[2023-06-07 18:15:32,128] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:15:32,131] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:15:32,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg75e192f4-33df-453c-bb0a-1da217acfd21/dqc_reference
[2023-06-07 18:15:33,355] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:15:33,356] [INFO] Task started: Prodigal
[2023-06-07 18:15:33,356] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb7e1bc8-042e-40fd-b346-ebb08d1fd7d8/GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:15:44,274] [INFO] Task succeeded: Prodigal
[2023-06-07 18:15:44,274] [INFO] Task started: HMMsearch
[2023-06-07 18:15:44,274] [INFO] Running command: hmmsearch --tblout GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75e192f4-33df-453c-bb0a-1da217acfd21/dqc_reference/reference_markers.hmm GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:15:44,513] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:15:44,514] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdb7e1bc8-042e-40fd-b346-ebb08d1fd7d8/GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-07 18:15:44,544] [INFO] Query marker FASTA was written to GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 18:15:44,544] [INFO] Task started: Blastn
[2023-06-07 18:15:44,545] [INFO] Running command: blastn -query GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg75e192f4-33df-453c-bb0a-1da217acfd21/dqc_reference/reference_markers.fasta -out GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:15:45,121] [INFO] Task succeeded: Blastn
[2023-06-07 18:15:45,126] [INFO] Selected 25 target genomes.
[2023-06-07 18:15:45,126] [INFO] Target genome list was writen to GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 18:15:45,128] [INFO] Task started: fastANI
[2023-06-07 18:15:45,128] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7e1bc8-042e-40fd-b346-ebb08d1fd7d8/GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:15:58,611] [INFO] Task succeeded: fastANI
[2023-06-07 18:15:58,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75e192f4-33df-453c-bb0a-1da217acfd21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:15:58,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75e192f4-33df-453c-bb0a-1da217acfd21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:15:58,618] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:15:58,618] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 18:15:58,618] [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 lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.5293	64	635	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.2007	72	635	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	75.9794	80	635	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	75.9147	62	635	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 18:15:58,620] [INFO] DFAST Taxonomy check result was written to GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 18:15:58,620] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:15:58,621] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:15:58,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75e192f4-33df-453c-bb0a-1da217acfd21/dqc_reference/checkm_data
[2023-06-07 18:15:58,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:15:58,649] [INFO] Task started: CheckM
[2023-06-07 18:15:58,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 18:16:33,805] [INFO] Task succeeded: CheckM
[2023-06-07 18:16:33,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 18:16:33,833] [INFO] ===== Completeness check finished =====
[2023-06-07 18:16:33,833] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:16:33,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 18:16:33,834] [INFO] Task started: Blastn
[2023-06-07 18:16:33,834] [INFO] Running command: blastn -query GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg75e192f4-33df-453c-bb0a-1da217acfd21/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:16:34,554] [INFO] Task succeeded: Blastn
[2023-06-07 18:16:34,559] [INFO] Selected 22 target genomes.
[2023-06-07 18:16:34,559] [INFO] Target genome list was writen to GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:16:34,565] [INFO] Task started: fastANI
[2023-06-07 18:16:34,565] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7e1bc8-042e-40fd-b346-ebb08d1fd7d8/GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:16:45,352] [INFO] Task succeeded: fastANI
[2023-06-07 18:16:45,368] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 18:16:45,368] [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_900315545.1	s__Prevotella sp900315545	98.688	589	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.56	97.68	0.91	0.82	8	conclusive
GCA_017627765.1	s__Prevotella sp017627765	78.3109	184	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.91	97.91	0.89	0.89	2	-
GCA_900315095.1	s__Prevotella sp900315095	76.8437	67	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.59	96.16	0.90	0.86	18	-
GCA_905216025.1	s__Prevotella sp905216025	76.4744	66	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.83	95.83	0.83	0.83	2	-
GCA_902776685.1	s__Prevotella sp902776685	76.445	63	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017940185.1	s__Prevotella sp017940185	76.3483	66	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549175.1	s__Prevotella sp900549175	76.1071	61	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.84	99.84	0.89	0.89	2	-
GCA_900317305.1	s__Prevotella sp900317305	76.0634	62	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	97.82	0.87	0.83	11	-
GCA_900313615.1	s__Prevotella sp900313615	76.0214	56	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.60	97.61	0.83	0.73	6	-
GCA_905234355.1	s__Prevotella sp905234355	75.9784	55	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 18:16:45,370] [INFO] GTDB search result was written to GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 18:16:45,371] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:16:45,374] [INFO] DFAST_QC result json was written to GCA_947166375.1_SRR8387716_bin.97_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 18:16:45,374] [INFO] DFAST_QC completed!
[2023-06-07 18:16:45,374] [INFO] Total running time: 0h1m13s