[2023-06-13 14:46:09,739] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:46:09,741] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:46:09,741] [INFO] DQC Reference Directory: /var/lib/cwl/stgd25586ed-a8fe-4c1a-b5d3-26b638bb0767/dqc_reference
[2023-06-13 14:46:10,884] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:46:10,884] [INFO] Task started: Prodigal
[2023-06-13 14:46:10,885] [INFO] Running command: gunzip -c /var/lib/cwl/stge55038ab-7a01-4b52-a69f-fcb7501a8896/GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna.gz | prodigal -d GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/cds.fna -a GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:46:17,266] [INFO] Task succeeded: Prodigal
[2023-06-13 14:46:17,267] [INFO] Task started: HMMsearch
[2023-06-13 14:46:17,267] [INFO] Running command: hmmsearch --tblout GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd25586ed-a8fe-4c1a-b5d3-26b638bb0767/dqc_reference/reference_markers.hmm GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:46:17,459] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:46:17,461] [INFO] Found 6/6 markers.
[2023-06-13 14:46:17,483] [INFO] Query marker FASTA was written to GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/markers.fasta
[2023-06-13 14:46:17,484] [INFO] Task started: Blastn
[2023-06-13 14:46:17,484] [INFO] Running command: blastn -query GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd25586ed-a8fe-4c1a-b5d3-26b638bb0767/dqc_reference/reference_markers.fasta -out GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:46:18,324] [INFO] Task succeeded: Blastn
[2023-06-13 14:46:18,327] [INFO] Selected 15 target genomes.
[2023-06-13 14:46:18,328] [INFO] Target genome list was writen to GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/target_genomes.txt
[2023-06-13 14:46:18,329] [INFO] Task started: fastANI
[2023-06-13 14:46:18,329] [INFO] Running command: fastANI --query /var/lib/cwl/stge55038ab-7a01-4b52-a69f-fcb7501a8896/GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna.gz --refList GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/target_genomes.txt --output GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:46:27,110] [INFO] Task succeeded: fastANI
[2023-06-13 14:46:27,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd25586ed-a8fe-4c1a-b5d3-26b638bb0767/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:46:27,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd25586ed-a8fe-4c1a-b5d3-26b638bb0767/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:46:27,123] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:46:27,123] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:46:27,123] [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
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	84.2311	505	611	95	below_threshold
Tepidimonas taiwanensis	strain=I1-1	GCA_007556675.1	307486	307486	type	True	83.379	495	611	95	below_threshold
Tepidimonas taiwanensis	strain=LMG 22826	GCA_020162115.1	307486	307486	type	True	83.3415	500	611	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	83.247	482	611	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	82.842	491	611	95	below_threshold
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	82.796	474	611	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	82.7923	473	611	95	below_threshold
Tepidimonas aquatica	strain=CLN-1	GCA_007556585.1	247482	247482	type	True	82.5992	470	611	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	81.5646	450	611	95	below_threshold
Tepidimonas charontis	strain=SPSP-6	GCA_007556685.1	2267262	2267262	type	True	81.4397	438	611	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.2948	370	611	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.8127	304	611	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.808	293	611	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.3654	285	611	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.237	241	611	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:46:27,125] [INFO] DFAST Taxonomy check result was written to GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/tc_result.tsv
[2023-06-13 14:46:27,126] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:46:27,126] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:46:27,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd25586ed-a8fe-4c1a-b5d3-26b638bb0767/dqc_reference/checkm_data
[2023-06-13 14:46:27,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:46:27,148] [INFO] Task started: CheckM
[2023-06-13 14:46:27,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/checkm_input GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/checkm_result
[2023-06-13 14:46:52,274] [INFO] Task succeeded: CheckM
[2023-06-13 14:46:52,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:46:52,293] [INFO] ===== Completeness check finished =====
[2023-06-13 14:46:52,293] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:46:52,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/markers.fasta)
[2023-06-13 14:46:52,293] [INFO] Task started: Blastn
[2023-06-13 14:46:52,293] [INFO] Running command: blastn -query GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd25586ed-a8fe-4c1a-b5d3-26b638bb0767/dqc_reference/reference_markers_gtdb.fasta -out GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:46:53,845] [INFO] Task succeeded: Blastn
[2023-06-13 14:46:53,849] [INFO] Selected 11 target genomes.
[2023-06-13 14:46:53,849] [INFO] Target genome list was writen to GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:46:53,854] [INFO] Task started: fastANI
[2023-06-13 14:46:53,854] [INFO] Running command: fastANI --query /var/lib/cwl/stge55038ab-7a01-4b52-a69f-fcb7501a8896/GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna.gz --refList GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:47:00,498] [INFO] Task succeeded: fastANI
[2023-06-13 14:47:00,508] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 14:47:00,509] [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_007556755.1	s__Tepidimonas fonticaldi	84.2121	506	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCF_007556675.1	s__Tepidimonas taiwanensis	83.3696	496	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	98.33	97.91	0.91	0.88	3	-
GCF_007556705.1	s__Tepidimonas thermarum	83.247	482	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556605.1	s__Tepidimonas sediminis	82.8537	490	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342625.1	s__Tepidimonas ignava	82.7846	474	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007556585.1	s__Tepidimonas aquatica	82.5995	469	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556595.1	s__Tepidimonas alkaliphilus	81.5646	450	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556685.1	s__Tepidimonas charontis	81.4496	439	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363315.1	s__Tepidicella xavieri	80.0978	360	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980595.1	s__Malikia granosa	79.2708	304	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828895.1	s__Serpentinomonas raichei	79.2342	317	611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:47:00,510] [INFO] GTDB search result was written to GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:47:00,511] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:47:00,515] [INFO] DFAST_QC result json was written to GCA_938045175.1_S1_Bin_METABAT_109_1_genomic.fna/dqc_result.json
[2023-06-13 14:47:00,515] [INFO] DFAST_QC completed!
[2023-06-13 14:47:00,515] [INFO] Total running time: 0h0m51s