[2024-01-24 11:51:09,886] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:09,888] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:09,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ae00bb7-9bdc-4699-909e-b08dbdc7af04/dqc_reference
[2024-01-24 11:51:11,231] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:11,233] [INFO] Task started: Prodigal
[2024-01-24 11:51:11,233] [INFO] Running command: gunzip -c /var/lib/cwl/stg61ffb6b6-96eb-4e9c-a9d7-7b5bcd186b9f/GCF_007556705.1_ASM755670v1_genomic.fna.gz | prodigal -d GCF_007556705.1_ASM755670v1_genomic.fna/cds.fna -a GCF_007556705.1_ASM755670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:20,571] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:20,571] [INFO] Task started: HMMsearch
[2024-01-24 11:51:20,572] [INFO] Running command: hmmsearch --tblout GCF_007556705.1_ASM755670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ae00bb7-9bdc-4699-909e-b08dbdc7af04/dqc_reference/reference_markers.hmm GCF_007556705.1_ASM755670v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:20,849] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:20,850] [INFO] Found 6/6 markers.
[2024-01-24 11:51:20,880] [INFO] Query marker FASTA was written to GCF_007556705.1_ASM755670v1_genomic.fna/markers.fasta
[2024-01-24 11:51:20,880] [INFO] Task started: Blastn
[2024-01-24 11:51:20,880] [INFO] Running command: blastn -query GCF_007556705.1_ASM755670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ae00bb7-9bdc-4699-909e-b08dbdc7af04/dqc_reference/reference_markers.fasta -out GCF_007556705.1_ASM755670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:21,875] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:21,878] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:21,879] [INFO] Target genome list was writen to GCF_007556705.1_ASM755670v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:21,884] [INFO] Task started: fastANI
[2024-01-24 11:51:21,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg61ffb6b6-96eb-4e9c-a9d7-7b5bcd186b9f/GCF_007556705.1_ASM755670v1_genomic.fna.gz --refList GCF_007556705.1_ASM755670v1_genomic.fna/target_genomes.txt --output GCF_007556705.1_ASM755670v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:32,167] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:32,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ae00bb7-9bdc-4699-909e-b08dbdc7af04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:32,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ae00bb7-9bdc-4699-909e-b08dbdc7af04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:32,183] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:32,184] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:32,184] [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 thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	100.0	838	843	95	conclusive
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	85.481	661	843	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	84.268	618	843	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	83.7684	619	843	95	below_threshold
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	83.7256	623	843	95	below_threshold
Tepidimonas taiwanensis	strain=LMG 22826	GCA_020162115.1	307486	307486	type	True	83.6335	612	843	95	below_threshold
Tepidimonas aquatica	strain=CLN-1	GCA_007556585.1	247482	247482	type	True	83.5872	619	843	95	below_threshold
Tepidimonas taiwanensis	strain=I1-1	GCA_007556675.1	307486	307486	type	True	83.5542	605	843	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	82.9008	577	843	95	below_threshold
Tepidimonas charontis	strain=SPSP-6	GCA_007556685.1	2267262	2267262	type	True	82.4104	576	843	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.0053	505	843	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.3263	402	843	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.1774	426	843	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.7931	407	843	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.2842	382	843	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:32,206] [INFO] DFAST Taxonomy check result was written to GCF_007556705.1_ASM755670v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:32,207] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:32,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:32,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ae00bb7-9bdc-4699-909e-b08dbdc7af04/dqc_reference/checkm_data
[2024-01-24 11:51:32,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:32,240] [INFO] Task started: CheckM
[2024-01-24 11:51:32,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007556705.1_ASM755670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007556705.1_ASM755670v1_genomic.fna/checkm_input GCF_007556705.1_ASM755670v1_genomic.fna/checkm_result
[2024-01-24 11:52:09,173] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:09,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:09,197] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:09,197] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:09,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007556705.1_ASM755670v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:09,198] [INFO] Task started: Blastn
[2024-01-24 11:52:09,198] [INFO] Running command: blastn -query GCF_007556705.1_ASM755670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ae00bb7-9bdc-4699-909e-b08dbdc7af04/dqc_reference/reference_markers_gtdb.fasta -out GCF_007556705.1_ASM755670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:11,297] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:11,301] [INFO] Selected 11 target genomes.
[2024-01-24 11:52:11,301] [INFO] Target genome list was writen to GCF_007556705.1_ASM755670v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:11,308] [INFO] Task started: fastANI
[2024-01-24 11:52:11,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg61ffb6b6-96eb-4e9c-a9d7-7b5bcd186b9f/GCF_007556705.1_ASM755670v1_genomic.fna.gz --refList GCF_007556705.1_ASM755670v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007556705.1_ASM755670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:18,189] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:18,199] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:18,200] [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_007556705.1	s__Tepidimonas thermarum	100.0	838	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007556755.1	s__Tepidimonas fonticaldi	85.481	661	843	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	84.2405	620	843	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	83.7386	621	843	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	83.5638	618	843	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	83.5611	604	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	98.33	97.91	0.91	0.88	3	-
GCF_007556595.1	s__Tepidimonas alkaliphilus	82.8901	578	843	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	82.4078	579	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837145.1	s__BK-30 sp002837145	80.8017	499	843	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_007655255.1	s__Extensimonas perlucida	79.0899	394	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Extensimonas	95.0	97.84	97.67	0.89	0.88	3	-
GCF_003337425.1	s__Extensimonas vulgaris	78.883	364	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Extensimonas	95.0	99.99	99.99	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:18,202] [INFO] GTDB search result was written to GCF_007556705.1_ASM755670v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:18,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:18,206] [INFO] DFAST_QC result json was written to GCF_007556705.1_ASM755670v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:18,206] [INFO] DFAST_QC completed!
[2024-01-24 11:52:18,207] [INFO] Total running time: 0h1m8s