[2023-06-28 20:56:04,284] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:56:04,285] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:56:04,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ce790a5-7cd0-429a-a363-c391db9279fe/dqc_reference
[2023-06-28 20:56:05,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:56:05,537] [INFO] Task started: Prodigal
[2023-06-28 20:56:05,538] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa724206-a7b2-4910-b6cf-8bfae05e4b45/GCA_019310085.1_ASM1931008v1_genomic.fna.gz | prodigal -d GCA_019310085.1_ASM1931008v1_genomic.fna/cds.fna -a GCA_019310085.1_ASM1931008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:56:11,766] [INFO] Task succeeded: Prodigal
[2023-06-28 20:56:11,766] [INFO] Task started: HMMsearch
[2023-06-28 20:56:11,766] [INFO] Running command: hmmsearch --tblout GCA_019310085.1_ASM1931008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ce790a5-7cd0-429a-a363-c391db9279fe/dqc_reference/reference_markers.hmm GCA_019310085.1_ASM1931008v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:56:11,958] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:56:11,959] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfa724206-a7b2-4910-b6cf-8bfae05e4b45/GCA_019310085.1_ASM1931008v1_genomic.fna.gz]
[2023-06-28 20:56:11,985] [INFO] Query marker FASTA was written to GCA_019310085.1_ASM1931008v1_genomic.fna/markers.fasta
[2023-06-28 20:56:11,986] [INFO] Task started: Blastn
[2023-06-28 20:56:11,986] [INFO] Running command: blastn -query GCA_019310085.1_ASM1931008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ce790a5-7cd0-429a-a363-c391db9279fe/dqc_reference/reference_markers.fasta -out GCA_019310085.1_ASM1931008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:56:12,617] [INFO] Task succeeded: Blastn
[2023-06-28 20:56:12,621] [INFO] Selected 20 target genomes.
[2023-06-28 20:56:12,621] [INFO] Target genome list was writen to GCA_019310085.1_ASM1931008v1_genomic.fna/target_genomes.txt
[2023-06-28 20:56:12,622] [INFO] Task started: fastANI
[2023-06-28 20:56:12,622] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa724206-a7b2-4910-b6cf-8bfae05e4b45/GCA_019310085.1_ASM1931008v1_genomic.fna.gz --refList GCA_019310085.1_ASM1931008v1_genomic.fna/target_genomes.txt --output GCA_019310085.1_ASM1931008v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:56:30,443] [INFO] Task succeeded: fastANI
[2023-06-28 20:56:30,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ce790a5-7cd0-429a-a363-c391db9279fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:56:30,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ce790a5-7cd0-429a-a363-c391db9279fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:56:30,448] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:56:30,448] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:56:30,448] [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
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.5664	63	507	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:56:30,449] [INFO] DFAST Taxonomy check result was written to GCA_019310085.1_ASM1931008v1_genomic.fna/tc_result.tsv
[2023-06-28 20:56:30,450] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:56:30,450] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:56:30,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ce790a5-7cd0-429a-a363-c391db9279fe/dqc_reference/checkm_data
[2023-06-28 20:56:30,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:56:30,482] [INFO] Task started: CheckM
[2023-06-28 20:56:30,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310085.1_ASM1931008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310085.1_ASM1931008v1_genomic.fna/checkm_input GCA_019310085.1_ASM1931008v1_genomic.fna/checkm_result
[2023-06-28 20:56:52,684] [INFO] Task succeeded: CheckM
[2023-06-28 20:56:52,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.36%
Contamintation: 11.81%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-06-28 20:56:52,709] [INFO] ===== Completeness check finished =====
[2023-06-28 20:56:52,709] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:56:52,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310085.1_ASM1931008v1_genomic.fna/markers.fasta)
[2023-06-28 20:56:52,709] [INFO] Task started: Blastn
[2023-06-28 20:56:52,709] [INFO] Running command: blastn -query GCA_019310085.1_ASM1931008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ce790a5-7cd0-429a-a363-c391db9279fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310085.1_ASM1931008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:56:53,797] [INFO] Task succeeded: Blastn
[2023-06-28 20:56:53,801] [INFO] Selected 17 target genomes.
[2023-06-28 20:56:53,801] [INFO] Target genome list was writen to GCA_019310085.1_ASM1931008v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:56:53,805] [INFO] Task started: fastANI
[2023-06-28 20:56:53,805] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa724206-a7b2-4910-b6cf-8bfae05e4b45/GCA_019310085.1_ASM1931008v1_genomic.fna.gz --refList GCA_019310085.1_ASM1931008v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310085.1_ASM1931008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:57:07,950] [INFO] Task succeeded: fastANI
[2023-06-28 20:57:07,956] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 20:57:07,956] [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_003647035.1	s__SG8-38 sp003647035	97.2806	380	507	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	96.70	96.70	0.74	0.74	2	conclusive
GCA_004283055.1	s__SG8-38 sp004283055	78.5788	193	507	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	99.78	99.72	0.93	0.90	8	-
GCA_013002645.1	s__SG8-38 sp013002645	78.3066	166	507	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001303415.1	s__SG8-38 sp001303415	77.4381	144	507	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744445.1	s__JAAYBZ01 sp012744445	76.4019	58	507	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAAYBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699025.1	s__GCA-2699025 sp002699025	76.027	65	507	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__GCA-2699025	95.0	99.90	99.85	0.97	0.97	3	-
GCA_016706685.1	s__JADJJE01 sp016706685	75.9652	50	507	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JADJJE01	95.0	99.15	99.06	0.93	0.90	7	-
GCF_000737325.1	s__Sandaracinus amylolyticus	75.5508	64	507	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:57:07,958] [INFO] GTDB search result was written to GCA_019310085.1_ASM1931008v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:57:07,959] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:57:07,961] [INFO] DFAST_QC result json was written to GCA_019310085.1_ASM1931008v1_genomic.fna/dqc_result.json
[2023-06-28 20:57:07,961] [INFO] DFAST_QC completed!
[2023-06-28 20:57:07,961] [INFO] Total running time: 0h1m4s