[2023-06-19 04:59:07,881] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:59:07,883] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:59:07,883] [INFO] DQC Reference Directory: /var/lib/cwl/stg823c2229-ec58-458a-9213-57899e0e672e/dqc_reference
[2023-06-19 04:59:09,153] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:59:09,154] [INFO] Task started: Prodigal
[2023-06-19 04:59:09,155] [INFO] Running command: gunzip -c /var/lib/cwl/stg61fecb0c-bb4c-40a4-8e31-b5328fba245c/GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna.gz | prodigal -d GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/cds.fna -a GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:59:13,582] [INFO] Task succeeded: Prodigal
[2023-06-19 04:59:13,583] [INFO] Task started: HMMsearch
[2023-06-19 04:59:13,583] [INFO] Running command: hmmsearch --tblout GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg823c2229-ec58-458a-9213-57899e0e672e/dqc_reference/reference_markers.hmm GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:59:13,881] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:59:13,882] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg61fecb0c-bb4c-40a4-8e31-b5328fba245c/GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna.gz]
[2023-06-19 04:59:13,918] [INFO] Query marker FASTA was written to GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/markers.fasta
[2023-06-19 04:59:13,919] [INFO] Task started: Blastn
[2023-06-19 04:59:13,919] [INFO] Running command: blastn -query GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg823c2229-ec58-458a-9213-57899e0e672e/dqc_reference/reference_markers.fasta -out GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:59:14,825] [INFO] Task succeeded: Blastn
[2023-06-19 04:59:14,830] [INFO] Selected 15 target genomes.
[2023-06-19 04:59:14,831] [INFO] Target genome list was writen to GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/target_genomes.txt
[2023-06-19 04:59:14,834] [INFO] Task started: fastANI
[2023-06-19 04:59:14,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg61fecb0c-bb4c-40a4-8e31-b5328fba245c/GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna.gz --refList GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/target_genomes.txt --output GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:59:23,726] [INFO] Task succeeded: fastANI
[2023-06-19 04:59:23,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg823c2229-ec58-458a-9213-57899e0e672e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:59:23,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg823c2229-ec58-458a-9213-57899e0e672e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:59:23,740] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:59:23,740] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 04:59:23,740] [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	88.3343	330	372	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	83.4247	286	372	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	82.9897	296	372	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	82.4463	262	372	95	below_threshold
Tepidimonas taiwanensis	strain=I1-1	GCA_007556675.1	307486	307486	type	True	82.1437	280	372	95	below_threshold
Tepidimonas taiwanensis	strain=LMG 22826	GCA_020162115.1	307486	307486	type	True	82.1231	284	372	95	below_threshold
Tepidimonas aquatica	strain=CLN-1	GCA_007556585.1	247482	247482	type	True	82.041	258	372	95	below_threshold
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	81.8637	269	372	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	81.7711	275	372	95	below_threshold
Tepidimonas charontis	strain=SPSP-6	GCA_007556685.1	2267262	2267262	type	True	81.2459	262	372	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.2462	203	372	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.8172	179	372	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.6269	177	372	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.3034	168	372	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.8109	139	372	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:59:23,742] [INFO] DFAST Taxonomy check result was written to GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/tc_result.tsv
[2023-06-19 04:59:23,743] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:59:23,743] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:59:23,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg823c2229-ec58-458a-9213-57899e0e672e/dqc_reference/checkm_data
[2023-06-19 04:59:23,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:59:23,772] [INFO] Task started: CheckM
[2023-06-19 04:59:23,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/checkm_input GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/checkm_result
[2023-06-19 04:59:43,969] [INFO] Task succeeded: CheckM
[2023-06-19 04:59:43,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 04:59:44,006] [INFO] ===== Completeness check finished =====
[2023-06-19 04:59:44,006] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:59:44,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/markers.fasta)
[2023-06-19 04:59:44,007] [INFO] Task started: Blastn
[2023-06-19 04:59:44,007] [INFO] Running command: blastn -query GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg823c2229-ec58-458a-9213-57899e0e672e/dqc_reference/reference_markers_gtdb.fasta -out GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:59:45,599] [INFO] Task succeeded: Blastn
[2023-06-19 04:59:45,606] [INFO] Selected 11 target genomes.
[2023-06-19 04:59:45,606] [INFO] Target genome list was writen to GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:59:45,611] [INFO] Task started: fastANI
[2023-06-19 04:59:45,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg61fecb0c-bb4c-40a4-8e31-b5328fba245c/GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna.gz --refList GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/target_genomes_gtdb.txt --output GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:59:50,799] [INFO] Task succeeded: fastANI
[2023-06-19 04:59:50,815] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 04:59:50,816] [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	88.349	329	372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCF_007556605.1	s__Tepidimonas sediminis	83.4247	286	372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556705.1	s__Tepidimonas thermarum	82.9897	296	372	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	82.4161	263	372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556675.1	s__Tepidimonas taiwanensis	82.1441	280	372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	98.33	97.91	0.91	0.88	3	-
GCF_007556585.1	s__Tepidimonas aquatica	82.041	258	372	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	81.7711	275	372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007556685.1	s__Tepidimonas charontis	81.2459	262	372	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	80.1717	209	372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837145.1	s__BK-30 sp002837145	79.7998	215	372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013432195.1	s__Tepidicella baoligensis	79.4907	190	372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:59:50,818] [INFO] GTDB search result was written to GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:59:50,819] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:59:50,825] [INFO] DFAST_QC result json was written to GCA_937949455.1_N1_Bin_METABAT_176_1_genomic.fna/dqc_result.json
[2023-06-19 04:59:50,825] [INFO] DFAST_QC completed!
[2023-06-19 04:59:50,825] [INFO] Total running time: 0h0m43s