[2024-01-24 13:57:14,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:14,715] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:14,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg61b5679c-ac01-499f-b26b-00bf5c928dc9/dqc_reference
[2024-01-24 13:57:15,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:15,934] [INFO] Task started: Prodigal
[2024-01-24 13:57:15,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg8763a4e7-d1d7-48e2-b88c-cd1a3ef25c3d/GCF_022811705.1_ASM2281170v1_genomic.fna.gz | prodigal -d GCF_022811705.1_ASM2281170v1_genomic.fna/cds.fna -a GCF_022811705.1_ASM2281170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:27,510] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:27,510] [INFO] Task started: HMMsearch
[2024-01-24 13:57:27,510] [INFO] Running command: hmmsearch --tblout GCF_022811705.1_ASM2281170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61b5679c-ac01-499f-b26b-00bf5c928dc9/dqc_reference/reference_markers.hmm GCF_022811705.1_ASM2281170v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:27,813] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:27,814] [INFO] Found 6/6 markers.
[2024-01-24 13:57:27,859] [INFO] Query marker FASTA was written to GCF_022811705.1_ASM2281170v1_genomic.fna/markers.fasta
[2024-01-24 13:57:27,860] [INFO] Task started: Blastn
[2024-01-24 13:57:27,860] [INFO] Running command: blastn -query GCF_022811705.1_ASM2281170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b5679c-ac01-499f-b26b-00bf5c928dc9/dqc_reference/reference_markers.fasta -out GCF_022811705.1_ASM2281170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:29,236] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:29,240] [INFO] Selected 25 target genomes.
[2024-01-24 13:57:29,241] [INFO] Target genome list was writen to GCF_022811705.1_ASM2281170v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:29,251] [INFO] Task started: fastANI
[2024-01-24 13:57:29,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg8763a4e7-d1d7-48e2-b88c-cd1a3ef25c3d/GCF_022811705.1_ASM2281170v1_genomic.fna.gz --refList GCF_022811705.1_ASM2281170v1_genomic.fna/target_genomes.txt --output GCF_022811705.1_ASM2281170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:50,865] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:50,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61b5679c-ac01-499f-b26b-00bf5c928dc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:50,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61b5679c-ac01-499f-b26b-00bf5c928dc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:50,883] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:50,883] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:50,884] [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 intestinalis	strain=KACC 19306	GCA_008365295.1	2592652	2592652	type	True	90.9081	1028	1335	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	83.0504	825	1335	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	82.7305	768	1335	95	below_threshold
Agromyces protaetiae	strain=FW100M-8	GCA_004135405.1	2509455	2509455	type	True	82.6572	806	1335	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	82.294	730	1335	95	below_threshold
Agromyces terreus	strain=JCM 14581	GCA_009749465.1	424795	424795	type	True	82.2885	749	1335	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	82.2384	719	1335	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	82.1911	546	1335	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_900104685.1	589382	589382	type	True	82.18	687	1335	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	82.1237	790	1335	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	82.111	691	1335	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	82.1094	733	1335	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	82.1006	685	1335	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	82.0484	754	1335	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	82.0056	738	1335	95	below_threshold
Agromyces bauzanensis	strain=CGMCC 1.8984	GCA_014645655.1	1308924	1308924	type	True	81.8694	669	1335	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	81.8483	730	1335	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	81.8158	665	1335	95	below_threshold
Agromyces kandeliae	strain=Q22	GCA_009674665.1	2666141	2666141	type	True	81.786	693	1335	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.9764	641	1335	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	74.9728	85	1335	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	74.913	80	1335	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:50,885] [INFO] DFAST Taxonomy check result was written to GCF_022811705.1_ASM2281170v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:50,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:50,886] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:50,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61b5679c-ac01-499f-b26b-00bf5c928dc9/dqc_reference/checkm_data
[2024-01-24 13:57:50,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:50,928] [INFO] Task started: CheckM
[2024-01-24 13:57:50,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022811705.1_ASM2281170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022811705.1_ASM2281170v1_genomic.fna/checkm_input GCF_022811705.1_ASM2281170v1_genomic.fna/checkm_result
[2024-01-24 13:58:55,808] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:55,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:55,826] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:55,827] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:55,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022811705.1_ASM2281170v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:55,827] [INFO] Task started: Blastn
[2024-01-24 13:58:55,828] [INFO] Running command: blastn -query GCF_022811705.1_ASM2281170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b5679c-ac01-499f-b26b-00bf5c928dc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_022811705.1_ASM2281170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:57,918] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:57,922] [INFO] Selected 24 target genomes.
[2024-01-24 13:58:57,923] [INFO] Target genome list was writen to GCF_022811705.1_ASM2281170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:57,956] [INFO] Task started: fastANI
[2024-01-24 13:58:57,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg8763a4e7-d1d7-48e2-b88c-cd1a3ef25c3d/GCF_022811705.1_ASM2281170v1_genomic.fna.gz --refList GCF_022811705.1_ASM2281170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022811705.1_ASM2281170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:20,019] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:20,044] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:20,044] [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_008365295.1	s__Agromyces intestinalis	90.9201	1026	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634985.1	s__Agromyces sp003634985	83.4904	835	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009647605.1	s__Agromyces sp009647605	83.0466	826	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135405.1	s__Agromyces protaetiae	82.6774	804	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006235.1	s__Agromyces sp004006235	82.6043	830	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907355.1	s__Agromyces aurantiacus	82.3268	729	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648575.1	s__Agromyces mediolanus	82.2655	717	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749405.1	s__Agromyces lapidis	82.2345	751	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710805.1	s__Agromyces tardus	82.1948	733	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104685.1	s__Agromyces flavus	82.1715	687	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009749385.1	s__Agromyces allii	82.1103	792	1335	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	82.098	734	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729855.1	s__Agromyces luteolus	82.0531	733	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709675.1	s__Agromyces bracchium	82.0378	756	1335	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	81.9971	748	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421565.1	s__Agromyces sp001421565	81.9704	804	1335	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	81.954	789	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674665.1	s__Agromyces kandeliae	81.8358	688	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018024495.1	s__WSTA01 sp018024495	80.9911	643	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__WSTA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759505.1	s__Curtobacterium flaccumfaciens_C	78.0226	395	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716265.1	s__JADJWQ01 sp016716265	74.8634	393	1335	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JADJWQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584315.1	s__CAADGN01 sp014584315	74.825	86	1335	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__CAADGN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:20,046] [INFO] GTDB search result was written to GCF_022811705.1_ASM2281170v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:20,047] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:20,052] [INFO] DFAST_QC result json was written to GCF_022811705.1_ASM2281170v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:20,052] [INFO] DFAST_QC completed!
[2024-01-24 13:59:20,052] [INFO] Total running time: 0h2m5s