[2023-07-01 02:12:38,905] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:12:38,909] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:12:38,909] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0bef445-1514-4016-ad12-906044754d27/dqc_reference
[2023-07-01 02:12:40,612] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:12:40,620] [INFO] Task started: Prodigal
[2023-07-01 02:12:40,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dc91f6c-05c6-41df-8372-08a6b4fcd5af/GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna.gz | prodigal -d GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/cds.fna -a GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:12:46,311] [INFO] Task succeeded: Prodigal
[2023-07-01 02:12:46,311] [INFO] Task started: HMMsearch
[2023-07-01 02:12:46,311] [INFO] Running command: hmmsearch --tblout GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0bef445-1514-4016-ad12-906044754d27/dqc_reference/reference_markers.hmm GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:12:46,575] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:12:46,577] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9dc91f6c-05c6-41df-8372-08a6b4fcd5af/GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna.gz]
[2023-07-01 02:12:46,607] [INFO] Query marker FASTA was written to GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/markers.fasta
[2023-07-01 02:12:46,607] [INFO] Task started: Blastn
[2023-07-01 02:12:46,607] [INFO] Running command: blastn -query GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0bef445-1514-4016-ad12-906044754d27/dqc_reference/reference_markers.fasta -out GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:12:47,268] [INFO] Task succeeded: Blastn
[2023-07-01 02:12:47,272] [INFO] Selected 23 target genomes.
[2023-07-01 02:12:47,272] [INFO] Target genome list was writen to GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/target_genomes.txt
[2023-07-01 02:12:47,273] [INFO] Task started: fastANI
[2023-07-01 02:12:47,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dc91f6c-05c6-41df-8372-08a6b4fcd5af/GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna.gz --refList GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/target_genomes.txt --output GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:13:02,190] [INFO] Task succeeded: fastANI
[2023-07-01 02:13:02,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0bef445-1514-4016-ad12-906044754d27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:13:02,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0bef445-1514-4016-ad12-906044754d27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:13:02,205] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:13:02,205] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 02:13:02,205] [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
Nevskia ramosa	strain=DSM 11499	GCA_000420645.1	64002	64002	type	True	92.3769	211	232	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	77.779	81	232	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	77.6082	72	232	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	77.5319	69	232	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	77.4598	86	232	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	77.3731	69	232	95	below_threshold
Hydrocarboniphaga daqingensis	strain=CGMCC 1.7049	GCA_900129825.1	490188	490188	type	True	77.0299	67	232	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	76.9522	63	232	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:13:02,212] [INFO] DFAST Taxonomy check result was written to GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/tc_result.tsv
[2023-07-01 02:13:02,212] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:13:02,212] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:13:02,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0bef445-1514-4016-ad12-906044754d27/dqc_reference/checkm_data
[2023-07-01 02:13:02,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:13:02,247] [INFO] Task started: CheckM
[2023-07-01 02:13:02,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/checkm_input GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/checkm_result
[2023-07-01 02:13:25,267] [INFO] Task succeeded: CheckM
[2023-07-01 02:13:25,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 02:13:25,290] [INFO] ===== Completeness check finished =====
[2023-07-01 02:13:25,290] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:13:25,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/markers.fasta)
[2023-07-01 02:13:25,291] [INFO] Task started: Blastn
[2023-07-01 02:13:25,291] [INFO] Running command: blastn -query GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0bef445-1514-4016-ad12-906044754d27/dqc_reference/reference_markers_gtdb.fasta -out GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:13:26,203] [INFO] Task succeeded: Blastn
[2023-07-01 02:13:26,229] [INFO] Selected 15 target genomes.
[2023-07-01 02:13:26,230] [INFO] Target genome list was writen to GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:13:26,257] [INFO] Task started: fastANI
[2023-07-01 02:13:26,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dc91f6c-05c6-41df-8372-08a6b4fcd5af/GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna.gz --refList GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/target_genomes_gtdb.txt --output GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:13:35,270] [INFO] Task succeeded: fastANI
[2023-07-01 02:13:35,283] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 02:13:35,284] [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_903885465.1	s__Nevskia sp903885465	99.4223	227	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000420645.1	s__Nevskia ramosa	92.3769	211	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823855.1	s__Nevskia sp013823855	82.9664	163	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822975.1	s__Nevskia sp903822975	77.8141	74	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000711955.1	s__Nevskia soli	77.779	81	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	77.6751	62	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	77.613	71	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	77.1746	50	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	77.1576	54	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129825.1	s__Hydrocarboniphaga daqingensis	77.0299	67	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970615.1	s__Nevskia sp903970615	76.9592	51	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730135.1	s__Stagnimonas aquatica	76.7569	65	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:13:35,286] [INFO] GTDB search result was written to GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/result_gtdb.tsv
[2023-07-01 02:13:35,286] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:13:35,290] [INFO] DFAST_QC result json was written to GCA_903894235.1_freshwater_MAG_---_MJ120827B_bin-085_genomic.fna/dqc_result.json
[2023-07-01 02:13:35,290] [INFO] DFAST_QC completed!
[2023-07-01 02:13:35,290] [INFO] Total running time: 0h0m56s