[2023-06-08 06:51:56,264] [INFO] DFAST_QC pipeline started.
[2023-06-08 06:51:56,268] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 06:51:56,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fc4333b-68c2-4051-ab2b-d356662a34a9/dqc_reference
[2023-06-08 06:51:57,774] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 06:51:57,775] [INFO] Task started: Prodigal
[2023-06-08 06:51:57,776] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe17b718-fbf4-4e63-85fd-591249db7737/GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 06:52:13,329] [INFO] Task succeeded: Prodigal
[2023-06-08 06:52:13,330] [INFO] Task started: HMMsearch
[2023-06-08 06:52:13,330] [INFO] Running command: hmmsearch --tblout GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fc4333b-68c2-4051-ab2b-d356662a34a9/dqc_reference/reference_markers.hmm GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 06:52:13,583] [INFO] Task succeeded: HMMsearch
[2023-06-08 06:52:13,586] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbe17b718-fbf4-4e63-85fd-591249db7737/GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 06:52:13,617] [INFO] Query marker FASTA was written to GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 06:52:13,618] [INFO] Task started: Blastn
[2023-06-08 06:52:13,618] [INFO] Running command: blastn -query GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fc4333b-68c2-4051-ab2b-d356662a34a9/dqc_reference/reference_markers.fasta -out GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:52:14,121] [INFO] Task succeeded: Blastn
[2023-06-08 06:52:14,125] [INFO] Selected 18 target genomes.
[2023-06-08 06:52:14,126] [INFO] Target genome list was writen to GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 06:52:14,127] [INFO] Task started: fastANI
[2023-06-08 06:52:14,127] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe17b718-fbf4-4e63-85fd-591249db7737/GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 06:52:23,133] [INFO] Task succeeded: fastANI
[2023-06-08 06:52:23,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fc4333b-68c2-4051-ab2b-d356662a34a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 06:52:23,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fc4333b-68c2-4051-ab2b-d356662a34a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 06:52:23,144] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 06:52:23,144] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 06:52:23,144] [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
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.3921	96	839	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.0415	55	839	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	75.9166	68	839	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 06:52:23,147] [INFO] DFAST Taxonomy check result was written to GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 06:52:23,147] [INFO] ===== Taxonomy check completed =====
[2023-06-08 06:52:23,147] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 06:52:23,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fc4333b-68c2-4051-ab2b-d356662a34a9/dqc_reference/checkm_data
[2023-06-08 06:52:23,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 06:52:23,193] [INFO] Task started: CheckM
[2023-06-08 06:52:23,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 06:53:10,722] [INFO] Task succeeded: CheckM
[2023-06-08 06:53:10,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 06:53:10,746] [INFO] ===== Completeness check finished =====
[2023-06-08 06:53:10,746] [INFO] ===== Start GTDB Search =====
[2023-06-08 06:53:10,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 06:53:10,747] [INFO] Task started: Blastn
[2023-06-08 06:53:10,747] [INFO] Running command: blastn -query GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fc4333b-68c2-4051-ab2b-d356662a34a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:53:11,216] [INFO] Task succeeded: Blastn
[2023-06-08 06:53:11,221] [INFO] Selected 15 target genomes.
[2023-06-08 06:53:11,221] [INFO] Target genome list was writen to GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 06:53:11,225] [INFO] Task started: fastANI
[2023-06-08 06:53:11,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe17b718-fbf4-4e63-85fd-591249db7737/GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 06:53:19,886] [INFO] Task succeeded: fastANI
[2023-06-08 06:53:19,902] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 06:53:19,902] [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_017402445.1	s__Prevotella sp017402445	98.2573	541	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002353205.1	s__Prevotella sp002353205	87.1079	532	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.92	99.92	0.98	0.98	2	-
GCA_017474515.1	s__Prevotella sp017474515	77.9114	257	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002392835.1	s__Prevotella sp002392835	77.7475	156	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.57	97.57	0.74	0.74	2	-
GCA_902790625.1	s__Prevotella sp902790625	77.6841	204	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.16	96.49	0.84	0.82	3	-
GCA_900314655.1	s__Prevotella sp900314655	77.5348	183	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	95.82	0.85	0.71	9	-
GCA_017483805.1	s__Prevotella sp017483805	77.5321	157	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394385.1	s__Prevotella sp002394385	77.3795	158	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.06	0.88	0.86	9	-
GCA_002395135.1	s__Prevotella sp002395135	77.1088	175	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.98	98.98	0.83	0.83	2	-
GCA_017459445.1	s__Prevotella sp017459445	77.0292	108	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792855.1	s__Prevotella sp902792855	76.9056	129	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.67	98.62	0.88	0.82	4	-
GCA_902765585.1	s__Prevotella sp902765585	76.7395	130	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016284895.1	s__Prevotella sp016284895	76.715	111	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017561825.1	s__Prevotella sp017561825	76.692	132	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 06:53:19,904] [INFO] GTDB search result was written to GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 06:53:19,904] [INFO] ===== GTDB Search completed =====
[2023-06-08 06:53:19,908] [INFO] DFAST_QC result json was written to GCA_947166085.1_SRR8387714_bin.63_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 06:53:19,908] [INFO] DFAST_QC completed!
[2023-06-08 06:53:19,908] [INFO] Total running time: 0h1m24s