[2024-01-24 13:09:50,889] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:50,905] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:50,905] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc8a1a15-e68c-43af-9522-710eacf56f67/dqc_reference
[2024-01-24 13:09:52,428] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:52,429] [INFO] Task started: Prodigal
[2024-01-24 13:09:52,429] [INFO] Running command: gunzip -c /var/lib/cwl/stgf271c5ef-b7f7-44d1-8ed6-61b1cbfbfae8/GCF_020162115.1_ASM2016211v1_genomic.fna.gz | prodigal -d GCF_020162115.1_ASM2016211v1_genomic.fna/cds.fna -a GCF_020162115.1_ASM2016211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:02,774] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:02,775] [INFO] Task started: HMMsearch
[2024-01-24 13:10:02,775] [INFO] Running command: hmmsearch --tblout GCF_020162115.1_ASM2016211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc8a1a15-e68c-43af-9522-710eacf56f67/dqc_reference/reference_markers.hmm GCF_020162115.1_ASM2016211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:03,096] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:03,098] [INFO] Found 6/6 markers.
[2024-01-24 13:10:03,126] [INFO] Query marker FASTA was written to GCF_020162115.1_ASM2016211v1_genomic.fna/markers.fasta
[2024-01-24 13:10:03,127] [INFO] Task started: Blastn
[2024-01-24 13:10:03,127] [INFO] Running command: blastn -query GCF_020162115.1_ASM2016211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc8a1a15-e68c-43af-9522-710eacf56f67/dqc_reference/reference_markers.fasta -out GCF_020162115.1_ASM2016211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:04,164] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:04,168] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:04,168] [INFO] Target genome list was writen to GCF_020162115.1_ASM2016211v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:04,173] [INFO] Task started: fastANI
[2024-01-24 13:10:04,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgf271c5ef-b7f7-44d1-8ed6-61b1cbfbfae8/GCF_020162115.1_ASM2016211v1_genomic.fna.gz --refList GCF_020162115.1_ASM2016211v1_genomic.fna/target_genomes.txt --output GCF_020162115.1_ASM2016211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:14,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:14,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc8a1a15-e68c-43af-9522-710eacf56f67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:14,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc8a1a15-e68c-43af-9522-710eacf56f67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:14,227] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:14,227] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:14,228] [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 taiwanensis	strain=LMG 22826	GCA_020162115.1	307486	307486	type	True	100.0	970	971	95	conclusive
Tepidimonas taiwanensis	strain=I1-1	GCA_007556675.1	307486	307486	type	True	99.9334	905	971	95	conclusive
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	84.4023	658	971	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	84.356	647	971	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	83.5367	624	971	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	83.2271	616	971	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	83.0037	590	971	95	below_threshold
Tepidimonas aquatica	strain=CLN-1	GCA_007556585.1	247482	247482	type	True	82.9768	634	971	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.0261	505	971	95	below_threshold
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	79.297	374	971	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.1432	438	971	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.9357	444	971	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.8029	361	971	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:14,229] [INFO] DFAST Taxonomy check result was written to GCF_020162115.1_ASM2016211v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:14,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:14,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:14,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc8a1a15-e68c-43af-9522-710eacf56f67/dqc_reference/checkm_data
[2024-01-24 13:10:14,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:14,265] [INFO] Task started: CheckM
[2024-01-24 13:10:14,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020162115.1_ASM2016211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020162115.1_ASM2016211v1_genomic.fna/checkm_input GCF_020162115.1_ASM2016211v1_genomic.fna/checkm_result
[2024-01-24 13:11:06,587] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:06,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:06,606] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:06,606] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:06,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020162115.1_ASM2016211v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:06,607] [INFO] Task started: Blastn
[2024-01-24 13:11:06,607] [INFO] Running command: blastn -query GCF_020162115.1_ASM2016211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc8a1a15-e68c-43af-9522-710eacf56f67/dqc_reference/reference_markers_gtdb.fasta -out GCF_020162115.1_ASM2016211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:08,390] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:08,394] [INFO] Selected 10 target genomes.
[2024-01-24 13:11:08,394] [INFO] Target genome list was writen to GCF_020162115.1_ASM2016211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:08,402] [INFO] Task started: fastANI
[2024-01-24 13:11:08,402] [INFO] Running command: fastANI --query /var/lib/cwl/stgf271c5ef-b7f7-44d1-8ed6-61b1cbfbfae8/GCF_020162115.1_ASM2016211v1_genomic.fna.gz --refList GCF_020162115.1_ASM2016211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020162115.1_ASM2016211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:14,884] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:14,897] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:14,897] [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_007556675.1	s__Tepidimonas taiwanensis	99.9334	905	971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	98.33	97.91	0.91	0.88	3	conclusive
GCF_007556605.1	s__Tepidimonas sediminis	84.3645	646	971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556755.1	s__Tepidimonas fonticaldi	84.3642	661	971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCF_007556705.1	s__Tepidimonas thermarum	83.546	626	971	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	83.2552	614	971	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	82.9942	633	971	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	82.9684	592	971	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	82.0927	578	971	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	80.1897	482	971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013432195.1	s__Tepidicella baoligensis	79.7887	438	971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:14,899] [INFO] GTDB search result was written to GCF_020162115.1_ASM2016211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:14,899] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:14,903] [INFO] DFAST_QC result json was written to GCF_020162115.1_ASM2016211v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:14,903] [INFO] DFAST_QC completed!
[2024-01-24 13:11:14,903] [INFO] Total running time: 0h1m24s