[2023-06-30 02:30:18,200] [INFO] DFAST_QC pipeline started.
[2023-06-30 02:30:18,203] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 02:30:18,203] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcd17f85-f841-412b-a2c7-e8496d4b6273/dqc_reference
[2023-06-30 02:30:19,567] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 02:30:19,568] [INFO] Task started: Prodigal
[2023-06-30 02:30:19,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg370f8d12-8b0c-4eb8-9ccb-722da9a76eb1/GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna.gz | prodigal -d GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/cds.fna -a GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 02:30:23,613] [INFO] Task succeeded: Prodigal
[2023-06-30 02:30:23,614] [INFO] Task started: HMMsearch
[2023-06-30 02:30:23,614] [INFO] Running command: hmmsearch --tblout GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcd17f85-f841-412b-a2c7-e8496d4b6273/dqc_reference/reference_markers.hmm GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/protein.faa > /dev/null
[2023-06-30 02:30:23,878] [INFO] Task succeeded: HMMsearch
[2023-06-30 02:30:23,880] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg370f8d12-8b0c-4eb8-9ccb-722da9a76eb1/GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna.gz]
[2023-06-30 02:30:23,905] [INFO] Query marker FASTA was written to GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/markers.fasta
[2023-06-30 02:30:23,905] [INFO] Task started: Blastn
[2023-06-30 02:30:23,905] [INFO] Running command: blastn -query GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcd17f85-f841-412b-a2c7-e8496d4b6273/dqc_reference/reference_markers.fasta -out GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:30:24,500] [INFO] Task succeeded: Blastn
[2023-06-30 02:30:24,504] [INFO] Selected 33 target genomes.
[2023-06-30 02:30:24,504] [INFO] Target genome list was writen to GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/target_genomes.txt
[2023-06-30 02:30:24,510] [INFO] Task started: fastANI
[2023-06-30 02:30:24,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg370f8d12-8b0c-4eb8-9ccb-722da9a76eb1/GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna.gz --refList GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/target_genomes.txt --output GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 02:30:46,024] [INFO] Task succeeded: fastANI
[2023-06-30 02:30:46,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcd17f85-f841-412b-a2c7-e8496d4b6273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 02:30:46,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcd17f85-f841-412b-a2c7-e8496d4b6273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 02:30:46,036] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 02:30:46,037] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 02:30:46,037] [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
Methylomonas denitrificans	strain=FJG1	GCA_000785705.2	1538553	1538553	type	True	76.9161	92	317	95	below_threshold
Methylomonas albis	strain=EbA	GCA_014850955.1	1854563	1854563	type	True	76.9085	86	317	95	below_threshold
Methylomonas koyamae	strain=JCM 16701	GCA_001312005.1	702114	702114	suspected-type	True	76.6678	61	317	95	below_threshold
Methylomonas koyamae	strain=Fw12E-Y	GCA_019669905.1	702114	702114	suspected-type	True	76.6576	63	317	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 02:30:46,039] [INFO] DFAST Taxonomy check result was written to GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/tc_result.tsv
[2023-06-30 02:30:46,040] [INFO] ===== Taxonomy check completed =====
[2023-06-30 02:30:46,040] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 02:30:46,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcd17f85-f841-412b-a2c7-e8496d4b6273/dqc_reference/checkm_data
[2023-06-30 02:30:46,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 02:30:46,071] [INFO] Task started: CheckM
[2023-06-30 02:30:46,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/checkm_input GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/checkm_result
[2023-06-30 02:31:06,144] [INFO] Task succeeded: CheckM
[2023-06-30 02:31:06,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.94%
Contamintation: 9.90%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-30 02:31:06,175] [INFO] ===== Completeness check finished =====
[2023-06-30 02:31:06,176] [INFO] ===== Start GTDB Search =====
[2023-06-30 02:31:06,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/markers.fasta)
[2023-06-30 02:31:06,177] [INFO] Task started: Blastn
[2023-06-30 02:31:06,177] [INFO] Running command: blastn -query GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcd17f85-f841-412b-a2c7-e8496d4b6273/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:31:06,983] [INFO] Task succeeded: Blastn
[2023-06-30 02:31:06,989] [INFO] Selected 29 target genomes.
[2023-06-30 02:31:06,989] [INFO] Target genome list was writen to GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 02:31:07,028] [INFO] Task started: fastANI
[2023-06-30 02:31:07,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg370f8d12-8b0c-4eb8-9ccb-722da9a76eb1/GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna.gz --refList GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/target_genomes_gtdb.txt --output GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 02:31:20,597] [INFO] Task succeeded: fastANI
[2023-06-30 02:31:20,614] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 02:31:20,614] [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_903918375.1	s__Methylomonas sp903918375	95.7798	260	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	98.06	95.20	0.87	0.72	8	conclusive
GCA_903931355.1	s__Methylomonas sp903931355	89.2373	193	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903902945.1	s__Methylomonas sp903902945	77.9325	98	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515215.1	s__Methylomonas sp000515215	77.5361	93	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	95.46	95.46	0.83	0.83	2	-
GCA_002928965.1	s__Methylomonas sp002928965	77.5209	74	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083615.1	s__Methylomonas sp002083615	77.2534	72	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214665.1	s__Methylomonas methanica_B	77.1673	66	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644035.1	s__Methylomonas methanica_A	77.1384	95	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	95.96	95.96	0.85	0.85	2	-
GCA_903858105.1	s__Methylomonas sp903858105	77.0148	71	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644015.1	s__Methylomonas lenta	76.9836	72	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903064715.1	s__Methylomonas sp903064715	76.936	85	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001644045.1	s__Methylomonas methanica	76.8729	92	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCA_903928685.1	s__Methylovulum sp903928685	76.4627	51	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum	95.0	99.91	99.86	0.97	0.96	8	-
--------------------------------------------------------------------------------
[2023-06-30 02:31:20,618] [INFO] GTDB search result was written to GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/result_gtdb.tsv
[2023-06-30 02:31:20,619] [INFO] ===== GTDB Search completed =====
[2023-06-30 02:31:20,622] [INFO] DFAST_QC result json was written to GCA_903830365.1_freshwater_MAG_---_Erken-D7_bin-0759_genomic.fna/dqc_result.json
[2023-06-30 02:31:20,622] [INFO] DFAST_QC completed!
[2023-06-30 02:31:20,622] [INFO] Total running time: 0h1m2s