[2024-01-24 12:30:52,522] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,525] [INFO] DQC Reference Directory: /var/lib/cwl/stge06f4ef3-ba69-4fa3-9775-57590d9eed4d/dqc_reference
[2024-01-24 12:30:53,899] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:53,900] [INFO] Task started: Prodigal
[2024-01-24 12:30:53,900] [INFO] Running command: gunzip -c /var/lib/cwl/stg4104be07-9faf-41d3-bea2-91aee9107d9f/GCF_009982895.1_ASM998289v1_genomic.fna.gz | prodigal -d GCF_009982895.1_ASM998289v1_genomic.fna/cds.fna -a GCF_009982895.1_ASM998289v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:07,174] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:07,175] [INFO] Task started: HMMsearch
[2024-01-24 12:31:07,175] [INFO] Running command: hmmsearch --tblout GCF_009982895.1_ASM998289v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge06f4ef3-ba69-4fa3-9775-57590d9eed4d/dqc_reference/reference_markers.hmm GCF_009982895.1_ASM998289v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:07,482] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:07,484] [INFO] Found 6/6 markers.
[2024-01-24 12:31:07,530] [INFO] Query marker FASTA was written to GCF_009982895.1_ASM998289v1_genomic.fna/markers.fasta
[2024-01-24 12:31:07,530] [INFO] Task started: Blastn
[2024-01-24 12:31:07,530] [INFO] Running command: blastn -query GCF_009982895.1_ASM998289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge06f4ef3-ba69-4fa3-9775-57590d9eed4d/dqc_reference/reference_markers.fasta -out GCF_009982895.1_ASM998289v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:08,203] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:08,208] [INFO] Selected 8 target genomes.
[2024-01-24 12:31:08,208] [INFO] Target genome list was writen to GCF_009982895.1_ASM998289v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:08,219] [INFO] Task started: fastANI
[2024-01-24 12:31:08,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg4104be07-9faf-41d3-bea2-91aee9107d9f/GCF_009982895.1_ASM998289v1_genomic.fna.gz --refList GCF_009982895.1_ASM998289v1_genomic.fna/target_genomes.txt --output GCF_009982895.1_ASM998289v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:15,274] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:15,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge06f4ef3-ba69-4fa3-9775-57590d9eed4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:15,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge06f4ef3-ba69-4fa3-9775-57590d9eed4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:15,291] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:15,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:15,292] [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 alpinitundrae	strain=LMG 24283	GCA_009982895.1	468913	468913	type	True	100.0	1477	1482	95	conclusive
Deinococcus rubellus	strain=Ant6	GCA_025244745.1	1889240	1889240	type	True	87.6583	837	1482	95	below_threshold
Deinococcus irradiatisoli	strain=17bor-2	GCA_003173015.1	2202254	2202254	type	True	83.4488	739	1482	95	below_threshold
Deinococcus psychrotolerans	strain=S14-83	GCA_003860465.1	2489213	2489213	type	True	81.4407	878	1482	95	below_threshold
Deinococcus detaillensis	strain=H1	GCA_007280555.1	2592048	2592048	type	True	81.3959	824	1482	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	78.7221	498	1482	95	below_threshold
Deinococcus wulumuqiensis	strain=R12	GCA_014875835.1	980427	980427	type	True	78.2895	382	1482	95	below_threshold
Deinococcus wulumuqiensis	strain=R12	GCA_014875975.1	980427	980427	type	True	78.1919	399	1482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:15,293] [INFO] DFAST Taxonomy check result was written to GCF_009982895.1_ASM998289v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:15,294] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:15,294] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:15,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge06f4ef3-ba69-4fa3-9775-57590d9eed4d/dqc_reference/checkm_data
[2024-01-24 12:31:15,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:15,342] [INFO] Task started: CheckM
[2024-01-24 12:31:15,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009982895.1_ASM998289v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009982895.1_ASM998289v1_genomic.fna/checkm_input GCF_009982895.1_ASM998289v1_genomic.fna/checkm_result
[2024-01-24 12:31:56,404] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:56,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:56,424] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:56,425] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:56,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009982895.1_ASM998289v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:56,426] [INFO] Task started: Blastn
[2024-01-24 12:31:56,426] [INFO] Running command: blastn -query GCF_009982895.1_ASM998289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge06f4ef3-ba69-4fa3-9775-57590d9eed4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009982895.1_ASM998289v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:57,452] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:57,456] [INFO] Selected 11 target genomes.
[2024-01-24 12:31:57,456] [INFO] Target genome list was writen to GCF_009982895.1_ASM998289v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:57,464] [INFO] Task started: fastANI
[2024-01-24 12:31:57,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg4104be07-9faf-41d3-bea2-91aee9107d9f/GCF_009982895.1_ASM998289v1_genomic.fna.gz --refList GCF_009982895.1_ASM998289v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009982895.1_ASM998289v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:07,151] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:07,164] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:07,165] [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_009982895.1	s__Deinococcus alpinitundrae	100.0	1477	1482	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_003173015.1	s__Deinococcus irradiatisoli	83.4189	742	1482	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860465.1	s__Deinococcus sp003860465	81.4276	880	1482	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	81.372	827	1482	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335125.1	s__Deinococcus radiopugnans	79.0169	547	1482	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
GCF_000252445.1	s__Deinococcus gobiensis	78.6835	500	1482	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	78.189	411	1482	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.82	97.50	0.97	0.83	19	-
GCF_014648095.1	s__Deinococcus ruber	78.1662	535	1482	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	78.1222	397	1482	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
GCF_003444775.1	s__Deinococcus ficus	77.5527	335	1482	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.33	97.44	0.95	0.88	4	-
GCF_000186385.1	s__Deinococcus_B maricopensis	76.8627	246	1482	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 12:32:07,167] [INFO] GTDB search result was written to GCF_009982895.1_ASM998289v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:07,167] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:07,170] [INFO] DFAST_QC result json was written to GCF_009982895.1_ASM998289v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:07,171] [INFO] DFAST_QC completed!
[2024-01-24 12:32:07,171] [INFO] Total running time: 0h1m15s