[2024-01-24 15:26:55,057] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,059] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,059] [INFO] DQC Reference Directory: /var/lib/cwl/stge19be4e8-dca7-45a6-a18b-4050f139ab0e/dqc_reference
[2024-01-24 15:26:56,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,452] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,453] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ac57296-28e8-498f-8eb2-d7f64088d544/GCF_003574355.1_ASM357435v1_genomic.fna.gz | prodigal -d GCF_003574355.1_ASM357435v1_genomic.fna/cds.fna -a GCF_003574355.1_ASM357435v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:05,538] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:05,539] [INFO] Task started: HMMsearch
[2024-01-24 15:27:05,539] [INFO] Running command: hmmsearch --tblout GCF_003574355.1_ASM357435v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge19be4e8-dca7-45a6-a18b-4050f139ab0e/dqc_reference/reference_markers.hmm GCF_003574355.1_ASM357435v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:05,781] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:05,782] [INFO] Found 6/6 markers.
[2024-01-24 15:27:05,819] [INFO] Query marker FASTA was written to GCF_003574355.1_ASM357435v1_genomic.fna/markers.fasta
[2024-01-24 15:27:05,820] [INFO] Task started: Blastn
[2024-01-24 15:27:05,820] [INFO] Running command: blastn -query GCF_003574355.1_ASM357435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge19be4e8-dca7-45a6-a18b-4050f139ab0e/dqc_reference/reference_markers.fasta -out GCF_003574355.1_ASM357435v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:06,484] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:06,487] [INFO] Selected 14 target genomes.
[2024-01-24 15:27:06,488] [INFO] Target genome list was writen to GCF_003574355.1_ASM357435v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:06,493] [INFO] Task started: fastANI
[2024-01-24 15:27:06,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ac57296-28e8-498f-8eb2-d7f64088d544/GCF_003574355.1_ASM357435v1_genomic.fna.gz --refList GCF_003574355.1_ASM357435v1_genomic.fna/target_genomes.txt --output GCF_003574355.1_ASM357435v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:15,521] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:15,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge19be4e8-dca7-45a6-a18b-4050f139ab0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:15,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge19be4e8-dca7-45a6-a18b-4050f139ab0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:15,533] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:15,534] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:15,534] [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
Meiothermus granaticius	strain=AF-68	GCA_003574355.1	863370	863370	type	True	100.0	1037	1041	95	conclusive
Meiothermus granaticius	strain=NBRC 107808	GCA_007990995.1	863370	863370	type	True	99.9703	1012	1041	95	conclusive
Meiothermus hypogaeus	strain=NBRC 106114	GCA_007990975.1	884155	884155	type	True	78.9648	322	1041	95	below_threshold
Meiothermus hypogaeus	strain=DSM 23238	GCA_003574035.1	884155	884155	type	True	78.8913	339	1041	95	below_threshold
Calidithermus roseus	strain=NBRC 110900	GCA_003574095.1	1644118	1644118	type	True	78.5432	324	1041	95	below_threshold
Meiothermus ruber	strain=DSM 1279	GCA_000376665.1	277	277	type	True	78.3041	348	1041	95	below_threshold
Meiothermus ruber	strain=DSM 1279	GCA_000024425.1	277	277	type	True	78.2756	354	1041	95	below_threshold
Meiothermus cerbereus	strain=DSM 11376	GCA_000620065.1	65552	65552	type	True	78.2017	298	1041	95	below_threshold
Calidithermus terrae	strain=DSM 26712	GCA_003574345.1	1408545	1408545	type	True	78.0407	324	1041	95	below_threshold
Calidithermus timidus	strain=DSM 17022	GCA_000373205.1	307124	307124	type	True	77.9446	325	1041	95	below_threshold
Calidithermus chliarophilus	strain=DSM 9957	GCA_000430045.1	52023	52023	type	True	77.8952	354	1041	95	below_threshold
Meiothermus rufus	strain=DSM 22234	GCA_000423425.1	604332	604332	type	True	77.7241	258	1041	95	below_threshold
Thermus igniterrae	strain=ATCC 700962	GCA_000376265.1	88189	88189	type	True	76.33	142	1041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:15,536] [INFO] DFAST Taxonomy check result was written to GCF_003574355.1_ASM357435v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:15,536] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:15,537] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:15,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge19be4e8-dca7-45a6-a18b-4050f139ab0e/dqc_reference/checkm_data
[2024-01-24 15:27:15,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:15,574] [INFO] Task started: CheckM
[2024-01-24 15:27:15,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003574355.1_ASM357435v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003574355.1_ASM357435v1_genomic.fna/checkm_input GCF_003574355.1_ASM357435v1_genomic.fna/checkm_result
[2024-01-24 15:27:46,945] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:46,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:46,964] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:46,964] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:46,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003574355.1_ASM357435v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:46,965] [INFO] Task started: Blastn
[2024-01-24 15:27:46,965] [INFO] Running command: blastn -query GCF_003574355.1_ASM357435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge19be4e8-dca7-45a6-a18b-4050f139ab0e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003574355.1_ASM357435v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:47,839] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:47,843] [INFO] Selected 16 target genomes.
[2024-01-24 15:27:47,843] [INFO] Target genome list was writen to GCF_003574355.1_ASM357435v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:47,853] [INFO] Task started: fastANI
[2024-01-24 15:27:47,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ac57296-28e8-498f-8eb2-d7f64088d544/GCF_003574355.1_ASM357435v1_genomic.fna.gz --refList GCF_003574355.1_ASM357435v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003574355.1_ASM357435v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:58,037] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:58,050] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:58,050] [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_003574355.1	s__Meiothermus granaticius	100.0	1037	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.97	99.97	0.97	0.97	2	conclusive
GCF_003574035.1	s__Meiothermus hypogaeus	78.8764	341	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.94	99.94	0.95	0.95	2	-
GCF_003574095.1	s__Calidithermus roseus	78.5073	327	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000482765.1	s__Meiothermus taiwanensis	78.3367	350	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.41	99.02	0.97	0.95	5	-
GCF_000024425.1	s__Meiothermus ruber	78.2694	354	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.09	97.58	0.97	0.94	5	-
GCA_011327565.1	s__Meiothermus ruber_A	78.1749	318	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620065.1	s__Meiothermus cerbereus	78.1738	302	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226535.1	s__Meiothermus_B sp003226535	78.1616	311	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus_B	95.0	99.73	99.73	0.99	0.99	2	-
GCF_000373205.1	s__Calidithermus timidus	77.9434	325	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430045.1	s__Calidithermus chliarophilus	77.8855	355	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus	95.0	96.07	96.07	0.89	0.89	2	-
GCA_015478585.1	s__Meiothermus sp015478585	77.8052	378	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574085.1	s__Meiothermus luteus	77.7716	268	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.87	99.87	0.92	0.92	2	-
GCF_000423425.1	s__Meiothermus rufus	77.7365	257	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376265.1	s__Thermus igniterrae	76.3171	143	1041	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:58,052] [INFO] GTDB search result was written to GCF_003574355.1_ASM357435v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:58,053] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:58,056] [INFO] DFAST_QC result json was written to GCF_003574355.1_ASM357435v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:58,056] [INFO] DFAST_QC completed!
[2024-01-24 15:27:58,057] [INFO] Total running time: 0h1m3s