[2023-06-05 18:59:43,219] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:59:43,221] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:59:43,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg214a5a3e-64c5-4f22-8423-f8583332209e/dqc_reference
[2023-06-05 18:59:44,446] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:59:44,446] [INFO] Task started: Prodigal
[2023-06-05 18:59:44,447] [INFO] Running command: gunzip -c /var/lib/cwl/stg5411389e-5381-4093-936b-23be2358c47f/GCA_004559095.1_ASM455909v1_genomic.fna.gz | prodigal -d GCA_004559095.1_ASM455909v1_genomic.fna/cds.fna -a GCA_004559095.1_ASM455909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:59:56,918] [INFO] Task succeeded: Prodigal
[2023-06-05 18:59:56,919] [INFO] Task started: HMMsearch
[2023-06-05 18:59:56,919] [INFO] Running command: hmmsearch --tblout GCA_004559095.1_ASM455909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg214a5a3e-64c5-4f22-8423-f8583332209e/dqc_reference/reference_markers.hmm GCA_004559095.1_ASM455909v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:59:57,118] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:59:57,120] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg5411389e-5381-4093-936b-23be2358c47f/GCA_004559095.1_ASM455909v1_genomic.fna.gz]
[2023-06-05 18:59:57,146] [INFO] Query marker FASTA was written to GCA_004559095.1_ASM455909v1_genomic.fna/markers.fasta
[2023-06-05 18:59:57,146] [INFO] Task started: Blastn
[2023-06-05 18:59:57,146] [INFO] Running command: blastn -query GCA_004559095.1_ASM455909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg214a5a3e-64c5-4f22-8423-f8583332209e/dqc_reference/reference_markers.fasta -out GCA_004559095.1_ASM455909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:59:57,661] [INFO] Task succeeded: Blastn
[2023-06-05 18:59:57,666] [INFO] Selected 9 target genomes.
[2023-06-05 18:59:57,666] [INFO] Target genome list was writen to GCA_004559095.1_ASM455909v1_genomic.fna/target_genomes.txt
[2023-06-05 18:59:57,671] [INFO] Task started: fastANI
[2023-06-05 18:59:57,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg5411389e-5381-4093-936b-23be2358c47f/GCA_004559095.1_ASM455909v1_genomic.fna.gz --refList GCA_004559095.1_ASM455909v1_genomic.fna/target_genomes.txt --output GCA_004559095.1_ASM455909v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:00:02,214] [INFO] Task succeeded: fastANI
[2023-06-05 19:00:02,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg214a5a3e-64c5-4f22-8423-f8583332209e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:00:02,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg214a5a3e-64c5-4f22-8423-f8583332209e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:00:02,222] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 19:00:02,223] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 19:00:02,223] [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 hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	79.3771	61	615	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.9113	51	615	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 19:00:02,225] [INFO] DFAST Taxonomy check result was written to GCA_004559095.1_ASM455909v1_genomic.fna/tc_result.tsv
[2023-06-05 19:00:02,226] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:00:02,226] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:00:02,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg214a5a3e-64c5-4f22-8423-f8583332209e/dqc_reference/checkm_data
[2023-06-05 19:00:02,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:00:02,256] [INFO] Task started: CheckM
[2023-06-05 19:00:02,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004559095.1_ASM455909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004559095.1_ASM455909v1_genomic.fna/checkm_input GCA_004559095.1_ASM455909v1_genomic.fna/checkm_result
[2023-06-05 19:00:42,813] [INFO] Task succeeded: CheckM
[2023-06-05 19:00:42,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 19:00:42,832] [INFO] ===== Completeness check finished =====
[2023-06-05 19:00:42,833] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:00:42,833] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004559095.1_ASM455909v1_genomic.fna/markers.fasta)
[2023-06-05 19:00:42,834] [INFO] Task started: Blastn
[2023-06-05 19:00:42,834] [INFO] Running command: blastn -query GCA_004559095.1_ASM455909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg214a5a3e-64c5-4f22-8423-f8583332209e/dqc_reference/reference_markers_gtdb.fasta -out GCA_004559095.1_ASM455909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:00:43,336] [INFO] Task succeeded: Blastn
[2023-06-05 19:00:43,339] [INFO] Selected 9 target genomes.
[2023-06-05 19:00:43,340] [INFO] Target genome list was writen to GCA_004559095.1_ASM455909v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:00:43,350] [INFO] Task started: fastANI
[2023-06-05 19:00:43,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg5411389e-5381-4093-936b-23be2358c47f/GCA_004559095.1_ASM455909v1_genomic.fna.gz --refList GCA_004559095.1_ASM455909v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004559095.1_ASM455909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:00:48,305] [INFO] Task succeeded: fastANI
[2023-06-05 19:00:48,321] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 19:00:48,322] [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
GCF_002251295.1	s__Prevotella sp002251295	98.7955	439	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.86	97.35	0.91	0.81	14	conclusive
GCA_016291595.1	s__Prevotella sp016291595	77.8982	59	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017474925.1	s__Prevotella sp017474925	77.8766	52	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.19	98.19	0.77	0.77	2	-
GCA_902799655.1	s__Prevotella sp902799655	77.2545	80	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554105.1	s__Prevotella sp017554105	76.9975	55	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000184945.1	s__Prevotella buccae	76.9113	51	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCA_900315075.1	s__Prevotella sp900315075	76.6489	50	615	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.41	0.92	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-05 19:00:48,324] [INFO] GTDB search result was written to GCA_004559095.1_ASM455909v1_genomic.fna/result_gtdb.tsv
[2023-06-05 19:00:48,325] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:00:48,330] [INFO] DFAST_QC result json was written to GCA_004559095.1_ASM455909v1_genomic.fna/dqc_result.json
[2023-06-05 19:00:48,330] [INFO] DFAST_QC completed!
[2023-06-05 19:00:48,330] [INFO] Total running time: 0h1m5s