[2024-01-24 11:26:54,317] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,321] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe659ad9-52e2-4b5c-bfb1-beb755887665/dqc_reference
[2024-01-24 11:26:58,224] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,226] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,227] [INFO] Running command: gunzip -c /var/lib/cwl/stge4ebd34a-e5f6-4bd1-a48f-96d1cac1fc41/GCF_003574095.1_ASM357409v1_genomic.fna.gz | prodigal -d GCF_003574095.1_ASM357409v1_genomic.fna/cds.fna -a GCF_003574095.1_ASM357409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:08,005] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:08,005] [INFO] Task started: HMMsearch
[2024-01-24 11:27:08,005] [INFO] Running command: hmmsearch --tblout GCF_003574095.1_ASM357409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe659ad9-52e2-4b5c-bfb1-beb755887665/dqc_reference/reference_markers.hmm GCF_003574095.1_ASM357409v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:08,296] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:08,298] [INFO] Found 6/6 markers.
[2024-01-24 11:27:08,333] [INFO] Query marker FASTA was written to GCF_003574095.1_ASM357409v1_genomic.fna/markers.fasta
[2024-01-24 11:27:08,334] [INFO] Task started: Blastn
[2024-01-24 11:27:08,334] [INFO] Running command: blastn -query GCF_003574095.1_ASM357409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe659ad9-52e2-4b5c-bfb1-beb755887665/dqc_reference/reference_markers.fasta -out GCF_003574095.1_ASM357409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:08,970] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:08,973] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:08,974] [INFO] Target genome list was writen to GCF_003574095.1_ASM357409v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:08,993] [INFO] Task started: fastANI
[2024-01-24 11:27:08,993] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ebd34a-e5f6-4bd1-a48f-96d1cac1fc41/GCF_003574095.1_ASM357409v1_genomic.fna.gz --refList GCF_003574095.1_ASM357409v1_genomic.fna/target_genomes.txt --output GCF_003574095.1_ASM357409v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:15,854] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:15,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe659ad9-52e2-4b5c-bfb1-beb755887665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:15,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe659ad9-52e2-4b5c-bfb1-beb755887665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:15,863] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:15,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:15,863] [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
Calidithermus roseus	strain=NBRC 110900	GCA_003574095.1	1644118	1644118	type	True	100.0	1130	1138	95	conclusive
Calidithermus timidus	strain=DSM 17022	GCA_000373205.1	307124	307124	type	True	90.532	844	1138	95	below_threshold
Calidithermus chliarophilus	strain=DSM 9957	GCA_000430045.1	52023	52023	type	True	88.2496	930	1138	95	below_threshold
Calidithermus terrae	strain=DSM 26712	GCA_003574345.1	1408545	1408545	type	True	88.0515	815	1138	95	below_threshold
Meiothermus ruber	strain=DSM 1279	GCA_000376665.1	277	277	type	True	79.3617	445	1138	95	below_threshold
Meiothermus cerbereus	strain=DSM 11376	GCA_000620065.1	65552	65552	type	True	78.5979	377	1138	95	below_threshold
Meiothermus granaticius	strain=AF-68	GCA_003574355.1	863370	863370	type	True	78.412	328	1138	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:15,865] [INFO] DFAST Taxonomy check result was written to GCF_003574095.1_ASM357409v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:15,866] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:15,866] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:15,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe659ad9-52e2-4b5c-bfb1-beb755887665/dqc_reference/checkm_data
[2024-01-24 11:27:15,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:15,908] [INFO] Task started: CheckM
[2024-01-24 11:27:15,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003574095.1_ASM357409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003574095.1_ASM357409v1_genomic.fna/checkm_input GCF_003574095.1_ASM357409v1_genomic.fna/checkm_result
[2024-01-24 11:27:47,539] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:47,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:47,561] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:47,562] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:47,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003574095.1_ASM357409v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:47,563] [INFO] Task started: Blastn
[2024-01-24 11:27:47,563] [INFO] Running command: blastn -query GCF_003574095.1_ASM357409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe659ad9-52e2-4b5c-bfb1-beb755887665/dqc_reference/reference_markers_gtdb.fasta -out GCF_003574095.1_ASM357409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:48,555] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:48,558] [INFO] Selected 10 target genomes.
[2024-01-24 11:27:48,558] [INFO] Target genome list was writen to GCF_003574095.1_ASM357409v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:48,578] [INFO] Task started: fastANI
[2024-01-24 11:27:48,579] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ebd34a-e5f6-4bd1-a48f-96d1cac1fc41/GCF_003574095.1_ASM357409v1_genomic.fna.gz --refList GCF_003574095.1_ASM357409v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003574095.1_ASM357409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:56,464] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:56,481] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:56,482] [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_003574095.1	s__Calidithermus roseus	100.0	1130	1138	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000373205.1	s__Calidithermus timidus	90.5228	845	1138	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	88.2246	933	1138	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus	95.0	96.07	96.07	0.89	0.89	2	-
GCF_003226535.1	s__Meiothermus_B sp003226535	81.6801	504	1138	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_000092125.1	s__Meiothermus_B silvanus	79.8466	440	1138	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus_B	95.0	97.39	97.39	0.91	0.91	2	-
GCA_000482765.1	s__Meiothermus taiwanensis	79.596	423	1138	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	79.3656	443	1138	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.09	97.58	0.97	0.94	5	-
GCF_000620065.1	s__Meiothermus cerbereus	78.6187	375	1138	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494055.1	s__Oceanithermus sp015494055	77.5846	191	1138	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	99.03	99.03	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:56,484] [INFO] GTDB search result was written to GCF_003574095.1_ASM357409v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:56,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:56,488] [INFO] DFAST_QC result json was written to GCF_003574095.1_ASM357409v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:56,489] [INFO] DFAST_QC completed!
[2024-01-24 11:27:56,489] [INFO] Total running time: 0h1m2s