[2024-01-24 14:19:18,889] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:18,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:18,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg1eed2366-bcfa-4e6a-9dbd-07f28ba03e7b/dqc_reference
[2024-01-24 14:19:20,255] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:20,255] [INFO] Task started: Prodigal
[2024-01-24 14:19:20,256] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bcc8b62-1893-4a5e-9bb7-9936c7838cc1/GCF_000375405.1_ASM37540v1_genomic.fna.gz | prodigal -d GCF_000375405.1_ASM37540v1_genomic.fna/cds.fna -a GCF_000375405.1_ASM37540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:30,131] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:30,132] [INFO] Task started: HMMsearch
[2024-01-24 14:19:30,132] [INFO] Running command: hmmsearch --tblout GCF_000375405.1_ASM37540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1eed2366-bcfa-4e6a-9dbd-07f28ba03e7b/dqc_reference/reference_markers.hmm GCF_000375405.1_ASM37540v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:30,420] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:30,421] [INFO] Found 6/6 markers.
[2024-01-24 14:19:30,447] [INFO] Query marker FASTA was written to GCF_000375405.1_ASM37540v1_genomic.fna/markers.fasta
[2024-01-24 14:19:30,448] [INFO] Task started: Blastn
[2024-01-24 14:19:30,448] [INFO] Running command: blastn -query GCF_000375405.1_ASM37540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eed2366-bcfa-4e6a-9dbd-07f28ba03e7b/dqc_reference/reference_markers.fasta -out GCF_000375405.1_ASM37540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:31,067] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:31,070] [INFO] Selected 17 target genomes.
[2024-01-24 14:19:31,071] [INFO] Target genome list was writen to GCF_000375405.1_ASM37540v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:31,081] [INFO] Task started: fastANI
[2024-01-24 14:19:31,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bcc8b62-1893-4a5e-9bb7-9936c7838cc1/GCF_000375405.1_ASM37540v1_genomic.fna.gz --refList GCF_000375405.1_ASM37540v1_genomic.fna/target_genomes.txt --output GCF_000375405.1_ASM37540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:42,062] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:42,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1eed2366-bcfa-4e6a-9dbd-07f28ba03e7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:42,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1eed2366-bcfa-4e6a-9dbd-07f28ba03e7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:42,070] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:42,070] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:42,070] [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
Bacteroides propionicifaciens	strain=DSM 19291	GCA_000375405.1	392838	392838	type	True	100.0	834	840	95	conclusive
Bacteroides propionicifaciens	strain=JCM 14649	GCA_000613745.1	392838	392838	type	True	99.9676	816	840	95	conclusive
Bacteroides coprosuis	strain=DSM 18011	GCA_000212915.1	151276	151276	type	True	78.9509	206	840	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	76.9582	50	840	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	76.9566	50	840	95	below_threshold
Bacteroides luti	strain=DSM 26991	GCA_900128905.1	1297750	1297750	type	True	76.8619	55	840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:42,072] [INFO] DFAST Taxonomy check result was written to GCF_000375405.1_ASM37540v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:42,073] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:42,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:42,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1eed2366-bcfa-4e6a-9dbd-07f28ba03e7b/dqc_reference/checkm_data
[2024-01-24 14:19:42,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:42,108] [INFO] Task started: CheckM
[2024-01-24 14:19:42,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000375405.1_ASM37540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000375405.1_ASM37540v1_genomic.fna/checkm_input GCF_000375405.1_ASM37540v1_genomic.fna/checkm_result
[2024-01-24 14:20:16,027] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:16,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:16,045] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:16,046] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:16,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000375405.1_ASM37540v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:16,046] [INFO] Task started: Blastn
[2024-01-24 14:20:16,047] [INFO] Running command: blastn -query GCF_000375405.1_ASM37540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eed2366-bcfa-4e6a-9dbd-07f28ba03e7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000375405.1_ASM37540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:16,951] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:16,955] [INFO] Selected 27 target genomes.
[2024-01-24 14:20:16,955] [INFO] Target genome list was writen to GCF_000375405.1_ASM37540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:16,975] [INFO] Task started: fastANI
[2024-01-24 14:20:16,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bcc8b62-1893-4a5e-9bb7-9936c7838cc1/GCF_000375405.1_ASM37540v1_genomic.fna.gz --refList GCF_000375405.1_ASM37540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000375405.1_ASM37540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:32,477] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:32,487] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:32,487] [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_000375405.1	s__Bacteroides_E propionicifaciens	100.0	834	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides_E	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_000212915.1	s__Bacteroides_E coprosuis	78.9723	205	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001688725.2	s__Bacteroides caecimuris	76.872	50	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_900128905.1	s__Bacteroides_G luti	76.8619	55	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:32,489] [INFO] GTDB search result was written to GCF_000375405.1_ASM37540v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:32,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:32,493] [INFO] DFAST_QC result json was written to GCF_000375405.1_ASM37540v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:32,494] [INFO] DFAST_QC completed!
[2024-01-24 14:20:32,494] [INFO] Total running time: 0h1m14s