[2023-06-19 06:19:46,947] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:19:46,949] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:19:46,949] [INFO] DQC Reference Directory: /var/lib/cwl/stg6103f884-c8bc-447e-bfbb-58574c6a387c/dqc_reference
[2023-06-19 06:19:48,307] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:19:48,308] [INFO] Task started: Prodigal
[2023-06-19 06:19:48,308] [INFO] Running command: gunzip -c /var/lib/cwl/stgd497c9a4-72ec-47db-b32c-bddb6301455d/GCA_018004735.1_ASM1800473v1_genomic.fna.gz | prodigal -d GCA_018004735.1_ASM1800473v1_genomic.fna/cds.fna -a GCA_018004735.1_ASM1800473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:19:52,443] [INFO] Task succeeded: Prodigal
[2023-06-19 06:19:52,443] [INFO] Task started: HMMsearch
[2023-06-19 06:19:52,443] [INFO] Running command: hmmsearch --tblout GCA_018004735.1_ASM1800473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6103f884-c8bc-447e-bfbb-58574c6a387c/dqc_reference/reference_markers.hmm GCA_018004735.1_ASM1800473v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:19:52,619] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:19:52,621] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgd497c9a4-72ec-47db-b32c-bddb6301455d/GCA_018004735.1_ASM1800473v1_genomic.fna.gz]
[2023-06-19 06:19:52,640] [INFO] Query marker FASTA was written to GCA_018004735.1_ASM1800473v1_genomic.fna/markers.fasta
[2023-06-19 06:19:52,640] [INFO] Task started: Blastn
[2023-06-19 06:19:52,640] [INFO] Running command: blastn -query GCA_018004735.1_ASM1800473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6103f884-c8bc-447e-bfbb-58574c6a387c/dqc_reference/reference_markers.fasta -out GCA_018004735.1_ASM1800473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:19:53,196] [INFO] Task succeeded: Blastn
[2023-06-19 06:19:53,201] [INFO] Selected 6 target genomes.
[2023-06-19 06:19:53,201] [INFO] Target genome list was writen to GCA_018004735.1_ASM1800473v1_genomic.fna/target_genomes.txt
[2023-06-19 06:19:53,203] [INFO] Task started: fastANI
[2023-06-19 06:19:53,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgd497c9a4-72ec-47db-b32c-bddb6301455d/GCA_018004735.1_ASM1800473v1_genomic.fna.gz --refList GCA_018004735.1_ASM1800473v1_genomic.fna/target_genomes.txt --output GCA_018004735.1_ASM1800473v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:19:55,931] [INFO] Task succeeded: fastANI
[2023-06-19 06:19:55,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6103f884-c8bc-447e-bfbb-58574c6a387c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:19:55,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6103f884-c8bc-447e-bfbb-58574c6a387c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:19:55,940] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 06:19:55,941] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 06:19:55,941] [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
Prevotella paludivivens	strain=DSM 17968	GCA_000373185.1	185294	185294	type	True	87.2195	166	239	95	below_threshold
Prevotella paludivivens	strain=JCM 13650	GCA_000613605.1	185294	185294	type	True	87.1705	169	239	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	86.3313	168	239	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 06:19:55,943] [INFO] DFAST Taxonomy check result was written to GCA_018004735.1_ASM1800473v1_genomic.fna/tc_result.tsv
[2023-06-19 06:19:55,944] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:19:55,944] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:19:55,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6103f884-c8bc-447e-bfbb-58574c6a387c/dqc_reference/checkm_data
[2023-06-19 06:19:55,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:19:55,964] [INFO] Task started: CheckM
[2023-06-19 06:19:55,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018004735.1_ASM1800473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018004735.1_ASM1800473v1_genomic.fna/checkm_input GCA_018004735.1_ASM1800473v1_genomic.fna/checkm_result
[2023-06-19 06:20:15,555] [INFO] Task succeeded: CheckM
[2023-06-19 06:20:15,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 06:20:15,585] [INFO] ===== Completeness check finished =====
[2023-06-19 06:20:15,585] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:20:15,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018004735.1_ASM1800473v1_genomic.fna/markers.fasta)
[2023-06-19 06:20:15,586] [INFO] Task started: Blastn
[2023-06-19 06:20:15,586] [INFO] Running command: blastn -query GCA_018004735.1_ASM1800473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6103f884-c8bc-447e-bfbb-58574c6a387c/dqc_reference/reference_markers_gtdb.fasta -out GCA_018004735.1_ASM1800473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:20:16,120] [INFO] Task succeeded: Blastn
[2023-06-19 06:20:16,127] [INFO] Selected 6 target genomes.
[2023-06-19 06:20:16,127] [INFO] Target genome list was writen to GCA_018004735.1_ASM1800473v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:20:16,131] [INFO] Task started: fastANI
[2023-06-19 06:20:16,131] [INFO] Running command: fastANI --query /var/lib/cwl/stgd497c9a4-72ec-47db-b32c-bddb6301455d/GCA_018004735.1_ASM1800473v1_genomic.fna.gz --refList GCA_018004735.1_ASM1800473v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018004735.1_ASM1800473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:20:19,169] [INFO] Task succeeded: fastANI
[2023-06-19 06:20:19,180] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:20:19,180] [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_018054505.1	s__Prevotella sp018054505	97.7197	150	239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.05	98.05	0.52	0.52	2	conclusive
GCA_018053665.1	s__Prevotella sp018053665	88.6981	157	239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.38	99.32	0.87	0.85	3	-
GCF_000373185.1	s__Prevotella paludivivens	87.2195	166	239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.98	0.99	0.99	2	-
GCF_017347605.1	s__Prevotella sp017347605	86.3313	168	239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:20:19,182] [INFO] GTDB search result was written to GCA_018004735.1_ASM1800473v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:20:19,183] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:20:19,185] [INFO] DFAST_QC result json was written to GCA_018004735.1_ASM1800473v1_genomic.fna/dqc_result.json
[2023-06-19 06:20:19,185] [INFO] DFAST_QC completed!
[2023-06-19 06:20:19,185] [INFO] Total running time: 0h0m32s