[2024-01-24 13:17:45,898] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:45,900] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:45,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d716d98-f89d-4e46-9918-fb706ea7d32b/dqc_reference
[2024-01-24 13:17:47,159] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:47,160] [INFO] Task started: Prodigal
[2024-01-24 13:17:47,160] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc0ff6f5-a542-464b-a326-4494e2d46e19/GCF_007556755.1_ASM755675v1_genomic.fna.gz | prodigal -d GCF_007556755.1_ASM755675v1_genomic.fna/cds.fna -a GCF_007556755.1_ASM755675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:56,863] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:56,863] [INFO] Task started: HMMsearch
[2024-01-24 13:17:56,864] [INFO] Running command: hmmsearch --tblout GCF_007556755.1_ASM755675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d716d98-f89d-4e46-9918-fb706ea7d32b/dqc_reference/reference_markers.hmm GCF_007556755.1_ASM755675v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:57,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:57,221] [INFO] Found 6/6 markers.
[2024-01-24 13:17:57,250] [INFO] Query marker FASTA was written to GCF_007556755.1_ASM755675v1_genomic.fna/markers.fasta
[2024-01-24 13:17:57,251] [INFO] Task started: Blastn
[2024-01-24 13:17:57,251] [INFO] Running command: blastn -query GCF_007556755.1_ASM755675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d716d98-f89d-4e46-9918-fb706ea7d32b/dqc_reference/reference_markers.fasta -out GCF_007556755.1_ASM755675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:58,282] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:58,287] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:58,287] [INFO] Target genome list was writen to GCF_007556755.1_ASM755675v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:58,293] [INFO] Task started: fastANI
[2024-01-24 13:17:58,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc0ff6f5-a542-464b-a326-4494e2d46e19/GCF_007556755.1_ASM755675v1_genomic.fna.gz --refList GCF_007556755.1_ASM755675v1_genomic.fna/target_genomes.txt --output GCF_007556755.1_ASM755675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:08,965] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:08,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d716d98-f89d-4e46-9918-fb706ea7d32b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:08,966] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d716d98-f89d-4e46-9918-fb706ea7d32b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:08,978] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:08,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:08,978] [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	100.0	953	965	95	conclusive
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	86.3887	648	965	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	85.4926	663	965	95	below_threshold
Tepidimonas aquatica	strain=CLN-1	GCA_007556585.1	247482	247482	type	True	85.3167	643	965	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	85.1481	583	965	95	below_threshold
Tepidimonas taiwanensis	strain=I1-1	GCA_007556675.1	307486	307486	type	True	84.4063	643	965	95	below_threshold
Tepidimonas taiwanensis	strain=LMG 22826	GCA_020162115.1	307486	307486	type	True	84.3494	675	965	95	below_threshold
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	83.9555	640	965	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	83.8998	635	965	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.482	547	965	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.0448	471	965	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.4142	403	965	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.3294	461	965	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.2455	336	965	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:08,980] [INFO] DFAST Taxonomy check result was written to GCF_007556755.1_ASM755675v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:08,980] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:08,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:08,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d716d98-f89d-4e46-9918-fb706ea7d32b/dqc_reference/checkm_data
[2024-01-24 13:18:08,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:09,024] [INFO] Task started: CheckM
[2024-01-24 13:18:09,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007556755.1_ASM755675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007556755.1_ASM755675v1_genomic.fna/checkm_input GCF_007556755.1_ASM755675v1_genomic.fna/checkm_result
[2024-01-24 13:18:50,052] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:50,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:50,071] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:50,071] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:50,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007556755.1_ASM755675v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:50,072] [INFO] Task started: Blastn
[2024-01-24 13:18:50,072] [INFO] Running command: blastn -query GCF_007556755.1_ASM755675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d716d98-f89d-4e46-9918-fb706ea7d32b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007556755.1_ASM755675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:51,996] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:52,000] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:52,000] [INFO] Target genome list was writen to GCF_007556755.1_ASM755675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:52,011] [INFO] Task started: fastANI
[2024-01-24 13:18:52,011] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc0ff6f5-a542-464b-a326-4494e2d46e19/GCF_007556755.1_ASM755675v1_genomic.fna.gz --refList GCF_007556755.1_ASM755675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007556755.1_ASM755675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:58,543] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:58,555] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:58,556] [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	100.0	953	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	conclusive
GCF_007556605.1	s__Tepidimonas sediminis	86.4223	646	965	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	85.4761	664	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556585.1	s__Tepidimonas aquatica	85.3197	643	965	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	85.1184	584	965	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	84.4206	644	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	98.33	97.91	0.91	0.88	3	-
GCF_004342625.1	s__Tepidimonas ignava	83.9049	636	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004363315.1	s__Tepidicella xavieri	82.0875	534	965	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	81.4349	519	965	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	81.2193	505	965	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 13:18:58,557] [INFO] GTDB search result was written to GCF_007556755.1_ASM755675v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:58,558] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:58,561] [INFO] DFAST_QC result json was written to GCF_007556755.1_ASM755675v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:58,561] [INFO] DFAST_QC completed!
[2024-01-24 13:18:58,561] [INFO] Total running time: 0h1m13s