[2023-06-29 23:15:55,328] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:15:55,333] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:15:55,333] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ba5bf51-a9e5-4e4c-a00a-28c05545bfc9/dqc_reference
[2023-06-29 23:15:56,524] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:15:56,525] [INFO] Task started: Prodigal
[2023-06-29 23:15:56,525] [INFO] Running command: gunzip -c /var/lib/cwl/stg828ec45a-6b5b-4af2-9e20-943ecbb22de7/GCA_016296405.1_ASM1629640v1_genomic.fna.gz | prodigal -d GCA_016296405.1_ASM1629640v1_genomic.fna/cds.fna -a GCA_016296405.1_ASM1629640v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:16:08,339] [INFO] Task succeeded: Prodigal
[2023-06-29 23:16:08,339] [INFO] Task started: HMMsearch
[2023-06-29 23:16:08,339] [INFO] Running command: hmmsearch --tblout GCA_016296405.1_ASM1629640v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ba5bf51-a9e5-4e4c-a00a-28c05545bfc9/dqc_reference/reference_markers.hmm GCA_016296405.1_ASM1629640v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:16:08,603] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:16:08,604] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg828ec45a-6b5b-4af2-9e20-943ecbb22de7/GCA_016296405.1_ASM1629640v1_genomic.fna.gz]
[2023-06-29 23:16:08,633] [INFO] Query marker FASTA was written to GCA_016296405.1_ASM1629640v1_genomic.fna/markers.fasta
[2023-06-29 23:16:08,634] [INFO] Task started: Blastn
[2023-06-29 23:16:08,634] [INFO] Running command: blastn -query GCA_016296405.1_ASM1629640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ba5bf51-a9e5-4e4c-a00a-28c05545bfc9/dqc_reference/reference_markers.fasta -out GCA_016296405.1_ASM1629640v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:16:09,303] [INFO] Task succeeded: Blastn
[2023-06-29 23:16:09,307] [INFO] Selected 23 target genomes.
[2023-06-29 23:16:09,308] [INFO] Target genome list was writen to GCA_016296405.1_ASM1629640v1_genomic.fna/target_genomes.txt
[2023-06-29 23:16:09,313] [INFO] Task started: fastANI
[2023-06-29 23:16:09,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg828ec45a-6b5b-4af2-9e20-943ecbb22de7/GCA_016296405.1_ASM1629640v1_genomic.fna.gz --refList GCA_016296405.1_ASM1629640v1_genomic.fna/target_genomes.txt --output GCA_016296405.1_ASM1629640v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:16:20,348] [INFO] Task succeeded: fastANI
[2023-06-29 23:16:20,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ba5bf51-a9e5-4e4c-a00a-28c05545bfc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:16:20,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ba5bf51-a9e5-4e4c-a00a-28c05545bfc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:16:20,355] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:16:20,356] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:16:20,356] [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 copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.9337	69	646	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.8976	70	646	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.7175	58	646	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.622	67	646	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:16:20,393] [INFO] DFAST Taxonomy check result was written to GCA_016296405.1_ASM1629640v1_genomic.fna/tc_result.tsv
[2023-06-29 23:16:20,393] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:16:20,394] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:16:20,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ba5bf51-a9e5-4e4c-a00a-28c05545bfc9/dqc_reference/checkm_data
[2023-06-29 23:16:20,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:16:20,429] [INFO] Task started: CheckM
[2023-06-29 23:16:20,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016296405.1_ASM1629640v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016296405.1_ASM1629640v1_genomic.fna/checkm_input GCA_016296405.1_ASM1629640v1_genomic.fna/checkm_result
[2023-06-29 23:16:59,698] [INFO] Task succeeded: CheckM
[2023-06-29 23:16:59,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:16:59,720] [INFO] ===== Completeness check finished =====
[2023-06-29 23:16:59,720] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:16:59,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016296405.1_ASM1629640v1_genomic.fna/markers.fasta)
[2023-06-29 23:16:59,721] [INFO] Task started: Blastn
[2023-06-29 23:16:59,721] [INFO] Running command: blastn -query GCA_016296405.1_ASM1629640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ba5bf51-a9e5-4e4c-a00a-28c05545bfc9/dqc_reference/reference_markers_gtdb.fasta -out GCA_016296405.1_ASM1629640v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:17:00,544] [INFO] Task succeeded: Blastn
[2023-06-29 23:17:00,549] [INFO] Selected 14 target genomes.
[2023-06-29 23:17:00,550] [INFO] Target genome list was writen to GCA_016296405.1_ASM1629640v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:17:00,561] [INFO] Task started: fastANI
[2023-06-29 23:17:00,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg828ec45a-6b5b-4af2-9e20-943ecbb22de7/GCA_016296405.1_ASM1629640v1_genomic.fna.gz --refList GCA_016296405.1_ASM1629640v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016296405.1_ASM1629640v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:17:08,370] [INFO] Task succeeded: fastANI
[2023-06-29 23:17:08,381] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:17:08,381] [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_900548195.1	s__Prevotella sp900548195	96.7096	524	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.71	95.27	0.80	0.75	7	conclusive
GCA_900552965.1	s__Prevotella sp900552965	89.5002	377	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.78	99.78	0.83	0.83	2	-
GCA_002317355.1	s__Prevotella sp002317355	78.5703	152	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798615.1	s__Prevotella sp902798615	78.4124	140	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.97	96.95	0.86	0.84	3	-
GCA_900769275.1	s__Prevotella sp900769275	78.3628	193	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801155.1	s__Prevotella sp902801155	78.0799	119	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.39	96.09	0.81	0.73	3	-
GCA_900315105.1	s__Prevotella sp900315105	78.0092	147	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.64	97.28	0.95	0.91	3	-
GCA_902801425.1	s__Prevotella sp902801425	77.8176	148	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.51	0.78	0.78	3	-
GCA_017478025.1	s__Prevotella sp017478025	77.1892	54	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.24	95.24	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-06-29 23:17:08,383] [INFO] GTDB search result was written to GCA_016296405.1_ASM1629640v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:17:08,384] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:17:08,387] [INFO] DFAST_QC result json was written to GCA_016296405.1_ASM1629640v1_genomic.fna/dqc_result.json
[2023-06-29 23:17:08,388] [INFO] DFAST_QC completed!
[2023-06-29 23:17:08,388] [INFO] Total running time: 0h1m13s