[2023-06-30 19:47:45,986] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:47:45,988] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:47:45,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg87f871a6-c0c6-489b-bfa4-e3c7a1db3130/dqc_reference
[2023-06-30 19:47:49,334] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:47:49,336] [INFO] Task started: Prodigal
[2023-06-30 19:47:49,336] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d779da3-14f1-4609-bbc0-e19a37be24d2/GCA_007130355.1_ASM713035v1_genomic.fna.gz | prodigal -d GCA_007130355.1_ASM713035v1_genomic.fna/cds.fna -a GCA_007130355.1_ASM713035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:47:54,501] [INFO] Task succeeded: Prodigal
[2023-06-30 19:47:54,501] [INFO] Task started: HMMsearch
[2023-06-30 19:47:54,501] [INFO] Running command: hmmsearch --tblout GCA_007130355.1_ASM713035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87f871a6-c0c6-489b-bfa4-e3c7a1db3130/dqc_reference/reference_markers.hmm GCA_007130355.1_ASM713035v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:47:54,862] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:47:54,864] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4d779da3-14f1-4609-bbc0-e19a37be24d2/GCA_007130355.1_ASM713035v1_genomic.fna.gz]
[2023-06-30 19:47:54,891] [INFO] Query marker FASTA was written to GCA_007130355.1_ASM713035v1_genomic.fna/markers.fasta
[2023-06-30 19:47:54,892] [INFO] Task started: Blastn
[2023-06-30 19:47:54,892] [INFO] Running command: blastn -query GCA_007130355.1_ASM713035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87f871a6-c0c6-489b-bfa4-e3c7a1db3130/dqc_reference/reference_markers.fasta -out GCA_007130355.1_ASM713035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:47:55,689] [INFO] Task succeeded: Blastn
[2023-06-30 19:47:55,693] [INFO] Selected 16 target genomes.
[2023-06-30 19:47:55,693] [INFO] Target genome list was writen to GCA_007130355.1_ASM713035v1_genomic.fna/target_genomes.txt
[2023-06-30 19:47:55,695] [INFO] Task started: fastANI
[2023-06-30 19:47:55,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d779da3-14f1-4609-bbc0-e19a37be24d2/GCA_007130355.1_ASM713035v1_genomic.fna.gz --refList GCA_007130355.1_ASM713035v1_genomic.fna/target_genomes.txt --output GCA_007130355.1_ASM713035v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:48:09,133] [INFO] Task succeeded: fastANI
[2023-06-30 19:48:09,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87f871a6-c0c6-489b-bfa4-e3c7a1db3130/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:48:09,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87f871a6-c0c6-489b-bfa4-e3c7a1db3130/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:48:09,147] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:48:09,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 19:48:09,147] [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
Oceanithermus desulfurans	strain=DSM 15757	GCA_014201675.1	227924	227924	type	True	75.8266	76	660	95	below_threshold
Oceanithermus desulfurans	strain=NBRC 100063	GCA_007991015.1	227924	227924	type	True	75.8235	76	660	95	below_threshold
Truepera radiovictrix	strain=DSM 17093	GCA_000092425.1	332249	332249	type	True	75.7917	117	660	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	75.7612	85	660	95	below_threshold
Deinococcus pimensis	strain=DSM 21231	GCA_000519345.1	309888	309888	type	True	75.4179	97	660	95	below_threshold
Deinococcus reticulitermitis	strain=CGMCC 1.10218	GCA_900109185.1	856736	856736	type	True	75.4099	62	660	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	75.3079	104	660	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	75.2896	65	660	95	below_threshold
Haloechinothrix alba	strain=DSM 45207	GCA_900188115.1	664784	664784	type	True	74.7822	57	660	95	below_threshold
Amycolatopsis suaedae	strain=8-3EHSu	GCA_004214935.1	2510978	2510978	type	True	74.7453	110	660	95	below_threshold
Amycolatopsis jiangsuensis	strain=DSM 45859	GCA_014204865.1	1181879	1181879	type	True	74.6879	104	660	95	below_threshold
Frankia saprophytica	strain=CN3	GCA_000235425.3	298655	298655	type	True	74.6819	174	660	95	below_threshold
Amycolatopsis marina	strain=CGMCC 4.3568	GCA_900111885.1	490629	490629	type	True	74.6809	76	660	95	below_threshold
Amycolatopsis palatopharyngis	strain=DSM 44832	GCA_003385185.1	187982	187982	type	True	74.6623	68	660	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:48:09,149] [INFO] DFAST Taxonomy check result was written to GCA_007130355.1_ASM713035v1_genomic.fna/tc_result.tsv
[2023-06-30 19:48:09,150] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:48:09,150] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:48:09,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87f871a6-c0c6-489b-bfa4-e3c7a1db3130/dqc_reference/checkm_data
[2023-06-30 19:48:09,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:48:09,184] [INFO] Task started: CheckM
[2023-06-30 19:48:09,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007130355.1_ASM713035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007130355.1_ASM713035v1_genomic.fna/checkm_input GCA_007130355.1_ASM713035v1_genomic.fna/checkm_result
[2023-06-30 19:48:38,563] [INFO] Task succeeded: CheckM
[2023-06-30 19:48:38,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:48:38,587] [INFO] ===== Completeness check finished =====
[2023-06-30 19:48:38,588] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:48:38,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007130355.1_ASM713035v1_genomic.fna/markers.fasta)
[2023-06-30 19:48:38,588] [INFO] Task started: Blastn
[2023-06-30 19:48:38,589] [INFO] Running command: blastn -query GCA_007130355.1_ASM713035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87f871a6-c0c6-489b-bfa4-e3c7a1db3130/dqc_reference/reference_markers_gtdb.fasta -out GCA_007130355.1_ASM713035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:48:39,373] [INFO] Task succeeded: Blastn
[2023-06-30 19:48:39,378] [INFO] Selected 12 target genomes.
[2023-06-30 19:48:39,378] [INFO] Target genome list was writen to GCA_007130355.1_ASM713035v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:48:39,385] [INFO] Task started: fastANI
[2023-06-30 19:48:39,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d779da3-14f1-4609-bbc0-e19a37be24d2/GCA_007130355.1_ASM713035v1_genomic.fna.gz --refList GCA_007130355.1_ASM713035v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007130355.1_ASM713035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:48:46,124] [INFO] Task succeeded: fastANI
[2023-06-30 19:48:46,142] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:48:46,142] [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
GCA_007130355.1	s__SLSQ01 sp007130355	100.0	650	660	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__SLSQ01	95.0	99.11	99.11	0.70	0.70	2	conclusive
GCA_012515535.1	s__JAAYYF01 sp012515535	77.3966	201	660	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__JAAYYF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007130855.1	s__CSSed10-48 sp007130855	77.1847	200	660	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__CSSed10-48	95.0	99.69	99.67	0.91	0.90	3	-
GCA_011390455.1	s__JAABTL01 sp011390455	77.1129	223	660	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__JAABTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121175.1	s__CSSed10-48 sp007121175	77.0176	123	660	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__CSSed10-48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390735.1	s__JAABTL01 sp011390735	76.959	173	660	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__JAABTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007695125.1	s__CSSed10-48 sp007695125	76.9254	219	660	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__CSSed10-48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007130445.1	s__CSSed10-48 sp007130445	76.6662	157	660	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__CSSed10-48	95.0	99.41	99.41	0.84	0.83	3	-
GCF_000235425.2	s__Frankia saprophytica	74.6848	174	660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	99.94	99.94	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-30 19:48:46,145] [INFO] GTDB search result was written to GCA_007130355.1_ASM713035v1_genomic.fna/result_gtdb.tsv
[2023-06-30 19:48:46,145] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:48:46,150] [INFO] DFAST_QC result json was written to GCA_007130355.1_ASM713035v1_genomic.fna/dqc_result.json
[2023-06-30 19:48:46,150] [INFO] DFAST_QC completed!
[2023-06-30 19:48:46,150] [INFO] Total running time: 0h1m0s