[2023-06-30 13:27:45,619] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:27:45,621] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:27:45,621] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf6ea6e8-476d-4a44-92a7-b82e6c33c92c/dqc_reference
[2023-06-30 13:27:46,933] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:27:46,934] [INFO] Task started: Prodigal
[2023-06-30 13:27:46,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e251581-1157-4a05-85fc-ee53e24cb5b9/GCA_019307595.1_ASM1930759v1_genomic.fna.gz | prodigal -d GCA_019307595.1_ASM1930759v1_genomic.fna/cds.fna -a GCA_019307595.1_ASM1930759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:27:54,783] [INFO] Task succeeded: Prodigal
[2023-06-30 13:27:54,784] [INFO] Task started: HMMsearch
[2023-06-30 13:27:54,784] [INFO] Running command: hmmsearch --tblout GCA_019307595.1_ASM1930759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf6ea6e8-476d-4a44-92a7-b82e6c33c92c/dqc_reference/reference_markers.hmm GCA_019307595.1_ASM1930759v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:27:55,082] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:27:55,083] [INFO] Found 6/6 markers.
[2023-06-30 13:27:55,114] [INFO] Query marker FASTA was written to GCA_019307595.1_ASM1930759v1_genomic.fna/markers.fasta
[2023-06-30 13:27:55,114] [INFO] Task started: Blastn
[2023-06-30 13:27:55,115] [INFO] Running command: blastn -query GCA_019307595.1_ASM1930759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf6ea6e8-476d-4a44-92a7-b82e6c33c92c/dqc_reference/reference_markers.fasta -out GCA_019307595.1_ASM1930759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:27:55,898] [INFO] Task succeeded: Blastn
[2023-06-30 13:27:55,902] [INFO] Selected 29 target genomes.
[2023-06-30 13:27:55,902] [INFO] Target genome list was writen to GCA_019307595.1_ASM1930759v1_genomic.fna/target_genomes.txt
[2023-06-30 13:27:55,909] [INFO] Task started: fastANI
[2023-06-30 13:27:55,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e251581-1157-4a05-85fc-ee53e24cb5b9/GCA_019307595.1_ASM1930759v1_genomic.fna.gz --refList GCA_019307595.1_ASM1930759v1_genomic.fna/target_genomes.txt --output GCA_019307595.1_ASM1930759v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:28:19,902] [INFO] Task succeeded: fastANI
[2023-06-30 13:28:19,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf6ea6e8-476d-4a44-92a7-b82e6c33c92c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:28:19,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf6ea6e8-476d-4a44-92a7-b82e6c33c92c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:28:19,912] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:28:19,912] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 13:28:19,912] [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	75.5923	103	759	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.5682	55	759	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.0394	57	759	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 13:28:19,915] [INFO] DFAST Taxonomy check result was written to GCA_019307595.1_ASM1930759v1_genomic.fna/tc_result.tsv
[2023-06-30 13:28:19,916] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:28:19,916] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:28:19,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf6ea6e8-476d-4a44-92a7-b82e6c33c92c/dqc_reference/checkm_data
[2023-06-30 13:28:19,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:28:19,959] [INFO] Task started: CheckM
[2023-06-30 13:28:19,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019307595.1_ASM1930759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019307595.1_ASM1930759v1_genomic.fna/checkm_input GCA_019307595.1_ASM1930759v1_genomic.fna/checkm_result
[2023-06-30 13:28:48,614] [INFO] Task succeeded: CheckM
[2023-06-30 13:28:48,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.64%
Contamintation: 8.33%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-30 13:28:48,645] [INFO] ===== Completeness check finished =====
[2023-06-30 13:28:48,646] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:28:48,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019307595.1_ASM1930759v1_genomic.fna/markers.fasta)
[2023-06-30 13:28:48,647] [INFO] Task started: Blastn
[2023-06-30 13:28:48,647] [INFO] Running command: blastn -query GCA_019307595.1_ASM1930759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf6ea6e8-476d-4a44-92a7-b82e6c33c92c/dqc_reference/reference_markers_gtdb.fasta -out GCA_019307595.1_ASM1930759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:28:49,681] [INFO] Task succeeded: Blastn
[2023-06-30 13:28:49,687] [INFO] Selected 13 target genomes.
[2023-06-30 13:28:49,687] [INFO] Target genome list was writen to GCA_019307595.1_ASM1930759v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:28:49,695] [INFO] Task started: fastANI
[2023-06-30 13:28:49,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e251581-1157-4a05-85fc-ee53e24cb5b9/GCA_019307595.1_ASM1930759v1_genomic.fna.gz --refList GCA_019307595.1_ASM1930759v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019307595.1_ASM1930759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:29:03,479] [INFO] Task succeeded: fastANI
[2023-06-30 13:29:03,492] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 13:29:03,492] [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	82.0132	495	759	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	78.6719	330	759	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	78.6664	396	759	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	77.7608	283	759	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_016706685.1	s__JADJJE01 sp016706685	76.2937	73	759	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	75.8864	82	759	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	75.8788	95	759	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418325.1	s__Sorangium cellulosum_D	75.1902	80	759	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCF_002950945.1	s__Sorangium cellulosum_E	75.0526	71	759	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:29:03,494] [INFO] GTDB search result was written to GCA_019307595.1_ASM1930759v1_genomic.fna/result_gtdb.tsv
[2023-06-30 13:29:03,494] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:29:03,497] [INFO] DFAST_QC result json was written to GCA_019307595.1_ASM1930759v1_genomic.fna/dqc_result.json
[2023-06-30 13:29:03,497] [INFO] DFAST_QC completed!
[2023-06-30 13:29:03,498] [INFO] Total running time: 0h1m18s