[2024-01-25 19:31:51,563] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,568] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5d89846-7a6c-4e5c-bca2-3d4eff61f5dc/dqc_reference
[2024-01-25 19:31:52,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,679] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fb1cdba-8e87-4e1a-9348-c7652b3581d7/GCF_014191775.1_ASM1419177v1_genomic.fna.gz | prodigal -d GCF_014191775.1_ASM1419177v1_genomic.fna/cds.fna -a GCF_014191775.1_ASM1419177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:02,177] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:02,177] [INFO] Task started: HMMsearch
[2024-01-25 19:32:02,177] [INFO] Running command: hmmsearch --tblout GCF_014191775.1_ASM1419177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5d89846-7a6c-4e5c-bca2-3d4eff61f5dc/dqc_reference/reference_markers.hmm GCF_014191775.1_ASM1419177v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:02,387] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:02,388] [INFO] Found 6/6 markers.
[2024-01-25 19:32:02,418] [INFO] Query marker FASTA was written to GCF_014191775.1_ASM1419177v1_genomic.fna/markers.fasta
[2024-01-25 19:32:02,418] [INFO] Task started: Blastn
[2024-01-25 19:32:02,418] [INFO] Running command: blastn -query GCF_014191775.1_ASM1419177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5d89846-7a6c-4e5c-bca2-3d4eff61f5dc/dqc_reference/reference_markers.fasta -out GCF_014191775.1_ASM1419177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:03,073] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:03,076] [INFO] Selected 27 target genomes.
[2024-01-25 19:32:03,077] [INFO] Target genome list was writen to GCF_014191775.1_ASM1419177v1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:03,097] [INFO] Task started: fastANI
[2024-01-25 19:32:03,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fb1cdba-8e87-4e1a-9348-c7652b3581d7/GCF_014191775.1_ASM1419177v1_genomic.fna.gz --refList GCF_014191775.1_ASM1419177v1_genomic.fna/target_genomes.txt --output GCF_014191775.1_ASM1419177v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:23,853] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:23,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5d89846-7a6c-4e5c-bca2-3d4eff61f5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:23,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5d89846-7a6c-4e5c-bca2-3d4eff61f5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:23,863] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:32:23,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:32:23,863] [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
Limibacillus halophilus	strain=CECT 8803	GCA_014191775.1	1579333	1579333	type	True	100.0	1150	1151	95	conclusive
Algihabitans albus	strain=HHTR 118	GCA_003572205.1	2164067	2164067	type	True	76.6316	67	1151	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	76.5486	73	1151	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.3964	121	1151	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.361	121	1151	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.2943	74	1151	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.1712	68	1151	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.1493	65	1151	95	below_threshold
Fodinicurvata sediminis	strain=DSM 21159	GCA_000420625.1	1121832	1121832	type	True	75.9478	72	1151	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8536	76	1151	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.7734	65	1151	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.5735	51	1151	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:23,867] [INFO] DFAST Taxonomy check result was written to GCF_014191775.1_ASM1419177v1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:23,867] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:23,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:23,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5d89846-7a6c-4e5c-bca2-3d4eff61f5dc/dqc_reference/checkm_data
[2024-01-25 19:32:23,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:23,906] [INFO] Task started: CheckM
[2024-01-25 19:32:23,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191775.1_ASM1419177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191775.1_ASM1419177v1_genomic.fna/checkm_input GCF_014191775.1_ASM1419177v1_genomic.fna/checkm_result
[2024-01-25 19:32:53,853] [INFO] Task succeeded: CheckM
[2024-01-25 19:32:53,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:32:53,873] [INFO] ===== Completeness check finished =====
[2024-01-25 19:32:53,873] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:32:53,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191775.1_ASM1419177v1_genomic.fna/markers.fasta)
[2024-01-25 19:32:53,874] [INFO] Task started: Blastn
[2024-01-25 19:32:53,874] [INFO] Running command: blastn -query GCF_014191775.1_ASM1419177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5d89846-7a6c-4e5c-bca2-3d4eff61f5dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191775.1_ASM1419177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:54,993] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:54,997] [INFO] Selected 28 target genomes.
[2024-01-25 19:32:54,997] [INFO] Target genome list was writen to GCF_014191775.1_ASM1419177v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:32:55,033] [INFO] Task started: fastANI
[2024-01-25 19:32:55,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fb1cdba-8e87-4e1a-9348-c7652b3581d7/GCF_014191775.1_ASM1419177v1_genomic.fna.gz --refList GCF_014191775.1_ASM1419177v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191775.1_ASM1419177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:33:21,444] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:21,456] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:33:21,456] [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_014191775.1	s__Limibacillus halophilus	100.0	1150	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__CECT-8803;g__Limibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003572205.1	s__Algihabitans albus	76.6316	67	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	76.4434	115	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.3773	120	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_001657395.1	s__Pelagibius sp001657395	76.3177	94	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	76.1076	68	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184795.1	s__Phaeospirillum sp900184795	76.0936	52	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365375.1	s__Azospirillum sp008365375	76.0324	64	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016806835.1	s__Skermanella rosea	75.9842	64	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	75.9717	60	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	75.9645	61	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730165.1	s__Nitrospirillum amazonense	75.905	65	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	97.38	95.62	0.93	0.89	4	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	75.8536	76	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828045.1	s__Nitrospirillum amazonense_C	75.8246	60	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590945.1	s__Zavarzinia sp003590945	75.8242	61	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992495.1	s__Reyranella soli	75.7947	64	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	75.7714	52	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859315.1	s__SYSU-D60007 sp007859315	75.7617	64	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:33:21,457] [INFO] GTDB search result was written to GCF_014191775.1_ASM1419177v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:33:21,458] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:33:21,462] [INFO] DFAST_QC result json was written to GCF_014191775.1_ASM1419177v1_genomic.fna/dqc_result.json
[2024-01-25 19:33:21,462] [INFO] DFAST_QC completed!
[2024-01-25 19:33:21,463] [INFO] Total running time: 0h1m30s