01-24 14:05:54,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e50936b-2f1c-4321-8ae0-28d27446900d/GCF_021228295.1_ASM2122829v1_genomic.fna.gz | prodigal -d GCF_021228295.1_ASM2122829v1_genomic.fna/cds.fna -a GCF_021228295.1_ASM2122829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:07,791] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:07,791] [INFO] Task started: HMMsearch
[2024-01-24 14:06:07,792] [INFO] Running command: hmmsearch --tblout GCF_021228295.1_ASM2122829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg852cf29d-2ac2-4730-a475-6cb7507d0b8c/dqc_reference/reference_markers.hmm GCF_021228295.1_ASM2122829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:08,130] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:08,131] [INFO] Found 6/6 markers.
[2024-01-24 14:06:08,177] [INFO] Query marker FASTA was written to GCF_021228295.1_ASM2122829v1_genomic.fna/markers.fasta
[2024-01-24 14:06:08,178] [INFO] Task started: Blastn
[2024-01-24 14:06:08,178] [INFO] Running command: blastn -query GCF_021228295.1_ASM2122829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg852cf29d-2ac2-4730-a475-6cb7507d0b8c/dqc_reference/reference_markers.fasta -out GCF_021228295.1_ASM2122829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:09,512] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:09,516] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:09,516] [INFO] Target genome list was writen to GCF_021228295.1_ASM2122829v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:09,526] [INFO] Task started: fastANI
[2024-01-24 14:06:09,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e50936b-2f1c-4321-8ae0-28d27446900d/GCF_021228295.1_ASM2122829v1_genomic.fna.gz --refList GCF_021228295.1_ASM2122829v1_genomic.fna/target_genomes.txt --output GCF_021228295.1_ASM2122829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:22,702] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:22,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg852cf29d-2ac2-4730-a475-6cb7507d0b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:22,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg852cf29d-2ac2-4730-a475-6cb7507d0b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:22,714] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:22,714] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:22,715] [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
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	100.0	1335	1336	95	conclusive
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	90.4119	1041	1336	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	83.6621	826	1336	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	83.6516	742	1336	95	below_threshold
Agromyces italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	83.4004	761	1336	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	83.374	579	1336	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.3714	889	1336	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	83.3245	841	1336	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	83.298	856	1336	95	below_threshold
Agromyces italicus	strain=DSM 16388	GCA_000421545.1	279572	279572	type	True	83.266	768	1336	95	below_threshold
Agromyces aureus	strain=AR33	GCA_001660485.1	453304	453304	type	True	82.3951	792	1336	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	81.649	770	1336	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	78.3717	421	1336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:22,716] [INFO] DFAST Taxonomy check result was written to GCF_021228295.1_ASM2122829v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:22,717] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:22,717] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:22,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg852cf29d-2ac2-4730-a475-6cb7507d0b8c/dqc_reference/checkm_data
[2024-01-24 14:06:22,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:22,760] [INFO] Task started: CheckM
[2024-01-24 14:06:22,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021228295.1_ASM2122829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021228295.1_ASM2122829v1_genomic.fna/checkm_input GCF_021228295.1_ASM2122829v1_genomic.fna/checkm_result
[2024-01-24 14:07:30,001] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:30,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:30,024] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:30,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:30,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021228295.1_ASM2122829v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:30,025] [INFO] Task started: Blastn
[2024-01-24 14:07:30,025] [INFO] Running command: blastn -query GCF_021228295.1_ASM2122829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg852cf29d-2ac2-4730-a475-6cb7507d0b8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_021228295.1_ASM2122829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:31,956] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:31,960] [INFO] Selected 16 target genomes.
[2024-01-24 14:07:31,961] [INFO] Target genome list was writen to GCF_021228295.1_ASM2122829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:31,974] [INFO] Task started: fastANI
[2024-01-24 14:07:31,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e50936b-2f1c-4321-8ae0-28d27446900d/GCF_021228295.1_ASM2122829v1_genomic.fna.gz --refList GCF_021228295.1_ASM2122829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021228295.1_ASM2122829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:46,832] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:46,852] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:07:46,852] [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_003070885.1	s__Agromyces badenianii	83.6304	744	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.76	98.76	0.96	0.96	2	-
GCF_009749405.1	s__Agromyces lapidis	83.619	830	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907835.1	s__Agromyces cerinus_A	83.5364	841	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410355.1	s__Agromyces hippuratus	83.5138	840	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142065.1	s__Agromyces cerinus	83.431	838	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429165.1	s__Agromyces sp001429165	83.4134	798	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	83.4051	885	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720255.1	s__Agromyces humi	83.3736	579	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216665.1	s__Agromyces ramosus	83.3469	851	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004134865.1	s__Agromyces fucosus	83.2926	844	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.23	98.22	0.96	0.96	3	-
GCF_000421545.1	s__Agromyces italicus	83.2345	772	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001428255.1	s__Agromyces sp001428255	82.9553	846	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959775.1	s__Agromyces sp004959775	82.8869	834	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715355.1	s__Agromyces sp006715355	82.8332	852	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749385.1	s__Agromyces allii	82.7428	805	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660485.1	s__Agromyces aureus	82.369	795	1336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:46,854] [INFO] GTDB search result was written to GCF_021228295.1_ASM2122829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:46,855] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:46,859] [INFO] DFAST_QC result json was written to GCF_021228295.1_ASM2122829v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:46,859] [INFO] DFAST_QC completed!
[2024-01-24 14:07:46,860] [INFO] Total running time: 0h1m53s