[2024-01-25 18:51:50,676] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:50,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:50,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg7621c523-3c7d-4eee-840a-ade83b9faf27/dqc_reference
[2024-01-25 18:51:51,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:51,952] [INFO] Task started: Prodigal
[2024-01-25 18:51:51,952] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2eadc5c-006e-4569-8ef5-93fa8fb46998/GCF_003052455.1_ASM305245v1_genomic.fna.gz | prodigal -d GCF_003052455.1_ASM305245v1_genomic.fna/cds.fna -a GCF_003052455.1_ASM305245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:01,455] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:01,455] [INFO] Task started: HMMsearch
[2024-01-25 18:52:01,455] [INFO] Running command: hmmsearch --tblout GCF_003052455.1_ASM305245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7621c523-3c7d-4eee-840a-ade83b9faf27/dqc_reference/reference_markers.hmm GCF_003052455.1_ASM305245v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:01,711] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:01,712] [INFO] Found 6/6 markers.
[2024-01-25 18:52:01,771] [INFO] Query marker FASTA was written to GCF_003052455.1_ASM305245v1_genomic.fna/markers.fasta
[2024-01-25 18:52:01,772] [INFO] Task started: Blastn
[2024-01-25 18:52:01,772] [INFO] Running command: blastn -query GCF_003052455.1_ASM305245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7621c523-3c7d-4eee-840a-ade83b9faf27/dqc_reference/reference_markers.fasta -out GCF_003052455.1_ASM305245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:03,095] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:03,099] [INFO] Selected 16 target genomes.
[2024-01-25 18:52:03,099] [INFO] Target genome list was writen to GCF_003052455.1_ASM305245v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:03,135] [INFO] Task started: fastANI
[2024-01-25 18:52:03,135] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2eadc5c-006e-4569-8ef5-93fa8fb46998/GCF_003052455.1_ASM305245v1_genomic.fna.gz --refList GCF_003052455.1_ASM305245v1_genomic.fna/target_genomes.txt --output GCF_003052455.1_ASM305245v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:20,403] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:20,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7621c523-3c7d-4eee-840a-ade83b9faf27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:20,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7621c523-3c7d-4eee-840a-ade83b9faf27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:20,414] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:52:20,414] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:20,414] [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	96.0261	1235	1392	95	conclusive
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	95.9415	1218	1392	95	conclusive
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	84.9747	943	1392	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	83.5224	882	1392	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	81.723	828	1392	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	81.7091	834	1392	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	81.5451	871	1392	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	81.5039	855	1392	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	81.3162	860	1392	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	81.1954	717	1392	95	below_threshold
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	80.109	697	1392	95	below_threshold
Isoptericola dokdonensis	strain=DS-3	GCA_001636295.1	372663	372663	type	True	79.9356	702	1392	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.863	670	1392	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	79.5434	654	1392	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.3297	696	1392	95	below_threshold
Myceligenerans salitolerans	strain=XHU 5031	GCA_017349295.1	1230528	1230528	type	True	78.9444	548	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:20,415] [INFO] DFAST Taxonomy check result was written to GCF_003052455.1_ASM305245v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:20,416] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:20,416] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:20,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7621c523-3c7d-4eee-840a-ade83b9faf27/dqc_reference/checkm_data
[2024-01-25 18:52:20,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:20,456] [INFO] Task started: CheckM
[2024-01-25 18:52:20,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003052455.1_ASM305245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003052455.1_ASM305245v1_genomic.fna/checkm_input GCF_003052455.1_ASM305245v1_genomic.fna/checkm_result
[2024-01-25 18:53:11,792] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:11,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:11,808] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:11,808] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:11,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003052455.1_ASM305245v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:11,809] [INFO] Task started: Blastn
[2024-01-25 18:53:11,809] [INFO] Running command: blastn -query GCF_003052455.1_ASM305245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7621c523-3c7d-4eee-840a-ade83b9faf27/dqc_reference/reference_markers_gtdb.fasta -out GCF_003052455.1_ASM305245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:14,036] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:14,039] [INFO] Selected 9 target genomes.
[2024-01-25 18:53:14,039] [INFO] Target genome list was writen to GCF_003052455.1_ASM305245v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:14,048] [INFO] Task started: fastANI
[2024-01-25 18:53:14,049] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2eadc5c-006e-4569-8ef5-93fa8fb46998/GCF_003052455.1_ASM305245v1_genomic.fna.gz --refList GCF_003052455.1_ASM305245v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003052455.1_ASM305245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:26,754] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:26,763] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:53:26,763] [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
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	100.0	1384	1392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	conclusive
GCF_004519295.1	s__Cellulosimicrobium funkei	96.0086	1236	1392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_016921195.1	s__Cellulosimicrobium cellulans_F	90.1584	1161	1392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	90.0888	1176	1392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	89.9471	1151	1392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	89.6707	1190	1392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	89.4226	1172	1392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	89.3241	1079	1392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	84.5506	908	1392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:26,764] [INFO] GTDB search result was written to GCF_003052455.1_ASM305245v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:26,765] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:26,767] [INFO] DFAST_QC result json was written to GCF_003052455.1_ASM305245v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:26,767] [INFO] DFAST_QC completed!
[2024-01-25 18:53:26,768] [INFO] Total running time: 0h1m36s