[2024-01-24 13:32:43,372] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:43,376] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:43,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg2103bac5-fc83-46e1-b24a-6530e1beb0ff/dqc_reference
[2024-01-24 13:32:44,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:44,824] [INFO] Task started: Prodigal
[2024-01-24 13:32:44,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg365638e1-a43a-40e2-935e-c0a41050f85c/GCF_000312445.1_ASM31244v1_genomic.fna.gz | prodigal -d GCF_000312445.1_ASM31244v1_genomic.fna/cds.fna -a GCF_000312445.1_ASM31244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:59,332] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:59,333] [INFO] Task started: HMMsearch
[2024-01-24 13:32:59,333] [INFO] Running command: hmmsearch --tblout GCF_000312445.1_ASM31244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2103bac5-fc83-46e1-b24a-6530e1beb0ff/dqc_reference/reference_markers.hmm GCF_000312445.1_ASM31244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:59,599] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:59,600] [INFO] Found 6/6 markers.
[2024-01-24 13:32:59,624] [INFO] Query marker FASTA was written to GCF_000312445.1_ASM31244v1_genomic.fna/markers.fasta
[2024-01-24 13:32:59,624] [INFO] Task started: Blastn
[2024-01-24 13:32:59,624] [INFO] Running command: blastn -query GCF_000312445.1_ASM31244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2103bac5-fc83-46e1-b24a-6530e1beb0ff/dqc_reference/reference_markers.fasta -out GCF_000312445.1_ASM31244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:00,301] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:00,303] [INFO] Selected 22 target genomes.
[2024-01-24 13:33:00,304] [INFO] Target genome list was writen to GCF_000312445.1_ASM31244v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:00,310] [INFO] Task started: fastANI
[2024-01-24 13:33:00,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg365638e1-a43a-40e2-935e-c0a41050f85c/GCF_000312445.1_ASM31244v1_genomic.fna.gz --refList GCF_000312445.1_ASM31244v1_genomic.fna/target_genomes.txt --output GCF_000312445.1_ASM31244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:16,410] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:16,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2103bac5-fc83-46e1-b24a-6530e1beb0ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:16,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2103bac5-fc83-46e1-b24a-6530e1beb0ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:16,416] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:16,416] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:16,416] [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
Phocaeicola abscessus	strain=CCUG 55929	GCA_000312445.1	555313	555313	type	True	100.0	839	840	95	conclusive
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	76.9982	50	840	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	76.8122	54	840	95	below_threshold
Phocaeicola sartorii	strain=JCM 17136	GCA_000614185.1	671267	671267	type	True	76.7195	57	840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:16,418] [INFO] DFAST Taxonomy check result was written to GCF_000312445.1_ASM31244v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:16,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:16,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:16,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2103bac5-fc83-46e1-b24a-6530e1beb0ff/dqc_reference/checkm_data
[2024-01-24 13:33:16,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:16,455] [INFO] Task started: CheckM
[2024-01-24 13:33:16,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000312445.1_ASM31244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000312445.1_ASM31244v1_genomic.fna/checkm_input GCF_000312445.1_ASM31244v1_genomic.fna/checkm_result
[2024-01-24 13:33:58,377] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:58,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:58,397] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:58,398] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:58,398] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000312445.1_ASM31244v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:58,398] [INFO] Task started: Blastn
[2024-01-24 13:33:58,399] [INFO] Running command: blastn -query GCF_000312445.1_ASM31244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2103bac5-fc83-46e1-b24a-6530e1beb0ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_000312445.1_ASM31244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:59,226] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:59,231] [INFO] Selected 25 target genomes.
[2024-01-24 13:33:59,231] [INFO] Target genome list was writen to GCF_000312445.1_ASM31244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:59,277] [INFO] Task started: fastANI
[2024-01-24 13:33:59,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg365638e1-a43a-40e2-935e-c0a41050f85c/GCF_000312445.1_ASM31244v1_genomic.fna.gz --refList GCF_000312445.1_ASM31244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000312445.1_ASM31244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:12,739] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:12,744] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:12,744] [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_000312445.1	s__Phocaeicola abscessus	100.0	839	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.49	99.45	0.95	0.95	3	conclusive
GCF_000614185.1	s__Phocaeicola sartorii	76.6644	56	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.95	98.44	0.85	0.76	7	-
GCA_900544675.1	s__Phocaeicola sp900544675	76.1883	52	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.98	99.96	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:12,746] [INFO] GTDB search result was written to GCF_000312445.1_ASM31244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:12,746] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:12,749] [INFO] DFAST_QC result json was written to GCF_000312445.1_ASM31244v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:12,749] [INFO] DFAST_QC completed!
[2024-01-24 13:34:12,749] [INFO] Total running time: 0h1m29s