[2024-01-24 12:53:41,643] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:41,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:41,646] [INFO] DQC Reference Directory: /var/lib/cwl/stgd28104f6-9741-400e-a8b4-531ac2b3eb1a/dqc_reference
[2024-01-24 12:53:43,150] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:43,151] [INFO] Task started: Prodigal
[2024-01-24 12:53:43,152] [INFO] Running command: gunzip -c /var/lib/cwl/stga78cc356-e31e-4482-b57f-8538215c4d74/GCF_007556685.1_ASM755668v1_genomic.fna.gz | prodigal -d GCF_007556685.1_ASM755668v1_genomic.fna/cds.fna -a GCF_007556685.1_ASM755668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:53,084] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:53,084] [INFO] Task started: HMMsearch
[2024-01-24 12:53:53,084] [INFO] Running command: hmmsearch --tblout GCF_007556685.1_ASM755668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd28104f6-9741-400e-a8b4-531ac2b3eb1a/dqc_reference/reference_markers.hmm GCF_007556685.1_ASM755668v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:53,342] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:53,347] [INFO] Found 6/6 markers.
[2024-01-24 12:53:53,377] [INFO] Query marker FASTA was written to GCF_007556685.1_ASM755668v1_genomic.fna/markers.fasta
[2024-01-24 12:53:53,378] [INFO] Task started: Blastn
[2024-01-24 12:53:53,378] [INFO] Running command: blastn -query GCF_007556685.1_ASM755668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd28104f6-9741-400e-a8b4-531ac2b3eb1a/dqc_reference/reference_markers.fasta -out GCF_007556685.1_ASM755668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:54,249] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:54,252] [INFO] Selected 15 target genomes.
[2024-01-24 12:53:54,253] [INFO] Target genome list was writen to GCF_007556685.1_ASM755668v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:54,258] [INFO] Task started: fastANI
[2024-01-24 12:53:54,259] [INFO] Running command: fastANI --query /var/lib/cwl/stga78cc356-e31e-4482-b57f-8538215c4d74/GCF_007556685.1_ASM755668v1_genomic.fna.gz --refList GCF_007556685.1_ASM755668v1_genomic.fna/target_genomes.txt --output GCF_007556685.1_ASM755668v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:05,305] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:05,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd28104f6-9741-400e-a8b4-531ac2b3eb1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:05,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd28104f6-9741-400e-a8b4-531ac2b3eb1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:05,323] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:05,324] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:05,324] [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 charontis	strain=SPSP-6	GCA_007556685.1	2267262	2267262	type	True	100.0	875	881	95	conclusive
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	83.4072	584	881	95	below_threshold
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	83.0797	587	881	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	83.0464	605	881	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	82.5176	562	881	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	82.1987	594	881	95	below_threshold
Tepidimonas taiwanensis	strain=LMG 22826	GCA_020162115.1	307486	307486	type	True	81.9943	594	881	95	below_threshold
Tepidimonas taiwanensis	strain=I1-1	GCA_007556675.1	307486	307486	type	True	81.9386	590	881	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	81.3899	533	881	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.6046	338	881	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.5129	339	881	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.3149	289	881	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.1192	352	881	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	78.0559	303	881	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	77.845	278	881	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:05,327] [INFO] DFAST Taxonomy check result was written to GCF_007556685.1_ASM755668v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:05,328] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:05,329] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:05,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd28104f6-9741-400e-a8b4-531ac2b3eb1a/dqc_reference/checkm_data
[2024-01-24 12:54:05,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:05,368] [INFO] Task started: CheckM
[2024-01-24 12:54:05,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007556685.1_ASM755668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007556685.1_ASM755668v1_genomic.fna/checkm_input GCF_007556685.1_ASM755668v1_genomic.fna/checkm_result
[2024-01-24 12:54:42,057] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:42,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:42,080] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:42,080] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:42,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007556685.1_ASM755668v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:42,081] [INFO] Task started: Blastn
[2024-01-24 12:54:42,081] [INFO] Running command: blastn -query GCF_007556685.1_ASM755668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd28104f6-9741-400e-a8b4-531ac2b3eb1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007556685.1_ASM755668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:44,811] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:44,816] [INFO] Selected 10 target genomes.
[2024-01-24 12:54:44,817] [INFO] Target genome list was writen to GCF_007556685.1_ASM755668v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:44,825] [INFO] Task started: fastANI
[2024-01-24 12:54:44,825] [INFO] Running command: fastANI --query /var/lib/cwl/stga78cc356-e31e-4482-b57f-8538215c4d74/GCF_007556685.1_ASM755668v1_genomic.fna.gz --refList GCF_007556685.1_ASM755668v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007556685.1_ASM755668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:52,337] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:52,384] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:52,385] [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_007556685.1	s__Tepidimonas charontis	100.0	875	881	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	83.3957	581	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCF_004342625.1	s__Tepidimonas ignava	83.13	599	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007556605.1	s__Tepidimonas sediminis	82.5319	561	881	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	82.4382	559	881	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	82.2078	596	881	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	81.9492	592	881	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	81.3706	534	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927045.1	s__Azohydromonas caseinilytica	78.0981	354	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903914615.1	s__Rubrivivax sp903914615	77.4769	291	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:52,387] [INFO] GTDB search result was written to GCF_007556685.1_ASM755668v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:52,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:52,394] [INFO] DFAST_QC result json was written to GCF_007556685.1_ASM755668v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:52,395] [INFO] DFAST_QC completed!
[2024-01-24 12:54:52,395] [INFO] Total running time: 0h1m11s