[2024-01-24 12:14:34,128] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,131] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c97af2f-0f14-449a-943e-4e60d4dfc53f/dqc_reference
[2024-01-24 12:14:35,351] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,351] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,352] [INFO] Running command: gunzip -c /var/lib/cwl/stga9037cb9-a4b2-44db-81ff-d0a7226ecbc1/GCF_024054555.1_ASM2405455v1_genomic.fna.gz | prodigal -d GCF_024054555.1_ASM2405455v1_genomic.fna/cds.fna -a GCF_024054555.1_ASM2405455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:48,239] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:48,239] [INFO] Task started: HMMsearch
[2024-01-24 12:14:48,239] [INFO] Running command: hmmsearch --tblout GCF_024054555.1_ASM2405455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c97af2f-0f14-449a-943e-4e60d4dfc53f/dqc_reference/reference_markers.hmm GCF_024054555.1_ASM2405455v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:48,546] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:48,547] [INFO] Found 6/6 markers.
[2024-01-24 12:14:48,571] [INFO] Query marker FASTA was written to GCF_024054555.1_ASM2405455v1_genomic.fna/markers.fasta
[2024-01-24 12:14:48,572] [INFO] Task started: Blastn
[2024-01-24 12:14:48,572] [INFO] Running command: blastn -query GCF_024054555.1_ASM2405455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c97af2f-0f14-449a-943e-4e60d4dfc53f/dqc_reference/reference_markers.fasta -out GCF_024054555.1_ASM2405455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:49,154] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:49,157] [INFO] Selected 22 target genomes.
[2024-01-24 12:14:49,157] [INFO] Target genome list was writen to GCF_024054555.1_ASM2405455v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:49,166] [INFO] Task started: fastANI
[2024-01-24 12:14:49,166] [INFO] Running command: fastANI --query /var/lib/cwl/stga9037cb9-a4b2-44db-81ff-d0a7226ecbc1/GCF_024054555.1_ASM2405455v1_genomic.fna.gz --refList GCF_024054555.1_ASM2405455v1_genomic.fna/target_genomes.txt --output GCF_024054555.1_ASM2405455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:01,159] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:01,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c97af2f-0f14-449a-943e-4e60d4dfc53f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:01,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c97af2f-0f14-449a-943e-4e60d4dfc53f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:01,166] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:01,166] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:01,166] [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 cerevisiae	strain=DSM 100619	GCA_024054555.1	2053716	2053716	type	True	100.0	1032	1037	95	conclusive
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.1642	68	1037	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.0912	51	1037	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.0873	70	1037	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.44	58	1037	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.3869	62	1037	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:01,167] [INFO] DFAST Taxonomy check result was written to GCF_024054555.1_ASM2405455v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:01,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:01,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:01,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c97af2f-0f14-449a-943e-4e60d4dfc53f/dqc_reference/checkm_data
[2024-01-24 12:15:01,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:01,202] [INFO] Task started: CheckM
[2024-01-24 12:15:01,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024054555.1_ASM2405455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024054555.1_ASM2405455v1_genomic.fna/checkm_input GCF_024054555.1_ASM2405455v1_genomic.fna/checkm_result
[2024-01-24 12:15:41,899] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:41,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,925] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:41,926] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:41,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024054555.1_ASM2405455v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:41,927] [INFO] Task started: Blastn
[2024-01-24 12:15:41,927] [INFO] Running command: blastn -query GCF_024054555.1_ASM2405455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c97af2f-0f14-449a-943e-4e60d4dfc53f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024054555.1_ASM2405455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:42,734] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:42,736] [INFO] Selected 29 target genomes.
[2024-01-24 12:15:42,737] [INFO] Target genome list was writen to GCF_024054555.1_ASM2405455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:42,754] [INFO] Task started: fastANI
[2024-01-24 12:15:42,754] [INFO] Running command: fastANI --query /var/lib/cwl/stga9037cb9-a4b2-44db-81ff-d0a7226ecbc1/GCF_024054555.1_ASM2405455v1_genomic.fna.gz --refList GCF_024054555.1_ASM2405455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024054555.1_ASM2405455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:56,706] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:56,712] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:15:56,712] [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_002409785.1	s__Prevotella sp002409785	79.7952	379	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.35	99.13	0.87	0.82	3	-
GCF_000426565.1	s__Prevotella albensis	77.0846	71	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000424185.1	s__Prevotella sp000424185	76.6602	69	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004535825.1	s__Prevotella hominis	76.3949	63	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.52	95.16	0.76	0.66	13	-
GCA_902775075.1	s__Prevotella sp902775075	76.3263	58	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316015.1	s__Prevotella sp900316015	76.3016	65	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.19	98.89	0.88	0.75	5	-
GCA_900317685.1	s__Prevotella sp900317685	76.2205	51	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.13	96.10	0.84	0.76	12	-
GCA_002353825.1	s__Prevotella sp002353825	75.9554	53	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.40	98.85	0.91	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:56,715] [INFO] GTDB search result was written to GCF_024054555.1_ASM2405455v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:56,715] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:56,718] [INFO] DFAST_QC result json was written to GCF_024054555.1_ASM2405455v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:56,718] [INFO] DFAST_QC completed!
[2024-01-24 12:15:56,718] [INFO] Total running time: 0h1m23s