[2024-01-24 13:41:26,507] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:26,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:26,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg4dade2cf-5be6-4003-bfbd-0d015b738be2/dqc_reference
[2024-01-24 13:41:27,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:27,879] [INFO] Task started: Prodigal
[2024-01-24 13:41:27,879] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ed64a7b-a3ed-448d-8553-100126925e5a/GCF_004115945.1_ASM411594v1_genomic.fna.gz | prodigal -d GCF_004115945.1_ASM411594v1_genomic.fna/cds.fna -a GCF_004115945.1_ASM411594v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:39,264] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:39,264] [INFO] Task started: HMMsearch
[2024-01-24 13:41:39,264] [INFO] Running command: hmmsearch --tblout GCF_004115945.1_ASM411594v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4dade2cf-5be6-4003-bfbd-0d015b738be2/dqc_reference/reference_markers.hmm GCF_004115945.1_ASM411594v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:39,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:39,602] [INFO] Found 6/6 markers.
[2024-01-24 13:41:39,643] [INFO] Query marker FASTA was written to GCF_004115945.1_ASM411594v1_genomic.fna/markers.fasta
[2024-01-24 13:41:39,644] [INFO] Task started: Blastn
[2024-01-24 13:41:39,644] [INFO] Running command: blastn -query GCF_004115945.1_ASM411594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dade2cf-5be6-4003-bfbd-0d015b738be2/dqc_reference/reference_markers.fasta -out GCF_004115945.1_ASM411594v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:40,347] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:40,352] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:40,353] [INFO] Target genome list was writen to GCF_004115945.1_ASM411594v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:40,358] [INFO] Task started: fastANI
[2024-01-24 13:41:40,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ed64a7b-a3ed-448d-8553-100126925e5a/GCF_004115945.1_ASM411594v1_genomic.fna.gz --refList GCF_004115945.1_ASM411594v1_genomic.fna/target_genomes.txt --output GCF_004115945.1_ASM411594v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:50,326] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4dade2cf-5be6-4003-bfbd-0d015b738be2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:50,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4dade2cf-5be6-4003-bfbd-0d015b738be2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:50,355] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:41:50,355] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:50,355] [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 metallilatus	strain=MA1002	GCA_004115945.1	1211322	1211322	type	True	100.0	1302	1308	95	conclusive
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	99.996	1282	1308	95	conclusive
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	99.9959	1299	1308	95	conclusive
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	86.3117	861	1308	95	below_threshold
Deinococcus aerius	strain=TR0125	GCA_002897375.1	200253	200253	type	True	85.5998	954	1308	95	below_threshold
Deinococcus geothermalis	strain=DSM 11300	GCA_000196275.1	68909	68909	type	True	83.7694	760	1308	95	below_threshold
Deinococcus planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	83.2785	831	1308	95	below_threshold
Deinococcus apachensis	strain=DSM 19763	GCA_000381345.1	309886	309886	type	True	83.1641	820	1308	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	82.8198	790	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,358] [INFO] DFAST Taxonomy check result was written to GCF_004115945.1_ASM411594v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:50,358] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:50,358] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:50,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4dade2cf-5be6-4003-bfbd-0d015b738be2/dqc_reference/checkm_data
[2024-01-24 13:41:50,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:50,405] [INFO] Task started: CheckM
[2024-01-24 13:41:50,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004115945.1_ASM411594v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004115945.1_ASM411594v1_genomic.fna/checkm_input GCF_004115945.1_ASM411594v1_genomic.fna/checkm_result
[2024-01-24 13:42:27,102] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:27,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:27,125] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:27,125] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:27,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004115945.1_ASM411594v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:27,126] [INFO] Task started: Blastn
[2024-01-24 13:42:27,126] [INFO] Running command: blastn -query GCF_004115945.1_ASM411594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dade2cf-5be6-4003-bfbd-0d015b738be2/dqc_reference/reference_markers_gtdb.fasta -out GCF_004115945.1_ASM411594v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:28,065] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:28,070] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:28,071] [INFO] Target genome list was writen to GCF_004115945.1_ASM411594v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:28,084] [INFO] Task started: fastANI
[2024-01-24 13:42:28,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ed64a7b-a3ed-448d-8553-100126925e5a/GCF_004115945.1_ASM411594v1_genomic.fna.gz --refList GCF_004115945.1_ASM411594v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004115945.1_ASM411594v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:39,996] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:40,053] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:40,054] [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_004758605.1	s__Deinococcus metallilatus	99.996	1282	1308	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	conclusive
GCF_000599865.1	s__Deinococcus phoenicis	86.3277	860	1308	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	85.5536	958	1308	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196275.1	s__Deinococcus geothermalis	83.7647	760	1308	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.28	97.91	0.91	0.89	4	-
GCF_002869765.1	s__Deinococcus planocerae	83.2583	833	1308	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	83.1567	821	1308	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	82.8253	790	1308	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	82.5978	833	1308	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	82.1475	696	1308	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	81.8414	706	1308	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901445.1	s__Deinococcus koreensis	79.7931	670	1308	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001949125.1	s__Deinococcus marmoris_A	79.1604	603	1308	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 13:42:40,055] [INFO] GTDB search result was written to GCF_004115945.1_ASM411594v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:40,056] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:40,059] [INFO] DFAST_QC result json was written to GCF_004115945.1_ASM411594v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:40,059] [INFO] DFAST_QC completed!
[2024-01-24 13:42:40,059] [INFO] Total running time: 0h1m14s