[2024-01-24 14:55:36,535] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:36,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:36,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a5187bb-6ea7-4537-bfb7-466ea4615954/dqc_reference
[2024-01-24 14:55:37,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:37,770] [INFO] Task started: Prodigal
[2024-01-24 14:55:37,770] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e47dc62-1ad7-49be-bca9-08e4c0b58006/GCF_007280555.1_ASM728055v1_genomic.fna.gz | prodigal -d GCF_007280555.1_ASM728055v1_genomic.fna/cds.fna -a GCF_007280555.1_ASM728055v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:49,500] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:49,500] [INFO] Task started: HMMsearch
[2024-01-24 14:55:49,500] [INFO] Running command: hmmsearch --tblout GCF_007280555.1_ASM728055v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a5187bb-6ea7-4537-bfb7-466ea4615954/dqc_reference/reference_markers.hmm GCF_007280555.1_ASM728055v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:49,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:49,789] [INFO] Found 6/6 markers.
[2024-01-24 14:55:49,830] [INFO] Query marker FASTA was written to GCF_007280555.1_ASM728055v1_genomic.fna/markers.fasta
[2024-01-24 14:55:49,831] [INFO] Task started: Blastn
[2024-01-24 14:55:49,831] [INFO] Running command: blastn -query GCF_007280555.1_ASM728055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a5187bb-6ea7-4537-bfb7-466ea4615954/dqc_reference/reference_markers.fasta -out GCF_007280555.1_ASM728055v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:50,497] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:50,501] [INFO] Selected 6 target genomes.
[2024-01-24 14:55:50,502] [INFO] Target genome list was writen to GCF_007280555.1_ASM728055v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:50,506] [INFO] Task started: fastANI
[2024-01-24 14:55:50,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e47dc62-1ad7-49be-bca9-08e4c0b58006/GCF_007280555.1_ASM728055v1_genomic.fna.gz --refList GCF_007280555.1_ASM728055v1_genomic.fna/target_genomes.txt --output GCF_007280555.1_ASM728055v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:56,162] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:56,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a5187bb-6ea7-4537-bfb7-466ea4615954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:56,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a5187bb-6ea7-4537-bfb7-466ea4615954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:56,169] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:56,170] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:56,170] [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
Deinococcus detaillensis	strain=H1	GCA_007280555.1	2592048	2592048	type	True	100.0	1281	1286	95	conclusive
Deinococcus psychrotolerans	strain=S14-83	GCA_003860465.1	2489213	2489213	type	True	94.2894	1090	1286	95	below_threshold
Deinococcus rubellus	strain=Ant6	GCA_025244745.1	1889240	1889240	type	True	81.8335	694	1286	95	below_threshold
Deinococcus alpinitundrae	strain=LMG 24283	GCA_009982895.1	468913	468913	type	True	81.3669	817	1286	95	below_threshold
Deinococcus irradiatisoli	strain=17bor-2	GCA_003173015.1	2202254	2202254	type	True	80.6998	593	1286	95	below_threshold
Deinococcus wulumuqiensis	strain=R12	GCA_014875835.1	980427	980427	type	True	77.4299	281	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:56,172] [INFO] DFAST Taxonomy check result was written to GCF_007280555.1_ASM728055v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:56,172] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:56,173] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:56,173] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a5187bb-6ea7-4537-bfb7-466ea4615954/dqc_reference/checkm_data
[2024-01-24 14:55:56,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:56,221] [INFO] Task started: CheckM
[2024-01-24 14:55:56,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007280555.1_ASM728055v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007280555.1_ASM728055v1_genomic.fna/checkm_input GCF_007280555.1_ASM728055v1_genomic.fna/checkm_result
[2024-01-24 14:56:34,209] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:34,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:34,233] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:34,234] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:34,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007280555.1_ASM728055v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:34,235] [INFO] Task started: Blastn
[2024-01-24 14:56:34,235] [INFO] Running command: blastn -query GCF_007280555.1_ASM728055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a5187bb-6ea7-4537-bfb7-466ea4615954/dqc_reference/reference_markers_gtdb.fasta -out GCF_007280555.1_ASM728055v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:35,223] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:35,226] [INFO] Selected 10 target genomes.
[2024-01-24 14:56:35,227] [INFO] Target genome list was writen to GCF_007280555.1_ASM728055v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:35,238] [INFO] Task started: fastANI
[2024-01-24 14:56:35,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e47dc62-1ad7-49be-bca9-08e4c0b58006/GCF_007280555.1_ASM728055v1_genomic.fna.gz --refList GCF_007280555.1_ASM728055v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007280555.1_ASM728055v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:43,605] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:43,614] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:43,614] [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_007280555.1	s__Deinococcus detaillensis	100.0	1281	1286	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003860465.1	s__Deinococcus sp003860465	94.2829	1091	1286	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009982895.1	s__Deinococcus alpinitundrae	81.3632	818	1286	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173015.1	s__Deinococcus irradiatisoli	80.6746	595	1286	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067105.1	s__Deinococcus wulumuqiensis	77.4074	290	1286	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.82	97.50	0.97	0.83	19	-
GCA_018260275.1	s__Deinococcus sp018260275	77.0088	215	1286	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004758605.1	s__Deinococcus metallilatus	77.0004	302	1286	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	-
GCF_000190555.1	s__Deinococcus proteolyticus	76.883	181	1286	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646915.1	s__Deinococcus aquiradiocola	76.8378	224	1286	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	76.5247	163	1286	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:43,616] [INFO] GTDB search result was written to GCF_007280555.1_ASM728055v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:43,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:43,620] [INFO] DFAST_QC result json was written to GCF_007280555.1_ASM728055v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:43,621] [INFO] DFAST_QC completed!
[2024-01-24 14:56:43,621] [INFO] Total running time: 0h1m7s