[2024-01-24 13:40:55,253] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,266] [INFO] DQC Reference Directory: /var/lib/cwl/stgddde1cc0-c620-4b7c-8522-b9484adde966/dqc_reference
[2024-01-24 13:40:56,380] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,381] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,381] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e6ea556-480c-460e-8b20-3c00f60fab4f/GCF_025997855.1_ASM2599785v1_genomic.fna.gz | prodigal -d GCF_025997855.1_ASM2599785v1_genomic.fna/cds.fna -a GCF_025997855.1_ASM2599785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:20,174] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:20,175] [INFO] Task started: HMMsearch
[2024-01-24 13:41:20,175] [INFO] Running command: hmmsearch --tblout GCF_025997855.1_ASM2599785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddde1cc0-c620-4b7c-8522-b9484adde966/dqc_reference/reference_markers.hmm GCF_025997855.1_ASM2599785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:20,462] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:20,463] [INFO] Found 6/6 markers.
[2024-01-24 13:41:20,501] [INFO] Query marker FASTA was written to GCF_025997855.1_ASM2599785v1_genomic.fna/markers.fasta
[2024-01-24 13:41:20,501] [INFO] Task started: Blastn
[2024-01-24 13:41:20,501] [INFO] Running command: blastn -query GCF_025997855.1_ASM2599785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddde1cc0-c620-4b7c-8522-b9484adde966/dqc_reference/reference_markers.fasta -out GCF_025997855.1_ASM2599785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:21,297] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:21,299] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:21,300] [INFO] Target genome list was writen to GCF_025997855.1_ASM2599785v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:21,303] [INFO] Task started: fastANI
[2024-01-24 13:41:21,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e6ea556-480c-460e-8b20-3c00f60fab4f/GCF_025997855.1_ASM2599785v1_genomic.fna.gz --refList GCF_025997855.1_ASM2599785v1_genomic.fna/target_genomes.txt --output GCF_025997855.1_ASM2599785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:30,643] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:30,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddde1cc0-c620-4b7c-8522-b9484adde966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:30,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddde1cc0-c620-4b7c-8522-b9484adde966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:30,651] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:30,651] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:30,651] [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 planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	88.8581	1008	1603	95	below_threshold
Deinococcus aerius	strain=TR0125	GCA_002897375.1	200253	200253	type	True	84.0956	969	1603	95	below_threshold
Deinococcus apachensis	strain=DSM 19763	GCA_000381345.1	309886	309886	type	True	83.1284	857	1603	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	82.6555	889	1603	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004115945.1	1211322	1211322	type	True	82.641	861	1603	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	82.5864	891	1603	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	81.8703	794	1603	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	81.6361	763	1603	95	below_threshold
Deinococcus terrestris	strain=SDU3-2	GCA_009377345.1	2651870	2651870	type	True	81.3954	699	1603	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:30,652] [INFO] DFAST Taxonomy check result was written to GCF_025997855.1_ASM2599785v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:30,653] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:30,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:30,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddde1cc0-c620-4b7c-8522-b9484adde966/dqc_reference/checkm_data
[2024-01-24 13:41:30,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:30,699] [INFO] Task started: CheckM
[2024-01-24 13:41:30,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025997855.1_ASM2599785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025997855.1_ASM2599785v1_genomic.fna/checkm_input GCF_025997855.1_ASM2599785v1_genomic.fna/checkm_result
[2024-01-24 13:42:22,299] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:22,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:22,314] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:22,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:22,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025997855.1_ASM2599785v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:22,315] [INFO] Task started: Blastn
[2024-01-24 13:42:22,315] [INFO] Running command: blastn -query GCF_025997855.1_ASM2599785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddde1cc0-c620-4b7c-8522-b9484adde966/dqc_reference/reference_markers_gtdb.fasta -out GCF_025997855.1_ASM2599785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:23,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:23,582] [INFO] Selected 11 target genomes.
[2024-01-24 13:42:23,583] [INFO] Target genome list was writen to GCF_025997855.1_ASM2599785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:23,589] [INFO] Task started: fastANI
[2024-01-24 13:42:23,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e6ea556-480c-460e-8b20-3c00f60fab4f/GCF_025997855.1_ASM2599785v1_genomic.fna.gz --refList GCF_025997855.1_ASM2599785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025997855.1_ASM2599785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:34,469] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:34,477] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:42:34,477] [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_002869765.1	s__Deinococcus planocerae	88.8797	1006	1603	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	88.4552	1119	1603	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897375.1	s__Deinococcus aerius	84.1012	969	1603	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	83.1107	859	1603	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	82.6488	890	1603	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	-
GCF_014201885.1	s__Deinococcus budaensis	81.8214	800	1603	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000599865.1	s__Deinococcus phoenicis	81.6833	756	1603	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	81.6826	708	1603	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	81.4188	696	1603	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002017875.1	s__Deinococcus sp002017875	78.9417	616	1603	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_001949125.1	s__Deinococcus marmoris_A	77.9704	535	1603	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 13:42:34,478] [INFO] GTDB search result was written to GCF_025997855.1_ASM2599785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:34,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:34,481] [INFO] DFAST_QC result json was written to GCF_025997855.1_ASM2599785v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:34,481] [INFO] DFAST_QC completed!
[2024-01-24 13:42:34,482] [INFO] Total running time: 0h1m39s