[2023-06-28 02:00:23,091] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:00:23,093] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:00:23,093] [INFO] DQC Reference Directory: /var/lib/cwl/stga77cf93e-01e3-4877-b482-2abd06d5385c/dqc_reference
[2023-06-28 02:00:24,332] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:00:24,333] [INFO] Task started: Prodigal
[2023-06-28 02:00:24,333] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9280510-229a-4250-84ca-9c687e4780d6/GCA_019310045.1_ASM1931004v1_genomic.fna.gz | prodigal -d GCA_019310045.1_ASM1931004v1_genomic.fna/cds.fna -a GCA_019310045.1_ASM1931004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:00:31,369] [INFO] Task succeeded: Prodigal
[2023-06-28 02:00:31,369] [INFO] Task started: HMMsearch
[2023-06-28 02:00:31,370] [INFO] Running command: hmmsearch --tblout GCA_019310045.1_ASM1931004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga77cf93e-01e3-4877-b482-2abd06d5385c/dqc_reference/reference_markers.hmm GCA_019310045.1_ASM1931004v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:00:31,595] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:00:31,596] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd9280510-229a-4250-84ca-9c687e4780d6/GCA_019310045.1_ASM1931004v1_genomic.fna.gz]
[2023-06-28 02:00:31,631] [INFO] Query marker FASTA was written to GCA_019310045.1_ASM1931004v1_genomic.fna/markers.fasta
[2023-06-28 02:00:31,632] [INFO] Task started: Blastn
[2023-06-28 02:00:31,632] [INFO] Running command: blastn -query GCA_019310045.1_ASM1931004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga77cf93e-01e3-4877-b482-2abd06d5385c/dqc_reference/reference_markers.fasta -out GCA_019310045.1_ASM1931004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:00:32,303] [INFO] Task succeeded: Blastn
[2023-06-28 02:00:32,307] [INFO] Selected 25 target genomes.
[2023-06-28 02:00:32,308] [INFO] Target genome list was writen to GCA_019310045.1_ASM1931004v1_genomic.fna/target_genomes.txt
[2023-06-28 02:00:32,316] [INFO] Task started: fastANI
[2023-06-28 02:00:32,316] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9280510-229a-4250-84ca-9c687e4780d6/GCA_019310045.1_ASM1931004v1_genomic.fna.gz --refList GCA_019310045.1_ASM1931004v1_genomic.fna/target_genomes.txt --output GCA_019310045.1_ASM1931004v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:00:51,475] [INFO] Task succeeded: fastANI
[2023-06-28 02:00:51,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga77cf93e-01e3-4877-b482-2abd06d5385c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:00:51,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga77cf93e-01e3-4877-b482-2abd06d5385c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:00:51,484] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:00:51,485] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 02:00:51,485] [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
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.5275	52	696	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.4905	103	696	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 02:00:51,487] [INFO] DFAST Taxonomy check result was written to GCA_019310045.1_ASM1931004v1_genomic.fna/tc_result.tsv
[2023-06-28 02:00:51,488] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:00:51,488] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:00:51,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga77cf93e-01e3-4877-b482-2abd06d5385c/dqc_reference/checkm_data
[2023-06-28 02:00:51,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:00:51,526] [INFO] Task started: CheckM
[2023-06-28 02:00:51,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310045.1_ASM1931004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310045.1_ASM1931004v1_genomic.fna/checkm_input GCA_019310045.1_ASM1931004v1_genomic.fna/checkm_result
[2023-06-28 02:01:18,147] [INFO] Task succeeded: CheckM
[2023-06-28 02:01:18,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.15%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 02:01:18,183] [INFO] ===== Completeness check finished =====
[2023-06-28 02:01:18,183] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:01:18,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310045.1_ASM1931004v1_genomic.fna/markers.fasta)
[2023-06-28 02:01:18,184] [INFO] Task started: Blastn
[2023-06-28 02:01:18,184] [INFO] Running command: blastn -query GCA_019310045.1_ASM1931004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga77cf93e-01e3-4877-b482-2abd06d5385c/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310045.1_ASM1931004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:01:19,150] [INFO] Task succeeded: Blastn
[2023-06-28 02:01:19,155] [INFO] Selected 11 target genomes.
[2023-06-28 02:01:19,155] [INFO] Target genome list was writen to GCA_019310045.1_ASM1931004v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:01:19,166] [INFO] Task started: fastANI
[2023-06-28 02:01:19,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9280510-229a-4250-84ca-9c687e4780d6/GCA_019310045.1_ASM1931004v1_genomic.fna.gz --refList GCA_019310045.1_ASM1931004v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310045.1_ASM1931004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:01:30,866] [INFO] Task succeeded: fastANI
[2023-06-28 02:01:30,878] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 02:01:30,879] [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	81.8126	456	696	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	-
GCA_013002645.1	s__SG8-38 sp013002645	78.841	305	696	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_004283055.1	s__SG8-38 sp004283055	78.5785	380	696	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_001303415.1	s__SG8-38 sp001303415	77.6196	264	696	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_002699025.1	s__GCA-2699025 sp002699025	76.0737	103	696	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	75.8851	67	696	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JADJJE01	95.0	99.15	99.06	0.93	0.90	7	-
GCA_002320815.1	s__UBA1660 sp002320815	75.7726	82	696	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	99.96	99.96	0.96	0.96	2	-
GCA_017644045.1	s__UBA1660 sp017644045	75.6651	94	696	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 02:01:30,881] [INFO] GTDB search result was written to GCA_019310045.1_ASM1931004v1_genomic.fna/result_gtdb.tsv
[2023-06-28 02:01:30,881] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:01:30,884] [INFO] DFAST_QC result json was written to GCA_019310045.1_ASM1931004v1_genomic.fna/dqc_result.json
[2023-06-28 02:01:30,884] [INFO] DFAST_QC completed!
[2023-06-28 02:01:30,884] [INFO] Total running time: 0h1m8s