[2024-01-24 13:37:04,901] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:04,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:04,904] [INFO] DQC Reference Directory: /var/lib/cwl/stgbebe6bb3-c20f-495f-b855-e38d1c19880b/dqc_reference
[2024-01-24 13:37:06,267] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,268] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,268] [INFO] Running command: gunzip -c /var/lib/cwl/stg2851de02-c813-4c09-b36b-abdc0b566408/GCF_014202645.1_ASM1420264v1_genomic.fna.gz | prodigal -d GCF_014202645.1_ASM1420264v1_genomic.fna/cds.fna -a GCF_014202645.1_ASM1420264v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:16,960] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:16,960] [INFO] Task started: HMMsearch
[2024-01-24 13:37:16,960] [INFO] Running command: hmmsearch --tblout GCF_014202645.1_ASM1420264v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbebe6bb3-c20f-495f-b855-e38d1c19880b/dqc_reference/reference_markers.hmm GCF_014202645.1_ASM1420264v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:17,353] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:17,354] [INFO] Found 6/6 markers.
[2024-01-24 13:37:17,391] [INFO] Query marker FASTA was written to GCF_014202645.1_ASM1420264v1_genomic.fna/markers.fasta
[2024-01-24 13:37:17,391] [INFO] Task started: Blastn
[2024-01-24 13:37:17,391] [INFO] Running command: blastn -query GCF_014202645.1_ASM1420264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbebe6bb3-c20f-495f-b855-e38d1c19880b/dqc_reference/reference_markers.fasta -out GCF_014202645.1_ASM1420264v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:18,164] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:18,168] [INFO] Selected 21 target genomes.
[2024-01-24 13:37:18,168] [INFO] Target genome list was writen to GCF_014202645.1_ASM1420264v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:18,175] [INFO] Task started: fastANI
[2024-01-24 13:37:18,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg2851de02-c813-4c09-b36b-abdc0b566408/GCF_014202645.1_ASM1420264v1_genomic.fna.gz --refList GCF_014202645.1_ASM1420264v1_genomic.fna/target_genomes.txt --output GCF_014202645.1_ASM1420264v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:33,453] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:33,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbebe6bb3-c20f-495f-b855-e38d1c19880b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:33,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbebe6bb3-c20f-495f-b855-e38d1c19880b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:33,471] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:33,471] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:33,471] [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
Deinobacterium chartae	strain=DSM 21458	GCA_014202645.1	521158	521158	type	True	100.0	1237	1240	95	conclusive
Deinococcus pimensis	strain=DSM 21231	GCA_000519345.1	309888	309888	type	True	77.8998	314	1240	95	below_threshold
Deinococcus irradiatisoli	strain=17bor-2	GCA_003173015.1	2202254	2202254	type	True	77.8051	271	1240	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	77.6116	260	1240	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	77.5671	311	1240	95	below_threshold
Deinococcus aerius	strain=TR0125	GCA_002897375.1	200253	200253	type	True	77.5352	252	1240	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	77.3963	301	1240	95	below_threshold
Deinococcus terrestris	strain=SDU3-2	GCA_009377345.1	2651870	2651870	type	True	77.3047	239	1240	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	77.2476	340	1240	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	77.2462	273	1240	95	below_threshold
Deinococcus planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	77.2287	257	1240	95	below_threshold
Deinococcus apachensis	strain=DSM 19763	GCA_000381345.1	309886	309886	type	True	77.1539	253	1240	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	77.1503	293	1240	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	77.1025	274	1240	95	below_threshold
Deinococcus rubellus	strain=Ant6	GCA_025244745.1	1889240	1889240	type	True	77.0497	230	1240	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	77.0432	287	1240	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	76.9392	314	1240	95	below_threshold
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	76.9347	249	1240	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	76.891	296	1240	95	below_threshold
Deinococcus psychrotolerans	strain=S14-83	GCA_003860465.1	2489213	2489213	type	True	76.4956	156	1240	95	below_threshold
Deinococcus detaillensis	strain=H1	GCA_007280555.1	2592048	2592048	type	True	76.413	150	1240	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:33,473] [INFO] DFAST Taxonomy check result was written to GCF_014202645.1_ASM1420264v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:33,473] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:33,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:33,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbebe6bb3-c20f-495f-b855-e38d1c19880b/dqc_reference/checkm_data
[2024-01-24 13:37:33,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:33,520] [INFO] Task started: CheckM
[2024-01-24 13:37:33,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202645.1_ASM1420264v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202645.1_ASM1420264v1_genomic.fna/checkm_input GCF_014202645.1_ASM1420264v1_genomic.fna/checkm_result
[2024-01-24 13:38:09,506] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:09,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:09,526] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:09,527] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:09,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202645.1_ASM1420264v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:09,528] [INFO] Task started: Blastn
[2024-01-24 13:38:09,528] [INFO] Running command: blastn -query GCF_014202645.1_ASM1420264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbebe6bb3-c20f-495f-b855-e38d1c19880b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202645.1_ASM1420264v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:10,635] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:10,639] [INFO] Selected 19 target genomes.
[2024-01-24 13:38:10,639] [INFO] Target genome list was writen to GCF_014202645.1_ASM1420264v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:10,664] [INFO] Task started: fastANI
[2024-01-24 13:38:10,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg2851de02-c813-4c09-b36b-abdc0b566408/GCF_014202645.1_ASM1420264v1_genomic.fna.gz --refList GCF_014202645.1_ASM1420264v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202645.1_ASM1420264v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:24,168] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:24,187] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:24,188] [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_014202645.1	s__Deinobacterium chartae	100.0	1237	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000519345.1	s__Deinococcus_A pimensis	77.9206	312	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173015.1	s__Deinococcus irradiatisoli	77.8347	268	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647075.1	s__Deinococcus aerophilus	77.6838	254	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252445.1	s__Deinococcus gobiensis	77.5564	312	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201885.1	s__Deinococcus budaensis	77.3959	301	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377345.1	s__Deinococcus sp009377345	77.2803	242	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953415.1	s__Deinococcus sp002953415	77.2731	271	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863415.1	s__Deinococcus sp018863415	77.2707	282	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201805.1	s__Deinococcus metalli	77.2582	338	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002869765.1	s__Deinococcus planocerae	77.2395	256	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381345.1	s__Deinococcus apachensis	77.157	253	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186385.1	s__Deinococcus_B maricopensis	77.1398	256	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000599865.1	s__Deinococcus phoenicis	77.1312	295	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648135.1	s__Deinococcus sedimenti	77.0781	275	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647435.1	s__Deinococcus radiotolerans	77.0434	287	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008565.1	s__Deinococcus radiodurans	76.9832	253	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
GCF_003860465.1	s__Deinococcus sp003860465	76.4938	155	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007280555.1	s__Deinococcus detaillensis	76.4264	149	1240	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:24,190] [INFO] GTDB search result was written to GCF_014202645.1_ASM1420264v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:24,190] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:24,195] [INFO] DFAST_QC result json was written to GCF_014202645.1_ASM1420264v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:24,195] [INFO] DFAST_QC completed!
[2024-01-24 13:38:24,195] [INFO] Total running time: 0h1m19s