[2024-01-24 13:57:13,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgf87138ab-d42f-4abc-8c5a-a1680771020c/dqc_reference
[2024-01-24 13:57:15,005] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:15,006] [INFO] Task started: Prodigal
[2024-01-24 13:57:15,006] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f614d23-a54d-455c-b482-dc272aa5de33/GCF_000698925.1_ASM69892v1_genomic.fna.gz | prodigal -d GCF_000698925.1_ASM69892v1_genomic.fna/cds.fna -a GCF_000698925.1_ASM69892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:34,809] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:34,810] [INFO] Task started: HMMsearch
[2024-01-24 13:57:34,810] [INFO] Running command: hmmsearch --tblout GCF_000698925.1_ASM69892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf87138ab-d42f-4abc-8c5a-a1680771020c/dqc_reference/reference_markers.hmm GCF_000698925.1_ASM69892v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:35,068] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:35,069] [INFO] Found 6/6 markers.
[2024-01-24 13:57:35,099] [INFO] Query marker FASTA was written to GCF_000698925.1_ASM69892v1_genomic.fna/markers.fasta
[2024-01-24 13:57:35,100] [INFO] Task started: Blastn
[2024-01-24 13:57:35,100] [INFO] Running command: blastn -query GCF_000698925.1_ASM69892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf87138ab-d42f-4abc-8c5a-a1680771020c/dqc_reference/reference_markers.fasta -out GCF_000698925.1_ASM69892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:35,671] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:35,674] [INFO] Selected 12 target genomes.
[2024-01-24 13:57:35,675] [INFO] Target genome list was writen to GCF_000698925.1_ASM69892v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:35,679] [INFO] Task started: fastANI
[2024-01-24 13:57:35,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f614d23-a54d-455c-b482-dc272aa5de33/GCF_000698925.1_ASM69892v1_genomic.fna.gz --refList GCF_000698925.1_ASM69892v1_genomic.fna/target_genomes.txt --output GCF_000698925.1_ASM69892v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:44,662] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:44,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf87138ab-d42f-4abc-8c5a-a1680771020c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:44,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf87138ab-d42f-4abc-8c5a-a1680771020c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:44,670] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:57:44,670] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:44,670] [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 loescheii	strain=ATCC 15930	GCA_000698925.1	840	840	type	True	100.0	1129	1132	95	conclusive
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	99.9747	1130	1132	95	conclusive
Prevotella loescheii	strain=JCM 12249	GCA_000613485.1	840	840	type	True	99.9426	1111	1132	95	conclusive
Prevotella shahii	strain=JCM 12083	GCA_000613445.1	228603	228603	type	True	81.9339	694	1132	95	below_threshold
Prevotella shahii	strain=DSM 15611	GCA_003201715.1	228603	228603	type	True	81.8894	722	1132	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.9929	105	1132	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.352	71	1132	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:44,672] [INFO] DFAST Taxonomy check result was written to GCF_000698925.1_ASM69892v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:44,672] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:44,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:44,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf87138ab-d42f-4abc-8c5a-a1680771020c/dqc_reference/checkm_data
[2024-01-24 13:57:44,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:44,708] [INFO] Task started: CheckM
[2024-01-24 13:57:44,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000698925.1_ASM69892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000698925.1_ASM69892v1_genomic.fna/checkm_input GCF_000698925.1_ASM69892v1_genomic.fna/checkm_result
[2024-01-24 13:58:42,547] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:42,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:42,566] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:42,567] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:42,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000698925.1_ASM69892v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:42,568] [INFO] Task started: Blastn
[2024-01-24 13:58:42,568] [INFO] Running command: blastn -query GCF_000698925.1_ASM69892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf87138ab-d42f-4abc-8c5a-a1680771020c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000698925.1_ASM69892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:43,506] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:43,510] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:43,510] [INFO] Target genome list was writen to GCF_000698925.1_ASM69892v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:43,527] [INFO] Task started: fastANI
[2024-01-24 13:58:43,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f614d23-a54d-455c-b482-dc272aa5de33/GCF_000698925.1_ASM69892v1_genomic.fna.gz --refList GCF_000698925.1_ASM69892v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000698925.1_ASM69892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:51,567] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:51,576] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:51,576] [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_000378085.1	s__Prevotella loescheii	99.9747	1130	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.09	95.73	0.96	0.93	5	conclusive
GCF_000312305.1	s__Prevotella conceptionensis	85.7875	871	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.86	95.59	0.91	0.86	4	-
GCF_000613445.1	s__Prevotella shahii	81.9098	697	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.54	98.05	0.93	0.90	5	-
GCA_905373605.1	s__Prevotella sp905373605	81.6652	561	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018127805.1	s__Prevotella sp018127805	80.824	234	1132	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	78.1234	101	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCF_016899955.1	s__Prevotella sp900540415	76.4828	65	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.08	0.94	0.91	6	-
GCF_000235885.1	s__Prevotella stercorea	76.3763	70	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	-
GCA_017474515.1	s__Prevotella sp017474515	76.1411	54	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315095.1	s__Prevotella sp900315095	75.9107	63	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.59	96.16	0.90	0.86	18	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:51,580] [INFO] GTDB search result was written to GCF_000698925.1_ASM69892v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:51,581] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:51,585] [INFO] DFAST_QC result json was written to GCF_000698925.1_ASM69892v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:51,585] [INFO] DFAST_QC completed!
[2024-01-24 13:58:51,586] [INFO] Total running time: 0h1m38s