[2024-01-24 13:41:40,905] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg82333e7b-b9c8-449d-bc07-4421ce23b030/dqc_reference
[2024-01-24 13:41:42,329] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,330] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,330] [INFO] Running command: gunzip -c /var/lib/cwl/stg577b8d13-5c4b-4c0d-9745-cc9862aeafeb/GCF_016342785.1_ASM1634278v1_genomic.fna.gz | prodigal -d GCF_016342785.1_ASM1634278v1_genomic.fna/cds.fna -a GCF_016342785.1_ASM1634278v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:51,843] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:51,843] [INFO] Task started: HMMsearch
[2024-01-24 13:41:51,843] [INFO] Running command: hmmsearch --tblout GCF_016342785.1_ASM1634278v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82333e7b-b9c8-449d-bc07-4421ce23b030/dqc_reference/reference_markers.hmm GCF_016342785.1_ASM1634278v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:52,123] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:52,124] [INFO] Found 6/6 markers.
[2024-01-24 13:41:52,160] [INFO] Query marker FASTA was written to GCF_016342785.1_ASM1634278v1_genomic.fna/markers.fasta
[2024-01-24 13:41:52,160] [INFO] Task started: Blastn
[2024-01-24 13:41:52,160] [INFO] Running command: blastn -query GCF_016342785.1_ASM1634278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82333e7b-b9c8-449d-bc07-4421ce23b030/dqc_reference/reference_markers.fasta -out GCF_016342785.1_ASM1634278v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:53,328] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:53,331] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:53,332] [INFO] Target genome list was writen to GCF_016342785.1_ASM1634278v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:53,337] [INFO] Task started: fastANI
[2024-01-24 13:41:53,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg577b8d13-5c4b-4c0d-9745-cc9862aeafeb/GCF_016342785.1_ASM1634278v1_genomic.fna.gz --refList GCF_016342785.1_ASM1634278v1_genomic.fna/target_genomes.txt --output GCF_016342785.1_ASM1634278v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:06,504] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:06,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82333e7b-b9c8-449d-bc07-4421ce23b030/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:06,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82333e7b-b9c8-449d-bc07-4421ce23b030/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:06,525] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:06,525] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:06,525] [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
Sanguibacter suaedae	strain=YZGR15	GCA_016342785.1	2795737	2795737	type	True	100.0	1043	1043	95	conclusive
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	81.1678	632	1043	95	below_threshold
Sanguibacter antarcticus	strain=DSM 18966	GCA_002564005.1	372484	372484	type	True	80.7591	595	1043	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	80.6499	596	1043	95	below_threshold
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	80.6052	589	1043	95	below_threshold
Sanguibacter gelidistatuariae	strain=ISLP-3	GCA_900096585.1	1814289	1814289	type	True	80.3963	563	1043	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.6569	486	1043	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	79.6451	472	1043	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	79.5669	518	1043	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.5423	498	1043	95	below_threshold
Flavimobilis marinus	strain=CGMCC 1.3457	GCA_014653315.1	285351	285351	type	True	79.516	462	1043	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.5042	490	1043	95	below_threshold
Flavimobilis marinus	strain=DSM 19083	GCA_900113055.1	285351	285351	type	True	79.4495	467	1043	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	79.4321	491	1043	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	78.7644	456	1043	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.7342	458	1043	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	78.7185	425	1043	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.6606	447	1043	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:06,527] [INFO] DFAST Taxonomy check result was written to GCF_016342785.1_ASM1634278v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:06,528] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:06,528] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:06,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82333e7b-b9c8-449d-bc07-4421ce23b030/dqc_reference/checkm_data
[2024-01-24 13:42:06,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:06,571] [INFO] Task started: CheckM
[2024-01-24 13:42:06,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016342785.1_ASM1634278v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016342785.1_ASM1634278v1_genomic.fna/checkm_input GCF_016342785.1_ASM1634278v1_genomic.fna/checkm_result
[2024-01-24 13:42:54,281] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:54,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:54,302] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:54,302] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:54,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016342785.1_ASM1634278v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:54,303] [INFO] Task started: Blastn
[2024-01-24 13:42:54,304] [INFO] Running command: blastn -query GCF_016342785.1_ASM1634278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82333e7b-b9c8-449d-bc07-4421ce23b030/dqc_reference/reference_markers_gtdb.fasta -out GCF_016342785.1_ASM1634278v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:56,106] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:56,111] [INFO] Selected 18 target genomes.
[2024-01-24 13:42:56,111] [INFO] Target genome list was writen to GCF_016342785.1_ASM1634278v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:56,160] [INFO] Task started: fastANI
[2024-01-24 13:42:56,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg577b8d13-5c4b-4c0d-9745-cc9862aeafeb/GCF_016342785.1_ASM1634278v1_genomic.fna.gz --refList GCF_016342785.1_ASM1634278v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016342785.1_ASM1634278v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:09,725] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:09,745] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:09,746] [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_016342785.1	s__Sanguibacter sp016342785	100.0	1043	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000024925.1	s__Sanguibacter keddieii	81.1891	630	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564005.1	s__Sanguibacter antarcticus	80.7654	594	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415325.1	s__Sanguibacter inulinus	80.6053	589	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	98.94	97.89	0.97	0.94	3	-
GCF_001552735.1	s__Sanguibacter suarezii	80.5882	602	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096585.1	s__Sanguibacter gelidistatuariae	80.386	564	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	79.8488	448	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836755.1	s__Oerskovia sp014836755	79.5152	501	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016921195.1	s__Cellulosimicrobium cellulans_F	79.5035	515	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718325.1	s__Oerskovia turbata	79.4323	491	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.78	99.34	0.96	0.90	4	-
GCF_900113055.1	s__Flavimobilis marinus	79.4283	469	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	79.2901	533	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538745.1	s__Cellulomonas cellasea	78.9708	530	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	-
GCF_002798015.1	s__Luteimicrobium subarcticum	78.9018	438	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009663185.1	s__Isoptericola sp009663185	78.786	403	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024965.1	s__Xylanimonas cellulosilytica	78.7166	395	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989825.1	s__Cellulomonas persica	78.6835	427	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	78.519	465	1043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:09,747] [INFO] GTDB search result was written to GCF_016342785.1_ASM1634278v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:09,748] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:09,752] [INFO] DFAST_QC result json was written to GCF_016342785.1_ASM1634278v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:09,752] [INFO] DFAST_QC completed!
[2024-01-24 13:43:09,752] [INFO] Total running time: 0h1m29s