[2024-01-24 12:39:41,784] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:41,786] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:41,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg50fde211-bf27-4506-8549-b20bc55b51bb/dqc_reference
[2024-01-24 12:39:43,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:43,153] [INFO] Task started: Prodigal
[2024-01-24 12:39:43,153] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4c2b726-d475-48ce-aa0d-2a711b4bc61b/GCF_000424685.1_ASM42468v1_genomic.fna.gz | prodigal -d GCF_000424685.1_ASM42468v1_genomic.fna/cds.fna -a GCF_000424685.1_ASM42468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:53,535] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:53,536] [INFO] Task started: HMMsearch
[2024-01-24 12:39:53,536] [INFO] Running command: hmmsearch --tblout GCF_000424685.1_ASM42468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50fde211-bf27-4506-8549-b20bc55b51bb/dqc_reference/reference_markers.hmm GCF_000424685.1_ASM42468v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:53,815] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:53,816] [INFO] Found 6/6 markers.
[2024-01-24 12:39:53,846] [INFO] Query marker FASTA was written to GCF_000424685.1_ASM42468v1_genomic.fna/markers.fasta
[2024-01-24 12:39:53,847] [INFO] Task started: Blastn
[2024-01-24 12:39:53,847] [INFO] Running command: blastn -query GCF_000424685.1_ASM42468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50fde211-bf27-4506-8549-b20bc55b51bb/dqc_reference/reference_markers.fasta -out GCF_000424685.1_ASM42468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:54,833] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:54,838] [INFO] Selected 17 target genomes.
[2024-01-24 12:39:54,838] [INFO] Target genome list was writen to GCF_000424685.1_ASM42468v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:54,844] [INFO] Task started: fastANI
[2024-01-24 12:39:54,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4c2b726-d475-48ce-aa0d-2a711b4bc61b/GCF_000424685.1_ASM42468v1_genomic.fna.gz --refList GCF_000424685.1_ASM42468v1_genomic.fna/target_genomes.txt --output GCF_000424685.1_ASM42468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:07,605] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:07,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50fde211-bf27-4506-8549-b20bc55b51bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:07,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50fde211-bf27-4506-8549-b20bc55b51bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:07,619] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:07,620] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:07,620] [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 capsulatus	strain=ATCC 19069	GCA_000424685.1	414	414	type	True	100.0	1075	1077	95	conclusive
Methylococcus capsulatus	strain=Texas	GCA_000297615.1	414	414	type	True	99.9359	1037	1077	95	conclusive
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	86.3875	875	1077	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	77.8901	222	1077	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	77.7423	245	1077	95	below_threshold
Methylomagnum ishizawai	strain=RS11D-Pr	GCA_019670005.1	1760988	1760988	type	True	77.4833	260	1077	95	below_threshold
Methylocaldum marinum	strain=S8	GCA_003584645.1	1432792	1432792	type	True	77.3443	184	1077	95	below_threshold
Methylotetracoccus oryzae	strain=C50C1	GCA_006175985.1	1919059	1919059	type	True	77.3043	195	1077	95	below_threshold
Methylomicrobium lacus	strain=LW14	GCA_000527095.1	136992	136992	type	True	77.2431	97	1077	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	77.2116	124	1077	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.3861	95	1077	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.3305	76	1077	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	76.3031	96	1077	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.0574	97	1077	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:07,623] [INFO] DFAST Taxonomy check result was written to GCF_000424685.1_ASM42468v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:07,623] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:07,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:07,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50fde211-bf27-4506-8549-b20bc55b51bb/dqc_reference/checkm_data
[2024-01-24 12:40:07,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:07,668] [INFO] Task started: CheckM
[2024-01-24 12:40:07,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000424685.1_ASM42468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000424685.1_ASM42468v1_genomic.fna/checkm_input GCF_000424685.1_ASM42468v1_genomic.fna/checkm_result
[2024-01-24 12:40:42,147] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:42,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:42,170] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:42,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:42,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000424685.1_ASM42468v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:42,171] [INFO] Task started: Blastn
[2024-01-24 12:40:42,171] [INFO] Running command: blastn -query GCF_000424685.1_ASM42468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50fde211-bf27-4506-8549-b20bc55b51bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000424685.1_ASM42468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:43,814] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:43,827] [INFO] Selected 13 target genomes.
[2024-01-24 12:40:43,828] [INFO] Target genome list was writen to GCF_000424685.1_ASM42468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:43,837] [INFO] Task started: fastANI
[2024-01-24 12:40:43,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4c2b726-d475-48ce-aa0d-2a711b4bc61b/GCF_000424685.1_ASM42468v1_genomic.fna.gz --refList GCF_000424685.1_ASM42468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000424685.1_ASM42468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:53,572] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:53,585] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:53,586] [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_000424685.1	s__Methylococcus capsulatus	100.0	1073	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	99.39	98.77	0.98	0.95	3	conclusive
GCF_016106025.1	s__Methylococcus sp016106025	89.2738	906	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012769535.1	s__Methylococcus sp012769535	86.3809	876	1077	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	78.3393	268	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__EFPC2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699185.1	s__Thiohalobacter sp002699185	77.8273	95	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934725.1	s__Methyloterricola oryzae	77.7149	247	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026715.1	s__VEPB01 sp012026715	77.686	183	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__VEPB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155475.1	s__Methylomagnum ishizawai	77.6028	246	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylomagnum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810705.1	s__CADDYU01 sp902810705	77.4111	183	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__CADDYU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584645.1	s__Methylocaldum marinum	77.32	182	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylocaldum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779595.1	s__Halomonas_B sp014779595	76.5262	72	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103845.1	s__Pseudomonas jinjuensis	76.2075	132	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:53,588] [INFO] GTDB search result was written to GCF_000424685.1_ASM42468v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:53,589] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:53,592] [INFO] DFAST_QC result json was written to GCF_000424685.1_ASM42468v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:53,593] [INFO] DFAST_QC completed!
[2024-01-24 12:40:53,593] [INFO] Total running time: 0h1m12s