[2024-01-24 14:22:04,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ab25a36-049b-4e0c-9e86-903ee069b02c/dqc_reference
[2024-01-24 14:22:05,939] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,940] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,940] [INFO] Running command: gunzip -c /var/lib/cwl/stgd00964be-f7bd-4471-a225-1ac7f9ea4001/GCF_012769535.1_ASM1276953v1_genomic.fna.gz | prodigal -d GCF_012769535.1_ASM1276953v1_genomic.fna/cds.fna -a GCF_012769535.1_ASM1276953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:16,377] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:16,378] [INFO] Task started: HMMsearch
[2024-01-24 14:22:16,378] [INFO] Running command: hmmsearch --tblout GCF_012769535.1_ASM1276953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ab25a36-049b-4e0c-9e86-903ee069b02c/dqc_reference/reference_markers.hmm GCF_012769535.1_ASM1276953v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:16,658] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:16,659] [INFO] Found 6/6 markers.
[2024-01-24 14:22:16,697] [INFO] Query marker FASTA was written to GCF_012769535.1_ASM1276953v1_genomic.fna/markers.fasta
[2024-01-24 14:22:16,698] [INFO] Task started: Blastn
[2024-01-24 14:22:16,698] [INFO] Running command: blastn -query GCF_012769535.1_ASM1276953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ab25a36-049b-4e0c-9e86-903ee069b02c/dqc_reference/reference_markers.fasta -out GCF_012769535.1_ASM1276953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:17,670] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:17,673] [INFO] Selected 17 target genomes.
[2024-01-24 14:22:17,673] [INFO] Target genome list was writen to GCF_012769535.1_ASM1276953v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:17,683] [INFO] Task started: fastANI
[2024-01-24 14:22:17,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgd00964be-f7bd-4471-a225-1ac7f9ea4001/GCF_012769535.1_ASM1276953v1_genomic.fna.gz --refList GCF_012769535.1_ASM1276953v1_genomic.fna/target_genomes.txt --output GCF_012769535.1_ASM1276953v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:31,749] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:31,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ab25a36-049b-4e0c-9e86-903ee069b02c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:31,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ab25a36-049b-4e0c-9e86-903ee069b02c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:31,770] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:31,771] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:31,771] [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
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	100.0	1122	1123	95	conclusive
Methylococcus capsulatus	strain=Texas	GCA_000297615.1	414	414	type	True	86.4156	849	1123	95	below_threshold
Methylococcus capsulatus	strain=ATCC 19069	GCA_000424685.1	414	414	type	True	86.3372	891	1123	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	78.3126	291	1123	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	78.0733	258	1123	95	below_threshold
Methylomagnum ishizawai	strain=RS11D-Pr	GCA_019670005.1	1760988	1760988	type	True	78.0435	300	1123	95	below_threshold
Methylogaea oryzae	strain=JCM 16910	GCA_001312345.1	1295382	1295382	type	True	77.9686	189	1123	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.5181	139	1123	95	below_threshold
Methylocaldum marinum	strain=S8	GCA_003584645.1	1432792	1432792	type	True	77.4543	208	1123	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	77.1897	130	1123	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.1537	146	1123	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	76.8265	107	1123	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.7979	162	1123	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.7675	155	1123	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.7578	154	1123	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	76.5651	127	1123	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.5415	160	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:31,773] [INFO] DFAST Taxonomy check result was written to GCF_012769535.1_ASM1276953v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:31,774] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:31,774] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:31,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ab25a36-049b-4e0c-9e86-903ee069b02c/dqc_reference/checkm_data
[2024-01-24 14:22:31,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:31,814] [INFO] Task started: CheckM
[2024-01-24 14:22:31,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012769535.1_ASM1276953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012769535.1_ASM1276953v1_genomic.fna/checkm_input GCF_012769535.1_ASM1276953v1_genomic.fna/checkm_result
[2024-01-24 14:23:06,872] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:06,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:06,895] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:06,895] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:06,896] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012769535.1_ASM1276953v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:06,896] [INFO] Task started: Blastn
[2024-01-24 14:23:06,896] [INFO] Running command: blastn -query GCF_012769535.1_ASM1276953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ab25a36-049b-4e0c-9e86-903ee069b02c/dqc_reference/reference_markers_gtdb.fasta -out GCF_012769535.1_ASM1276953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:08,703] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:08,708] [INFO] Selected 13 target genomes.
[2024-01-24 14:23:08,708] [INFO] Target genome list was writen to GCF_012769535.1_ASM1276953v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:08,723] [INFO] Task started: fastANI
[2024-01-24 14:23:08,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgd00964be-f7bd-4471-a225-1ac7f9ea4001/GCF_012769535.1_ASM1276953v1_genomic.fna.gz --refList GCF_012769535.1_ASM1276953v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012769535.1_ASM1276953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:19,045] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:19,059] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:19,059] [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_012769535.1	s__Methylococcus sp012769535	100.0	1121	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000424685.1	s__Methylococcus capsulatus	86.3287	892	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	99.39	98.77	0.98	0.95	3	-
GCF_016106025.1	s__Methylococcus sp016106025	85.881	878	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016925495.1	s__EFPC2 sp016925495	78.6618	291	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__EFPC2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934725.1	s__Methyloterricola oryzae	78.2987	290	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001312345.1	s__Methylogaea oryzae	77.9686	189	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylogaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155475.1	s__Methylomagnum ishizawai	77.9408	283	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylomagnum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005105.1	s__Methylocaldum sp002005105	77.6465	197	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylocaldum	95.0	98.51	98.17	0.91	0.88	6	-
GCA_902810705.1	s__CADDYU01 sp902810705	77.6193	211	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__CADDYU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	77.4962	140	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014268885.2	s__Pseudomonas_E sp014268885	76.8138	107	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103845.1	s__Pseudomonas jinjuensis	76.7008	151	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014779595.1	s__Halomonas_B sp014779595	76.2259	105	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:19,061] [INFO] GTDB search result was written to GCF_012769535.1_ASM1276953v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:19,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:19,065] [INFO] DFAST_QC result json was written to GCF_012769535.1_ASM1276953v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:19,065] [INFO] DFAST_QC completed!
[2024-01-24 14:23:19,065] [INFO] Total running time: 0h1m15s