[2023-07-01 03:25:49,039] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:25:49,041] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:25:49,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b18d1fe-9031-44b8-80b2-19238b5975c5/dqc_reference
[2023-07-01 03:25:50,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:25:50,307] [INFO] Task started: Prodigal
[2023-07-01 03:25:50,307] [INFO] Running command: gunzip -c /var/lib/cwl/stg52bb2e99-0333-42a5-8943-e70c530c236a/GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna.gz | prodigal -d GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/cds.fna -a GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:25:54,956] [INFO] Task succeeded: Prodigal
[2023-07-01 03:25:54,957] [INFO] Task started: HMMsearch
[2023-07-01 03:25:54,957] [INFO] Running command: hmmsearch --tblout GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b18d1fe-9031-44b8-80b2-19238b5975c5/dqc_reference/reference_markers.hmm GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:25:55,220] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:25:55,222] [INFO] Found 6/6 markers.
[2023-07-01 03:25:55,257] [INFO] Query marker FASTA was written to GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/markers.fasta
[2023-07-01 03:25:55,257] [INFO] Task started: Blastn
[2023-07-01 03:25:55,258] [INFO] Running command: blastn -query GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b18d1fe-9031-44b8-80b2-19238b5975c5/dqc_reference/reference_markers.fasta -out GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:25:55,845] [INFO] Task succeeded: Blastn
[2023-07-01 03:25:55,849] [INFO] Selected 40 target genomes.
[2023-07-01 03:25:55,850] [INFO] Target genome list was writen to GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/target_genomes.txt
[2023-07-01 03:25:55,851] [INFO] Task started: fastANI
[2023-07-01 03:25:55,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg52bb2e99-0333-42a5-8943-e70c530c236a/GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna.gz --refList GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/target_genomes.txt --output GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:26:18,502] [INFO] Task succeeded: fastANI
[2023-07-01 03:26:18,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b18d1fe-9031-44b8-80b2-19238b5975c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:26:18,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b18d1fe-9031-44b8-80b2-19238b5975c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:26:18,515] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:26:18,516] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 03:26:18,516] [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
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	77.2739	70	725	95	below_threshold
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	76.8045	51	725	95	below_threshold
Methylovulum miyakonense	strain=HT12	GCA_000384075.1	645578	645578	type	True	76.4839	54	725	95	below_threshold
Methylocucumis oryzae	strain=Sn10-6	GCA_000963695.1	1632867	1632867	type	True	76.0857	72	725	95	below_threshold
Crenothrix polyspora		GCA_900163755.1	360316	360316	reftype	True	76.0547	78	725	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 03:26:18,518] [INFO] DFAST Taxonomy check result was written to GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/tc_result.tsv
[2023-07-01 03:26:18,519] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:26:18,519] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:26:18,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b18d1fe-9031-44b8-80b2-19238b5975c5/dqc_reference/checkm_data
[2023-07-01 03:26:18,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:26:18,553] [INFO] Task started: CheckM
[2023-07-01 03:26:18,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/checkm_input GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/checkm_result
[2023-07-01 03:26:39,632] [INFO] Task succeeded: CheckM
[2023-07-01 03:26:39,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 03:26:39,654] [INFO] ===== Completeness check finished =====
[2023-07-01 03:26:39,654] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:26:39,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/markers.fasta)
[2023-07-01 03:26:39,655] [INFO] Task started: Blastn
[2023-07-01 03:26:39,655] [INFO] Running command: blastn -query GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b18d1fe-9031-44b8-80b2-19238b5975c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:26:40,420] [INFO] Task succeeded: Blastn
[2023-07-01 03:26:40,426] [INFO] Selected 13 target genomes.
[2023-07-01 03:26:40,426] [INFO] Target genome list was writen to GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:26:40,427] [INFO] Task started: fastANI
[2023-07-01 03:26:40,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg52bb2e99-0333-42a5-8943-e70c530c236a/GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna.gz --refList GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/target_genomes_gtdb.txt --output GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:26:47,057] [INFO] Task succeeded: fastANI
[2023-07-01 03:26:47,068] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 03:26:47,068] [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_903863905.1	s__KS41 sp903863905	99.5901	669	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.63	99.29	0.91	0.83	33	conclusive
GCA_003584865.1	s__KS41 sp003584865	80.6919	250	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.03	97.03	0.84	0.75	9	-
GCA_903839855.1	s__KS41 sp903839855	80.1811	327	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.93	99.90	0.95	0.94	3	-
GCA_903859415.1	s__KS41 sp903859415	80.079	325	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.28	98.83	0.89	0.85	3	-
GCA_903866825.1	s__KS41 sp903866825	79.888	313	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.82	99.82	0.85	0.85	2	-
GCA_903917345.1	s__KS41 sp903917345	78.7275	235	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.26	98.86	0.95	0.89	10	-
GCA_903903365.1	s__KS41 sp903903365	77.913	183	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003584895.1	s__KS41 sp003584895	77.742	154	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.75	98.03	0.85	0.79	12	-
GCA_903839795.1	s__KS41 sp903839795	77.687	166	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903765.1	s__KS41 sp903903765	77.6124	133	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934035.1	s__KS41 sp903934035	77.4054	162	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.03	98.98	0.89	0.84	3	-
GCA_903910205.1	s__KS41 sp903910205	77.125	137	725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.01	98.01	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-07-01 03:26:47,070] [INFO] GTDB search result was written to GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/result_gtdb.tsv
[2023-07-01 03:26:47,071] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:26:47,074] [INFO] DFAST_QC result json was written to GCA_903853375.1_freshwater_MAG_---_MJ120620B_bin-075_genomic.fna/dqc_result.json
[2023-07-01 03:26:47,074] [INFO] DFAST_QC completed!
[2023-07-01 03:26:47,075] [INFO] Total running time: 0h0m58s