[2024-01-24 13:01:52,150] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:52,157] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:52,157] [INFO] DQC Reference Directory: /var/lib/cwl/stg9695fed8-f284-428f-ba88-51988f233f4b/dqc_reference
[2024-01-24 13:01:53,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:53,481] [INFO] Task started: Prodigal
[2024-01-24 13:01:53,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b656ebb-1626-475b-851f-5c006ac898fa/GCF_006539945.1_ASM653994v1_genomic.fna.gz | prodigal -d GCF_006539945.1_ASM653994v1_genomic.fna/cds.fna -a GCF_006539945.1_ASM653994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:05,740] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:05,740] [INFO] Task started: HMMsearch
[2024-01-24 13:02:05,740] [INFO] Running command: hmmsearch --tblout GCF_006539945.1_ASM653994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9695fed8-f284-428f-ba88-51988f233f4b/dqc_reference/reference_markers.hmm GCF_006539945.1_ASM653994v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:06,108] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:06,109] [INFO] Found 6/6 markers.
[2024-01-24 13:02:06,153] [INFO] Query marker FASTA was written to GCF_006539945.1_ASM653994v1_genomic.fna/markers.fasta
[2024-01-24 13:02:06,154] [INFO] Task started: Blastn
[2024-01-24 13:02:06,154] [INFO] Running command: blastn -query GCF_006539945.1_ASM653994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9695fed8-f284-428f-ba88-51988f233f4b/dqc_reference/reference_markers.fasta -out GCF_006539945.1_ASM653994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:07,577] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:07,581] [INFO] Selected 17 target genomes.
[2024-01-24 13:02:07,582] [INFO] Target genome list was writen to GCF_006539945.1_ASM653994v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:07,587] [INFO] Task started: fastANI
[2024-01-24 13:02:07,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b656ebb-1626-475b-851f-5c006ac898fa/GCF_006539945.1_ASM653994v1_genomic.fna.gz --refList GCF_006539945.1_ASM653994v1_genomic.fna/target_genomes.txt --output GCF_006539945.1_ASM653994v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:25,598] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:25,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9695fed8-f284-428f-ba88-51988f233f4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:25,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9695fed8-f284-428f-ba88-51988f233f4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:25,617] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:02:25,617] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:02:25,618] [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
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	89.8506	1211	1501	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	89.8128	1172	1501	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	84.8793	1012	1501	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	83.335	955	1501	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	81.6645	834	1501	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	81.6038	839	1501	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	81.565	856	1501	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	81.4068	857	1501	95	below_threshold
Oerskovia jenensis	strain=DSM 46000	GCA_016907235.1	162169	162169	type	True	81.4063	873	1501	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	81.3967	883	1501	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	81.0847	727	1501	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	79.9113	695	1501	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	79.7962	751	1501	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.6025	684	1501	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	79.5014	642	1501	95	below_threshold
Isoptericola sediminis	strain=JC619	GCA_013085345.1	2733572	2733572	type	True	79.3031	562	1501	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.1105	647	1501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:25,620] [INFO] DFAST Taxonomy check result was written to GCF_006539945.1_ASM653994v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:25,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:25,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:25,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9695fed8-f284-428f-ba88-51988f233f4b/dqc_reference/checkm_data
[2024-01-24 13:02:25,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:25,666] [INFO] Task started: CheckM
[2024-01-24 13:02:25,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539945.1_ASM653994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539945.1_ASM653994v1_genomic.fna/checkm_input GCF_006539945.1_ASM653994v1_genomic.fna/checkm_result
[2024-01-24 13:03:24,943] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:24,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:25,028] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:25,028] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:25,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539945.1_ASM653994v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:25,029] [INFO] Task started: Blastn
[2024-01-24 13:03:25,030] [INFO] Running command: blastn -query GCF_006539945.1_ASM653994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9695fed8-f284-428f-ba88-51988f233f4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539945.1_ASM653994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:27,251] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:27,256] [INFO] Selected 8 target genomes.
[2024-01-24 13:03:27,257] [INFO] Target genome list was writen to GCF_006539945.1_ASM653994v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:27,264] [INFO] Task started: fastANI
[2024-01-24 13:03:27,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b656ebb-1626-475b-851f-5c006ac898fa/GCF_006539945.1_ASM653994v1_genomic.fna.gz --refList GCF_006539945.1_ASM653994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539945.1_ASM653994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:39,108] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:39,123] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:39,124] [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_006539945.1	s__Cellulosimicrobium cellulans	100.0	1499	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	94.9159	1297	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	93.261	1319	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_016921195.1	s__Cellulosimicrobium cellulans_F	93.0209	1268	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	91.8204	1260	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519295.1	s__Cellulosimicrobium funkei	89.8743	1209	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	89.4606	1140	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	85.1776	826	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:39,135] [INFO] GTDB search result was written to GCF_006539945.1_ASM653994v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:39,135] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:39,139] [INFO] DFAST_QC result json was written to GCF_006539945.1_ASM653994v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:39,139] [INFO] DFAST_QC completed!
[2024-01-24 13:03:39,139] [INFO] Total running time: 0h1m47s