[2024-01-25 19:45:50,439] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:50,441] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:50,441] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfc1ba3f-c404-4990-9d42-fc30e957ec7a/dqc_reference
[2024-01-25 19:45:51,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:51,718] [INFO] Task started: Prodigal
[2024-01-25 19:45:51,718] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4f82578-8f5d-4d33-ac99-5d48c3b9c261/GCF_030159795.1_ASM3015979v1_genomic.fna.gz | prodigal -d GCF_030159795.1_ASM3015979v1_genomic.fna/cds.fna -a GCF_030159795.1_ASM3015979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:58,262] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:58,263] [INFO] Task started: HMMsearch
[2024-01-25 19:45:58,263] [INFO] Running command: hmmsearch --tblout GCF_030159795.1_ASM3015979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfc1ba3f-c404-4990-9d42-fc30e957ec7a/dqc_reference/reference_markers.hmm GCF_030159795.1_ASM3015979v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:58,487] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:58,489] [INFO] Found 6/6 markers.
[2024-01-25 19:45:58,514] [INFO] Query marker FASTA was written to GCF_030159795.1_ASM3015979v1_genomic.fna/markers.fasta
[2024-01-25 19:45:58,514] [INFO] Task started: Blastn
[2024-01-25 19:45:58,514] [INFO] Running command: blastn -query GCF_030159795.1_ASM3015979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfc1ba3f-c404-4990-9d42-fc30e957ec7a/dqc_reference/reference_markers.fasta -out GCF_030159795.1_ASM3015979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:59,140] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:59,143] [INFO] Selected 19 target genomes.
[2024-01-25 19:45:59,144] [INFO] Target genome list was writen to GCF_030159795.1_ASM3015979v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:59,152] [INFO] Task started: fastANI
[2024-01-25 19:45:59,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4f82578-8f5d-4d33-ac99-5d48c3b9c261/GCF_030159795.1_ASM3015979v1_genomic.fna.gz --refList GCF_030159795.1_ASM3015979v1_genomic.fna/target_genomes.txt --output GCF_030159795.1_ASM3015979v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:12,222] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:12,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfc1ba3f-c404-4990-9d42-fc30e957ec7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:12,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfc1ba3f-c404-4990-9d42-fc30e957ec7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:12,229] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:12,229] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:12,229] [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
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	97.1729	920	1038	95	conclusive
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	87.155	806	1038	95	below_threshold
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	78.2757	245	1038	95	below_threshold
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	77.7601	147	1038	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	77.7543	142	1038	95	below_threshold
Methylophaga lonarensis	strain=MPL	GCA_000349205.1	999151	999151	type	True	77.3339	104	1038	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:12,230] [INFO] DFAST Taxonomy check result was written to GCF_030159795.1_ASM3015979v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:12,231] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:12,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:12,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfc1ba3f-c404-4990-9d42-fc30e957ec7a/dqc_reference/checkm_data
[2024-01-25 19:46:12,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:12,263] [INFO] Task started: CheckM
[2024-01-25 19:46:12,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030159795.1_ASM3015979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030159795.1_ASM3015979v1_genomic.fna/checkm_input GCF_030159795.1_ASM3015979v1_genomic.fna/checkm_result
[2024-01-25 19:46:36,858] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:36,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:36,874] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:36,874] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:36,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030159795.1_ASM3015979v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:36,875] [INFO] Task started: Blastn
[2024-01-25 19:46:36,875] [INFO] Running command: blastn -query GCF_030159795.1_ASM3015979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfc1ba3f-c404-4990-9d42-fc30e957ec7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030159795.1_ASM3015979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:37,894] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:37,897] [INFO] Selected 9 target genomes.
[2024-01-25 19:46:37,897] [INFO] Target genome list was writen to GCF_030159795.1_ASM3015979v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:37,906] [INFO] Task started: fastANI
[2024-01-25 19:46:37,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4f82578-8f5d-4d33-ac99-5d48c3b9c261/GCF_030159795.1_ASM3015979v1_genomic.fna.gz --refList GCF_030159795.1_ASM3015979v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030159795.1_ASM3015979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:43,133] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:43,139] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:43,140] [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_000214595.1	s__Methylophaga aminisulfidivorans	97.1729	920	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.12	97.07	0.93	0.92	4	conclusive
GCF_900114205.1	s__Methylophaga sulfidovorans	87.155	806	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706095.1	s__Methylophaga sp002706095	84.5936	748	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.12	97.28	0.92	0.89	8	-
GCA_011052985.1	s__Methylophaga aminisulfidivorans_A	79.0832	246	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696735.1	s__Methylophaga sp002696735	78.6584	158	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.51	97.89	0.93	0.90	20	-
GCF_000156355.1	s__Methylophaga thiooxydans	78.2611	245	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	96.48	96.37	0.89	0.88	3	-
GCA_014859375.1	s__GCA-002733105 sp014859375	76.9506	110	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163115.1	s__41-12-T18 sp002163115	76.545	98	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:43,141] [INFO] GTDB search result was written to GCF_030159795.1_ASM3015979v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:43,141] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:43,144] [INFO] DFAST_QC result json was written to GCF_030159795.1_ASM3015979v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:43,144] [INFO] DFAST_QC completed!
[2024-01-25 19:46:43,144] [INFO] Total running time: 0h0m53s