[2023-06-08 16:16:11,734] [INFO] DFAST_QC pipeline started.
[2023-06-08 16:16:11,737] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 16:16:11,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d57218b-00f0-49d4-93ee-3892e917b375/dqc_reference
[2023-06-08 16:16:12,977] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 16:16:12,977] [INFO] Task started: Prodigal
[2023-06-08 16:16:12,978] [INFO] Running command: gunzip -c /var/lib/cwl/stg3baa7608-66f6-4339-bfbf-d94a87bd78cb/GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 16:16:22,905] [INFO] Task succeeded: Prodigal
[2023-06-08 16:16:22,905] [INFO] Task started: HMMsearch
[2023-06-08 16:16:22,906] [INFO] Running command: hmmsearch --tblout GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d57218b-00f0-49d4-93ee-3892e917b375/dqc_reference/reference_markers.hmm GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 16:16:23,171] [INFO] Task succeeded: HMMsearch
[2023-06-08 16:16:23,173] [INFO] Found 6/6 markers.
[2023-06-08 16:16:23,210] [INFO] Query marker FASTA was written to GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 16:16:23,211] [INFO] Task started: Blastn
[2023-06-08 16:16:23,211] [INFO] Running command: blastn -query GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d57218b-00f0-49d4-93ee-3892e917b375/dqc_reference/reference_markers.fasta -out GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:16:23,867] [INFO] Task succeeded: Blastn
[2023-06-08 16:16:23,872] [INFO] Selected 15 target genomes.
[2023-06-08 16:16:23,873] [INFO] Target genome list was writen to GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 16:16:23,874] [INFO] Task started: fastANI
[2023-06-08 16:16:23,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg3baa7608-66f6-4339-bfbf-d94a87bd78cb/GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 16:16:32,211] [INFO] Task succeeded: fastANI
[2023-06-08 16:16:32,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d57218b-00f0-49d4-93ee-3892e917b375/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 16:16:32,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d57218b-00f0-49d4-93ee-3892e917b375/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 16:16:32,222] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 16:16:32,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 16:16:32,222] [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
Hallerella succinigenes	strain=UWS3	GCA_002797675.1	1896222	1896222	type	True	82.2487	241	1196	95	below_threshold
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000146505.1	834	833	type	True	81.0563	446	1196	95	below_threshold
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000024665.1	834	833	type	True	81.0534	448	1196	95	below_threshold
Hallerella porci	strain=UWS4	GCA_003148885.1	1945871	1945871	type	True	80.3437	106	1196	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 16:16:32,224] [INFO] DFAST Taxonomy check result was written to GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 16:16:32,225] [INFO] ===== Taxonomy check completed =====
[2023-06-08 16:16:32,225] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 16:16:32,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d57218b-00f0-49d4-93ee-3892e917b375/dqc_reference/checkm_data
[2023-06-08 16:16:32,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 16:16:32,267] [INFO] Task started: CheckM
[2023-06-08 16:16:32,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 16:17:06,072] [INFO] Task succeeded: CheckM
[2023-06-08 16:17:06,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 16:17:06,094] [INFO] ===== Completeness check finished =====
[2023-06-08 16:17:06,095] [INFO] ===== Start GTDB Search =====
[2023-06-08 16:17:06,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 16:17:06,095] [INFO] Task started: Blastn
[2023-06-08 16:17:06,096] [INFO] Running command: blastn -query GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d57218b-00f0-49d4-93ee-3892e917b375/dqc_reference/reference_markers_gtdb.fasta -out GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:17:07,164] [INFO] Task succeeded: Blastn
[2023-06-08 16:17:07,169] [INFO] Selected 14 target genomes.
[2023-06-08 16:17:07,169] [INFO] Target genome list was writen to GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 16:17:07,174] [INFO] Task started: fastANI
[2023-06-08 16:17:07,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg3baa7608-66f6-4339-bfbf-d94a87bd78cb/GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 16:17:17,566] [INFO] Task succeeded: fastANI
[2023-06-08 16:17:17,581] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 16:17:17,581] [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_900142475.1	s__Fibrobacter sp900142475	95.0194	887	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	95.25	95.07	0.84	0.80	4	conclusive
GCA_001603905.1	s__Fibrobacter sp001603905	91.7038	786	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.67	95.34	0.91	0.84	3	-
GCA_902756345.1	s__Fibrobacter sp900142495	86.3909	696	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	98.15	97.22	0.91	0.83	8	-
GCF_900177705.1	s__Fibrobacter sp900177705	86.1912	692	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	99.87	99.82	0.99	0.99	3	-
GCF_002210295.1	s__Fibrobacter sp002210295	85.5402	680	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142545.1	s__Fibrobacter sp900142545	85.0133	676	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017526585.1	s__Fibrobacter sp017526585	84.9471	588	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761355.1	s__Fibrobacter succinogenes_M	84.5615	600	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799745.1	s__Fibrobacter succinogenes_Q	84.5173	616	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017530965.1	s__Fibrobacter sp017530965	84.1242	575	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143055.1	s__Fibrobacter sp900143055	83.7486	556	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	96.51	95.61	0.84	0.74	8	-
GCA_016295375.1	s__Fibrobacter sp016295375	83.353	359	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550445.1	s__Fibrobacter sp017550445	82.9831	573	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017615055.1	s__Fibrobacter sp017615055	80.1571	399	1196	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 16:17:17,584] [INFO] GTDB search result was written to GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 16:17:17,584] [INFO] ===== GTDB Search completed =====
[2023-06-08 16:17:17,588] [INFO] DFAST_QC result json was written to GCA_945487085.1_SRR7188236_bin.34_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 16:17:17,588] [INFO] DFAST_QC completed!
[2023-06-08 16:17:17,588] [INFO] Total running time: 0h1m6s