[2024-01-24 13:30:12,416] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:30:12,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:30:12,418] [INFO] DQC Reference Directory: /var/lib/cwl/stg9622eecf-b218-4e10-b0ee-e4a1631875d1/dqc_reference
[2024-01-24 13:30:13,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:30:13,686] [INFO] Task started: Prodigal
[2024-01-24 13:30:13,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg53d28ebb-f441-48a2-8771-6db3e2230ae1/GCF_000092425.1_ASM9242v1_genomic.fna.gz | prodigal -d GCF_000092425.1_ASM9242v1_genomic.fna/cds.fna -a GCF_000092425.1_ASM9242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:30:22,249] [INFO] Task succeeded: Prodigal
[2024-01-24 13:30:22,250] [INFO] Task started: HMMsearch
[2024-01-24 13:30:22,250] [INFO] Running command: hmmsearch --tblout GCF_000092425.1_ASM9242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9622eecf-b218-4e10-b0ee-e4a1631875d1/dqc_reference/reference_markers.hmm GCF_000092425.1_ASM9242v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:30:22,488] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:30:22,489] [INFO] Found 6/6 markers.
[2024-01-24 13:30:22,521] [INFO] Query marker FASTA was written to GCF_000092425.1_ASM9242v1_genomic.fna/markers.fasta
[2024-01-24 13:30:22,522] [INFO] Task started: Blastn
[2024-01-24 13:30:22,522] [INFO] Running command: blastn -query GCF_000092425.1_ASM9242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9622eecf-b218-4e10-b0ee-e4a1631875d1/dqc_reference/reference_markers.fasta -out GCF_000092425.1_ASM9242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:23,247] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:23,251] [INFO] Selected 20 target genomes.
[2024-01-24 13:30:23,251] [INFO] Target genome list was writen to GCF_000092425.1_ASM9242v1_genomic.fna/target_genomes.txt
[2024-01-24 13:30:23,308] [INFO] Task started: fastANI
[2024-01-24 13:30:23,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg53d28ebb-f441-48a2-8771-6db3e2230ae1/GCF_000092425.1_ASM9242v1_genomic.fna.gz --refList GCF_000092425.1_ASM9242v1_genomic.fna/target_genomes.txt --output GCF_000092425.1_ASM9242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:30:34,657] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:34,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9622eecf-b218-4e10-b0ee-e4a1631875d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:30:34,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9622eecf-b218-4e10-b0ee-e4a1631875d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:30:34,684] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:30:34,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:30:34,684] [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
Truepera radiovictrix	strain=DSM 17093	GCA_000092425.1	332249	332249	type	True	100.0	1086	1086	95	conclusive
Thermus thermophilus	strain=JCM10941	GCA_019973715.1	274	274	type	True	76.0214	53	1086	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	75.9435	86	1086	95	below_threshold
Thermus thermophilus	strain=HB8	GCA_000091545.1	274	274	type	True	75.9314	51	1086	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	75.8885	121	1086	95	below_threshold
Calidithermus chliarophilus	strain=DSM 9957	GCA_000430045.1	52023	52023	type	True	75.8295	169	1086	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	75.8178	114	1086	95	below_threshold
Calidithermus terrae	strain=DSM 26712	GCA_003574345.1	1408545	1408545	type	True	75.7851	150	1086	95	below_threshold
Deinococcus hopiensis	strain=KR-140	GCA_900176165.1	309885	309885	type	True	75.7171	71	1086	95	below_threshold
Deinococcus terrestris	strain=SDU3-2	GCA_009377345.1	2651870	2651870	type	True	75.7123	79	1086	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	75.6804	82	1086	95	below_threshold
Deinococcus planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	75.6134	97	1086	95	below_threshold
Oceanithermus desulfurans	strain=DSM 15757	GCA_014201675.1	227924	227924	type	True	75.5884	117	1086	95	below_threshold
Deinococcus aerius	strain=TR0125	GCA_002897375.1	200253	200253	type	True	75.573	106	1086	95	below_threshold
Deinococcus pimensis	strain=DSM 21231	GCA_000519345.1	309888	309888	type	True	75.5347	148	1086	95	below_threshold
Deinococcus murrayi	strain=DSM 11303	GCA_000482805.1	68910	68910	type	True	75.5215	83	1086	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	75.5198	67	1086	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	75.4386	76	1086	95	below_threshold
Deinococcus sedimenti	strain=JCM 31405	GCA_014648135.1	1867090	1867090	type	True	75.2804	86	1086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:30:34,686] [INFO] DFAST Taxonomy check result was written to GCF_000092425.1_ASM9242v1_genomic.fna/tc_result.tsv
[2024-01-24 13:30:34,687] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:30:34,687] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:30:34,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9622eecf-b218-4e10-b0ee-e4a1631875d1/dqc_reference/checkm_data
[2024-01-24 13:30:34,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:30:34,726] [INFO] Task started: CheckM
[2024-01-24 13:30:34,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092425.1_ASM9242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092425.1_ASM9242v1_genomic.fna/checkm_input GCF_000092425.1_ASM9242v1_genomic.fna/checkm_result
[2024-01-24 13:31:03,613] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:03,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:03,640] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:03,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:03,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092425.1_ASM9242v1_genomic.fna/markers.fasta)
[2024-01-24 13:31:03,641] [INFO] Task started: Blastn
[2024-01-24 13:31:03,641] [INFO] Running command: blastn -query GCF_000092425.1_ASM9242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9622eecf-b218-4e10-b0ee-e4a1631875d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092425.1_ASM9242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:04,853] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:04,858] [INFO] Selected 14 target genomes.
[2024-01-24 13:31:04,858] [INFO] Target genome list was writen to GCF_000092425.1_ASM9242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:05,092] [INFO] Task started: fastANI
[2024-01-24 13:31:05,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg53d28ebb-f441-48a2-8771-6db3e2230ae1/GCF_000092425.1_ASM9242v1_genomic.fna.gz --refList GCF_000092425.1_ASM9242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092425.1_ASM9242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:12,880] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:12,895] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:12,896] [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_000092425.1	s__Truepera radiovictrix	100.0	1086	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__Truepera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902806425.1	s__Truepera sp902806425	77.5655	348	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__Truepera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515535.1	s__JAAYYF01 sp012515535	76.8912	217	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__JAAYYF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003567075.1	s__CSSed10-48 sp003567075	76.5929	145	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__CSSed10-48	95.0	99.00	98.79	0.83	0.81	3	-
GCA_007130855.1	s__CSSed10-48 sp007130855	76.4047	162	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__CSSed10-48	95.0	99.69	99.67	0.91	0.90	3	-
GCA_011390455.1	s__JAABTL01 sp011390455	76.3353	206	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__JAABTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333895.1	s__JAGXSJ01 sp018333895	76.3161	116	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__JAGXSJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389865.1	s__JAABTL01 sp011389865	76.3053	204	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__JAABTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121175.1	s__CSSed10-48 sp007121175	76.0836	129	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__CSSed10-48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697735.1	s__SKWV01 sp013697735	76.0547	162	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__SKWV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430045.1	s__Calidithermus chliarophilus	75.8632	169	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus	95.0	96.07	96.07	0.89	0.89	2	-
GCF_000183745.1	s__Oceanithermus profundus	75.8064	113	1086	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:12,898] [INFO] GTDB search result was written to GCF_000092425.1_ASM9242v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:12,898] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:12,902] [INFO] DFAST_QC result json was written to GCF_000092425.1_ASM9242v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:12,903] [INFO] DFAST_QC completed!
[2024-01-24 13:31:12,903] [INFO] Total running time: 0h1m0s