[2024-01-24 11:43:43,102] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:43,105] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:43,106] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b86a938-af11-4533-a952-4cfc8ac1f3fa/dqc_reference
[2024-01-24 11:43:44,407] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:44,408] [INFO] Task started: Prodigal
[2024-01-24 11:43:44,408] [INFO] Running command: gunzip -c /var/lib/cwl/stg50b3aa6c-8fdc-419e-b6c1-ae41672d48c5/GCF_030296755.1_ASM3029675v1_genomic.fna.gz | prodigal -d GCF_030296755.1_ASM3029675v1_genomic.fna/cds.fna -a GCF_030296755.1_ASM3029675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:52,180] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:52,180] [INFO] Task started: HMMsearch
[2024-01-24 11:43:52,180] [INFO] Running command: hmmsearch --tblout GCF_030296755.1_ASM3029675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b86a938-af11-4533-a952-4cfc8ac1f3fa/dqc_reference/reference_markers.hmm GCF_030296755.1_ASM3029675v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:52,528] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:52,530] [INFO] Found 6/6 markers.
[2024-01-24 11:43:52,556] [INFO] Query marker FASTA was written to GCF_030296755.1_ASM3029675v1_genomic.fna/markers.fasta
[2024-01-24 11:43:52,557] [INFO] Task started: Blastn
[2024-01-24 11:43:52,557] [INFO] Running command: blastn -query GCF_030296755.1_ASM3029675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b86a938-af11-4533-a952-4cfc8ac1f3fa/dqc_reference/reference_markers.fasta -out GCF_030296755.1_ASM3029675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:53,236] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:53,239] [INFO] Selected 22 target genomes.
[2024-01-24 11:43:53,240] [INFO] Target genome list was writen to GCF_030296755.1_ASM3029675v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:53,247] [INFO] Task started: fastANI
[2024-01-24 11:43:53,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b3aa6c-8fdc-419e-b6c1-ae41672d48c5/GCF_030296755.1_ASM3029675v1_genomic.fna.gz --refList GCF_030296755.1_ASM3029675v1_genomic.fna/target_genomes.txt --output GCF_030296755.1_ASM3029675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:06,441] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:06,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b86a938-af11-4533-a952-4cfc8ac1f3fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:06,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b86a938-af11-4533-a952-4cfc8ac1f3fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:06,448] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:06,448] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:06,448] [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 sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	84.3123	741	1035	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	84.0487	765	1035	95	below_threshold
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	79.2503	233	1035	95	below_threshold
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	78.9484	137	1035	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	77.7913	130	1035	95	below_threshold
Methylophaga lonarensis	strain=MPL	GCA_000349205.1	999151	999151	type	True	77.2659	103	1035	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:06,450] [INFO] DFAST Taxonomy check result was written to GCF_030296755.1_ASM3029675v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:06,450] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:06,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:06,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b86a938-af11-4533-a952-4cfc8ac1f3fa/dqc_reference/checkm_data
[2024-01-24 11:44:06,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:06,481] [INFO] Task started: CheckM
[2024-01-24 11:44:06,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030296755.1_ASM3029675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030296755.1_ASM3029675v1_genomic.fna/checkm_input GCF_030296755.1_ASM3029675v1_genomic.fna/checkm_result
[2024-01-24 11:44:36,757] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:36,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:36,777] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:36,778] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:36,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030296755.1_ASM3029675v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:36,779] [INFO] Task started: Blastn
[2024-01-24 11:44:36,779] [INFO] Running command: blastn -query GCF_030296755.1_ASM3029675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b86a938-af11-4533-a952-4cfc8ac1f3fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_030296755.1_ASM3029675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:37,637] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:37,642] [INFO] Selected 16 target genomes.
[2024-01-24 11:44:37,643] [INFO] Target genome list was writen to GCF_030296755.1_ASM3029675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:37,656] [INFO] Task started: fastANI
[2024-01-24 11:44:37,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b3aa6c-8fdc-419e-b6c1-ae41672d48c5/GCF_030296755.1_ASM3029675v1_genomic.fna.gz --refList GCF_030296755.1_ASM3029675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030296755.1_ASM3029675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:47,007] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:47,022] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:47,022] [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_002706095.1	s__Methylophaga sp002706095	97.4547	939	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.12	97.28	0.92	0.89	8	conclusive
GCF_900114205.1	s__Methylophaga sulfidovorans	84.2995	742	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214595.1	s__Methylophaga aminisulfidivorans	84.0487	765	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.12	97.07	0.93	0.92	4	-
GCA_011052985.1	s__Methylophaga aminisulfidivorans_A	79.5061	231	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156355.1	s__Methylophaga thiooxydans	79.2539	231	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	96.48	96.37	0.89	0.88	3	-
GCA_009711715.1	s__Methylophaga sp009711715	78.498	163	1035	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	78.2987	147	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.51	97.89	0.93	0.90	20	-
GCA_002363955.1	s__Methylophaga sp002363955	77.1925	129	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.95	98.64	0.94	0.91	14	-
GCA_002163115.1	s__41-12-T18 sp002163115	76.7099	93	1035	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	-
GCA_905479985.1	s__GCA-002733105 sp905479985	76.6504	71	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:47,024] [INFO] GTDB search result was written to GCF_030296755.1_ASM3029675v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:47,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:47,028] [INFO] DFAST_QC result json was written to GCF_030296755.1_ASM3029675v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:47,028] [INFO] DFAST_QC completed!
[2024-01-24 11:44:47,028] [INFO] Total running time: 0h1m4s