[2024-01-24 13:40:45,188] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:45,190] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:45,190] [INFO] DQC Reference Directory: /var/lib/cwl/stga4d14f52-4384-46af-a66c-f88c4dab4229/dqc_reference
[2024-01-24 13:40:46,461] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:46,462] [INFO] Task started: Prodigal
[2024-01-24 13:40:46,463] [INFO] Running command: gunzip -c /var/lib/cwl/stg40257225-40aa-4ba7-8b8d-1b84f8489c30/GCF_000430045.1_ASM43004v1_genomic.fna.gz | prodigal -d GCF_000430045.1_ASM43004v1_genomic.fna/cds.fna -a GCF_000430045.1_ASM43004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:59,035] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:59,036] [INFO] Task started: HMMsearch
[2024-01-24 13:40:59,036] [INFO] Running command: hmmsearch --tblout GCF_000430045.1_ASM43004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4d14f52-4384-46af-a66c-f88c4dab4229/dqc_reference/reference_markers.hmm GCF_000430045.1_ASM43004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:59,330] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:59,332] [INFO] Found 6/6 markers.
[2024-01-24 13:40:59,373] [INFO] Query marker FASTA was written to GCF_000430045.1_ASM43004v1_genomic.fna/markers.fasta
[2024-01-24 13:40:59,374] [INFO] Task started: Blastn
[2024-01-24 13:40:59,374] [INFO] Running command: blastn -query GCF_000430045.1_ASM43004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4d14f52-4384-46af-a66c-f88c4dab4229/dqc_reference/reference_markers.fasta -out GCF_000430045.1_ASM43004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:59,993] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:59,996] [INFO] Selected 9 target genomes.
[2024-01-24 13:40:59,997] [INFO] Target genome list was writen to GCF_000430045.1_ASM43004v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:00,017] [INFO] Task started: fastANI
[2024-01-24 13:41:00,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg40257225-40aa-4ba7-8b8d-1b84f8489c30/GCF_000430045.1_ASM43004v1_genomic.fna.gz --refList GCF_000430045.1_ASM43004v1_genomic.fna/target_genomes.txt --output GCF_000430045.1_ASM43004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:13,313] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:13,314] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4d14f52-4384-46af-a66c-f88c4dab4229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:13,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4d14f52-4384-46af-a66c-f88c4dab4229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:13,329] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:13,330] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:41:13,330] [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 chliarophilus	strain=DSM 9957	GCA_000430045.1	52023	52023	type	True	100.0	1557	1559	95	inconclusive
Calidithermus terrae	strain=DSM 26712	GCA_003574345.1	1408545	1408545	type	True	95.8011	1107	1559	95	inconclusive
Calidithermus roseus	strain=NBRC 110900	GCA_003574095.1	1644118	1644118	type	True	88.2999	909	1559	95	below_threshold
Calidithermus timidus	strain=DSM 17022	GCA_000373205.1	307124	307124	type	True	87.6063	856	1559	95	below_threshold
Meiothermus ruber	strain=DSM 1279	GCA_000376665.1	277	277	type	True	79.453	506	1559	95	below_threshold
Meiothermus ruber	strain=DSM 1279	GCA_000024425.1	277	277	type	True	79.3574	515	1559	95	below_threshold
Meiothermus granaticius	strain=AF-68	GCA_003574355.1	863370	863370	type	True	77.9704	351	1559	95	below_threshold
Thermus igniterrae	strain=ATCC 700962	GCA_000376265.1	88189	88189	type	True	77.7619	291	1559	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_001535545.1	456163	456163	type	True	77.5137	245	1559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,333] [INFO] DFAST Taxonomy check result was written to GCF_000430045.1_ASM43004v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:13,333] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:13,334] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:13,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4d14f52-4384-46af-a66c-f88c4dab4229/dqc_reference/checkm_data
[2024-01-24 13:41:13,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:13,384] [INFO] Task started: CheckM
[2024-01-24 13:41:13,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430045.1_ASM43004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430045.1_ASM43004v1_genomic.fna/checkm_input GCF_000430045.1_ASM43004v1_genomic.fna/checkm_result
[2024-01-24 13:41:50,574] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:50,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,640] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:50,641] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:50,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430045.1_ASM43004v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:50,642] [INFO] Task started: Blastn
[2024-01-24 13:41:50,642] [INFO] Running command: blastn -query GCF_000430045.1_ASM43004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4d14f52-4384-46af-a66c-f88c4dab4229/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430045.1_ASM43004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:51,518] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:51,521] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:51,522] [INFO] Target genome list was writen to GCF_000430045.1_ASM43004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:51,649] [INFO] Task started: fastANI
[2024-01-24 13:41:51,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg40257225-40aa-4ba7-8b8d-1b84f8489c30/GCF_000430045.1_ASM43004v1_genomic.fna.gz --refList GCF_000430045.1_ASM43004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430045.1_ASM43004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:04,619] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:04,634] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:04,635] [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_000430045.1	s__Calidithermus chliarophilus	100.0	1557	1559	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus	95.0	96.07	96.07	0.89	0.89	2	conclusive
GCF_003574095.1	s__Calidithermus roseus	88.3308	906	1559	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373205.1	s__Calidithermus timidus	87.6567	853	1559	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226535.1	s__Meiothermus_B sp003226535	81.6588	568	1559	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	80.8432	514	1559	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	80.155	492	1559	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	79.3855	511	1559	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.09	97.58	0.97	0.94	5	-
GCF_003351145.1	s__Meiothermus sp003351145	78.7556	453	1559	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	77.8438	271	1559	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	99.03	99.03	0.84	0.84	2	-
GCF_000376265.1	s__Thermus igniterrae	77.8167	289	1559	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001535545.1	s__Thermus parvatiensis	77.5082	244	1559	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.79	98.79	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:04,636] [INFO] GTDB search result was written to GCF_000430045.1_ASM43004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:04,637] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:04,640] [INFO] DFAST_QC result json was written to GCF_000430045.1_ASM43004v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:04,640] [INFO] DFAST_QC completed!
[2024-01-24 13:42:04,640] [INFO] Total running time: 0h1m19s