[2024-01-24 11:26:38,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg3983e8a9-4ee0-440c-adb9-ef499279fdeb/dqc_reference
[2024-01-24 11:26:39,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:39,444] [INFO] Task started: Prodigal
[2024-01-24 11:26:39,445] [INFO] Running command: gunzip -c /var/lib/cwl/stg38cecf26-d0a9-4e6b-955f-4b2fe1f6df76/GCF_022568795.1_ASM2256879v1_genomic.fna.gz | prodigal -d GCF_022568795.1_ASM2256879v1_genomic.fna/cds.fna -a GCF_022568795.1_ASM2256879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:49,633] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:49,633] [INFO] Task started: HMMsearch
[2024-01-24 11:26:49,633] [INFO] Running command: hmmsearch --tblout GCF_022568795.1_ASM2256879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3983e8a9-4ee0-440c-adb9-ef499279fdeb/dqc_reference/reference_markers.hmm GCF_022568795.1_ASM2256879v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:49,898] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:49,899] [INFO] Found 6/6 markers.
[2024-01-24 11:26:49,928] [INFO] Query marker FASTA was written to GCF_022568795.1_ASM2256879v1_genomic.fna/markers.fasta
[2024-01-24 11:26:49,929] [INFO] Task started: Blastn
[2024-01-24 11:26:49,929] [INFO] Running command: blastn -query GCF_022568795.1_ASM2256879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3983e8a9-4ee0-440c-adb9-ef499279fdeb/dqc_reference/reference_markers.fasta -out GCF_022568795.1_ASM2256879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:51,160] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:51,163] [INFO] Selected 12 target genomes.
[2024-01-24 11:26:51,163] [INFO] Target genome list was writen to GCF_022568795.1_ASM2256879v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:51,170] [INFO] Task started: fastANI
[2024-01-24 11:26:51,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg38cecf26-d0a9-4e6b-955f-4b2fe1f6df76/GCF_022568795.1_ASM2256879v1_genomic.fna.gz --refList GCF_022568795.1_ASM2256879v1_genomic.fna/target_genomes.txt --output GCF_022568795.1_ASM2256879v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:01,118] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:01,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3983e8a9-4ee0-440c-adb9-ef499279fdeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:01,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3983e8a9-4ee0-440c-adb9-ef499279fdeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:01,129] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:01,129] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:01,129] [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
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	100.0	1162	1169	95	conclusive
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	82.6752	749	1169	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	82.502	722	1169	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	80.3046	524	1169	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	79.1274	428	1169	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	78.7228	433	1169	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	78.7106	371	1169	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	78.5694	433	1169	95	below_threshold
Intrasporangium calvum	strain=DSM 43043	GCA_000184685.1	53358	53358	type	True	78.5381	350	1169	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	78.3635	341	1169	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	78.3591	341	1169	95	below_threshold
Streptomyces colonosanans	strain=MUSC 93	GCA_001866645.1	1428652	1428652	type	True	76.9698	272	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:01,131] [INFO] DFAST Taxonomy check result was written to GCF_022568795.1_ASM2256879v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:01,131] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:01,132] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:01,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3983e8a9-4ee0-440c-adb9-ef499279fdeb/dqc_reference/checkm_data
[2024-01-24 11:27:01,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:01,167] [INFO] Task started: CheckM
[2024-01-24 11:27:01,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022568795.1_ASM2256879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022568795.1_ASM2256879v1_genomic.fna/checkm_input GCF_022568795.1_ASM2256879v1_genomic.fna/checkm_result
[2024-01-24 11:28:02,782] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:02,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:02,805] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:02,805] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:02,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022568795.1_ASM2256879v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:02,806] [INFO] Task started: Blastn
[2024-01-24 11:28:02,806] [INFO] Running command: blastn -query GCF_022568795.1_ASM2256879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3983e8a9-4ee0-440c-adb9-ef499279fdeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_022568795.1_ASM2256879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:04,761] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:04,765] [INFO] Selected 15 target genomes.
[2024-01-24 11:28:04,765] [INFO] Target genome list was writen to GCF_022568795.1_ASM2256879v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:04,779] [INFO] Task started: fastANI
[2024-01-24 11:28:04,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg38cecf26-d0a9-4e6b-955f-4b2fe1f6df76/GCF_022568795.1_ASM2256879v1_genomic.fna.gz --refList GCF_022568795.1_ASM2256879v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022568795.1_ASM2256879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:17,504] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:17,519] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:28:17,519] [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_001189535.1	s__Arsenicicoccus sp001189535	82.9752	777	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426385.1	s__Arsenicicoccus bolidensis	82.6865	749	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	98.16	98.06	0.89	0.88	4	-
GCF_009707125.1	s__Arsenicicoccus sp009707125	82.5073	722	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	79.2791	475	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	79.1113	430	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_013041615.1	s__Pedococcus sp013041615	78.9439	441	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717025.1	s__Terrabacter lapilli	78.7846	428	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	95.88	95.88	0.91	0.91	2	-
GCF_001570945.1	s__Janibacter anophelis	78.7211	370	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_000184685.1	s__Intrasporangium calvum	78.5443	350	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Intrasporangium	95.0	99.10	99.10	0.92	0.92	2	-
GCF_016887965.1	s__Phycicoccus sp016887965	78.4852	445	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428505.1	s__Terrabacter sp001428505	78.4778	438	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.23	99.23	0.97	0.97	2	-
GCF_006716185.1	s__Ornithinicoccus hortensis	78.303	365	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCA_014857905.1	s__JACYXE01 sp014857905	78.0481	427	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__JACYXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082195.1	s__Streptomyces gilvosporeus	77.003	330	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCF_001866645.1	s__Streptomyces colonosanans	76.9874	270	1169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:17,522] [INFO] GTDB search result was written to GCF_022568795.1_ASM2256879v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:17,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:17,526] [INFO] DFAST_QC result json was written to GCF_022568795.1_ASM2256879v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:17,526] [INFO] DFAST_QC completed!
[2024-01-24 11:28:17,527] [INFO] Total running time: 0h1m39s