[2023-06-28 21:04:50,310] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:04:50,312] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:04:50,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ef3e176-de42-4a12-9a00-637c63ceaed8/dqc_reference
[2023-06-28 21:04:51,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:04:51,515] [INFO] Task started: Prodigal
[2023-06-28 21:04:51,515] [INFO] Running command: gunzip -c /var/lib/cwl/stg07d800a4-0880-4762-a15c-d57ca98c8056/GCA_015488785.1_ASM1548878v1_genomic.fna.gz | prodigal -d GCA_015488785.1_ASM1548878v1_genomic.fna/cds.fna -a GCA_015488785.1_ASM1548878v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:05:02,001] [INFO] Task succeeded: Prodigal
[2023-06-28 21:05:02,002] [INFO] Task started: HMMsearch
[2023-06-28 21:05:02,002] [INFO] Running command: hmmsearch --tblout GCA_015488785.1_ASM1548878v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ef3e176-de42-4a12-9a00-637c63ceaed8/dqc_reference/reference_markers.hmm GCA_015488785.1_ASM1548878v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:05:02,269] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:05:02,271] [INFO] Found 6/6 markers.
[2023-06-28 21:05:02,308] [INFO] Query marker FASTA was written to GCA_015488785.1_ASM1548878v1_genomic.fna/markers.fasta
[2023-06-28 21:05:02,308] [INFO] Task started: Blastn
[2023-06-28 21:05:02,309] [INFO] Running command: blastn -query GCA_015488785.1_ASM1548878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ef3e176-de42-4a12-9a00-637c63ceaed8/dqc_reference/reference_markers.fasta -out GCA_015488785.1_ASM1548878v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:05:02,951] [INFO] Task succeeded: Blastn
[2023-06-28 21:05:02,962] [INFO] Selected 30 target genomes.
[2023-06-28 21:05:02,963] [INFO] Target genome list was writen to GCA_015488785.1_ASM1548878v1_genomic.fna/target_genomes.txt
[2023-06-28 21:05:02,971] [INFO] Task started: fastANI
[2023-06-28 21:05:02,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg07d800a4-0880-4762-a15c-d57ca98c8056/GCA_015488785.1_ASM1548878v1_genomic.fna.gz --refList GCA_015488785.1_ASM1548878v1_genomic.fna/target_genomes.txt --output GCA_015488785.1_ASM1548878v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:05:19,877] [INFO] Task succeeded: fastANI
[2023-06-28 21:05:19,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ef3e176-de42-4a12-9a00-637c63ceaed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:05:19,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ef3e176-de42-4a12-9a00-637c63ceaed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:05:19,884] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:05:19,884] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 21:05:19,884] [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
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.8415	52	940	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	75.4801	51	940	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	75.2025	51	940	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:05:19,886] [INFO] DFAST Taxonomy check result was written to GCA_015488785.1_ASM1548878v1_genomic.fna/tc_result.tsv
[2023-06-28 21:05:19,887] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:05:19,887] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:05:19,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ef3e176-de42-4a12-9a00-637c63ceaed8/dqc_reference/checkm_data
[2023-06-28 21:05:19,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:05:19,927] [INFO] Task started: CheckM
[2023-06-28 21:05:19,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015488785.1_ASM1548878v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015488785.1_ASM1548878v1_genomic.fna/checkm_input GCA_015488785.1_ASM1548878v1_genomic.fna/checkm_result
[2023-06-28 21:05:56,623] [INFO] Task succeeded: CheckM
[2023-06-28 21:05:56,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 20.83%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:05:56,662] [INFO] ===== Completeness check finished =====
[2023-06-28 21:05:56,662] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:05:56,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015488785.1_ASM1548878v1_genomic.fna/markers.fasta)
[2023-06-28 21:05:56,663] [INFO] Task started: Blastn
[2023-06-28 21:05:56,663] [INFO] Running command: blastn -query GCA_015488785.1_ASM1548878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ef3e176-de42-4a12-9a00-637c63ceaed8/dqc_reference/reference_markers_gtdb.fasta -out GCA_015488785.1_ASM1548878v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:05:57,624] [INFO] Task succeeded: Blastn
[2023-06-28 21:05:57,629] [INFO] Selected 26 target genomes.
[2023-06-28 21:05:57,629] [INFO] Target genome list was writen to GCA_015488785.1_ASM1548878v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:05:57,694] [INFO] Task started: fastANI
[2023-06-28 21:05:57,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg07d800a4-0880-4762-a15c-d57ca98c8056/GCA_015488785.1_ASM1548878v1_genomic.fna.gz --refList GCA_015488785.1_ASM1548878v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015488785.1_ASM1548878v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:06:10,565] [INFO] Task succeeded: fastANI
[2023-06-28 21:06:10,572] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:06:10,573] [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_015488785.1	s__S010-51 sp015488785	100.0	923	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__S010-51	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018401455.1	s__CECT-30217 sp018401455	76.3166	50	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__CECT-30217	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260195.1	s__Lutibacter citreus	75.8415	52	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:06:10,575] [INFO] GTDB search result was written to GCA_015488785.1_ASM1548878v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:06:10,575] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:06:10,578] [INFO] DFAST_QC result json was written to GCA_015488785.1_ASM1548878v1_genomic.fna/dqc_result.json
[2023-06-28 21:06:10,578] [INFO] DFAST_QC completed!
[2023-06-28 21:06:10,578] [INFO] Total running time: 0h1m20s