[2023-06-29 00:28:30,184] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:28:30,186] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:28:30,186] [INFO] DQC Reference Directory: /var/lib/cwl/stg099629ad-fbdb-464d-931c-2fcecf0ae628/dqc_reference
[2023-06-29 00:28:31,375] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:28:31,376] [INFO] Task started: Prodigal
[2023-06-29 00:28:31,376] [INFO] Running command: gunzip -c /var/lib/cwl/stgadb978fb-4fd5-4b22-9e4d-6cd7af546f07/GCA_017406765.1_ASM1740676v1_genomic.fna.gz | prodigal -d GCA_017406765.1_ASM1740676v1_genomic.fna/cds.fna -a GCA_017406765.1_ASM1740676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:28:37,777] [INFO] Task succeeded: Prodigal
[2023-06-29 00:28:37,777] [INFO] Task started: HMMsearch
[2023-06-29 00:28:37,777] [INFO] Running command: hmmsearch --tblout GCA_017406765.1_ASM1740676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg099629ad-fbdb-464d-931c-2fcecf0ae628/dqc_reference/reference_markers.hmm GCA_017406765.1_ASM1740676v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:28:37,993] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:28:37,994] [INFO] Found 6/6 markers.
[2023-06-29 00:28:38,020] [INFO] Query marker FASTA was written to GCA_017406765.1_ASM1740676v1_genomic.fna/markers.fasta
[2023-06-29 00:28:38,021] [INFO] Task started: Blastn
[2023-06-29 00:28:38,021] [INFO] Running command: blastn -query GCA_017406765.1_ASM1740676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg099629ad-fbdb-464d-931c-2fcecf0ae628/dqc_reference/reference_markers.fasta -out GCA_017406765.1_ASM1740676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:28:38,575] [INFO] Task succeeded: Blastn
[2023-06-29 00:28:38,578] [INFO] Selected 20 target genomes.
[2023-06-29 00:28:38,579] [INFO] Target genome list was writen to GCA_017406765.1_ASM1740676v1_genomic.fna/target_genomes.txt
[2023-06-29 00:28:38,582] [INFO] Task started: fastANI
[2023-06-29 00:28:38,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgadb978fb-4fd5-4b22-9e4d-6cd7af546f07/GCA_017406765.1_ASM1740676v1_genomic.fna.gz --refList GCA_017406765.1_ASM1740676v1_genomic.fna/target_genomes.txt --output GCA_017406765.1_ASM1740676v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:28:55,088] [INFO] Task succeeded: fastANI
[2023-06-29 00:28:55,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg099629ad-fbdb-464d-931c-2fcecf0ae628/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:28:55,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg099629ad-fbdb-464d-931c-2fcecf0ae628/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:28:55,092] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:28:55,093] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:28:55,093] [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
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.456	50	895	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:28:55,095] [INFO] DFAST Taxonomy check result was written to GCA_017406765.1_ASM1740676v1_genomic.fna/tc_result.tsv
[2023-06-29 00:28:55,095] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:28:55,095] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:28:55,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg099629ad-fbdb-464d-931c-2fcecf0ae628/dqc_reference/checkm_data
[2023-06-29 00:28:55,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:28:55,130] [INFO] Task started: CheckM
[2023-06-29 00:28:55,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017406765.1_ASM1740676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017406765.1_ASM1740676v1_genomic.fna/checkm_input GCA_017406765.1_ASM1740676v1_genomic.fna/checkm_result
[2023-06-29 00:29:18,660] [INFO] Task succeeded: CheckM
[2023-06-29 00:29:18,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:29:18,678] [INFO] ===== Completeness check finished =====
[2023-06-29 00:29:18,678] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:29:18,679] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017406765.1_ASM1740676v1_genomic.fna/markers.fasta)
[2023-06-29 00:29:18,679] [INFO] Task started: Blastn
[2023-06-29 00:29:18,679] [INFO] Running command: blastn -query GCA_017406765.1_ASM1740676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg099629ad-fbdb-464d-931c-2fcecf0ae628/dqc_reference/reference_markers_gtdb.fasta -out GCA_017406765.1_ASM1740676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:29:19,461] [INFO] Task succeeded: Blastn
[2023-06-29 00:29:19,465] [INFO] Selected 16 target genomes.
[2023-06-29 00:29:19,465] [INFO] Target genome list was writen to GCA_017406765.1_ASM1740676v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:29:19,468] [INFO] Task started: fastANI
[2023-06-29 00:29:19,468] [INFO] Running command: fastANI --query /var/lib/cwl/stgadb978fb-4fd5-4b22-9e4d-6cd7af546f07/GCA_017406765.1_ASM1740676v1_genomic.fna.gz --refList GCA_017406765.1_ASM1740676v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017406765.1_ASM1740676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:29:30,151] [INFO] Task succeeded: fastANI
[2023-06-29 00:29:30,160] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:29:30,160] [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_017434455.1	s__RUG695 sp017434455	99.2331	868	895	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG695	95.0	98.46	97.69	0.95	0.94	3	conclusive
GCA_902797455.1	s__RUG695 sp902797455	92.0308	538	895	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG695	95.0	99.11	99.11	0.94	0.94	2	-
GCA_902766935.1	s__RUG695 sp902766935	77.0354	97	895	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG695	95.0	97.68	97.68	0.94	0.94	2	-
GCA_017405595.1	s__RUG695 sp017405595	77.0141	91	895	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG695	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321495.1	s__RUG695 sp900321495	76.9401	96	895	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG695	95.0	99.09	98.95	0.81	0.80	3	-
GCA_902796885.1	s__RUG695 sp902796885	76.7101	104	895	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG695	95.0	98.58	98.58	0.93	0.93	2	-
GCA_017559825.1	s__RUG369 sp017559825	75.6572	53	895	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937485.1	s__RUG369 sp017937485	75.5516	63	895	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435375.1	s__RUG369 sp017435375	75.4001	51	895	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:29:30,190] [INFO] GTDB search result was written to GCA_017406765.1_ASM1740676v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:29:30,190] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:29:30,192] [INFO] DFAST_QC result json was written to GCA_017406765.1_ASM1740676v1_genomic.fna/dqc_result.json
[2023-06-29 00:29:30,192] [INFO] DFAST_QC completed!
[2023-06-29 00:29:30,193] [INFO] Total running time: 0h1m0s