[2023-06-08 08:43:32,951] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:43:32,957] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:43:32,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b07a0bf-5052-427b-be43-1f45184a81bb/dqc_reference
[2023-06-08 08:43:34,185] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:43:34,186] [INFO] Task started: Prodigal
[2023-06-08 08:43:34,187] [INFO] Running command: gunzip -c /var/lib/cwl/stgb45ebc6c-bfa4-4c2f-bc22-31aab3db86f0/GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:43:47,886] [INFO] Task succeeded: Prodigal
[2023-06-08 08:43:47,886] [INFO] Task started: HMMsearch
[2023-06-08 08:43:47,887] [INFO] Running command: hmmsearch --tblout GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b07a0bf-5052-427b-be43-1f45184a81bb/dqc_reference/reference_markers.hmm GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:43:48,109] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:43:48,110] [INFO] Found 6/6 markers.
[2023-06-08 08:43:48,137] [INFO] Query marker FASTA was written to GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 08:43:48,138] [INFO] Task started: Blastn
[2023-06-08 08:43:48,138] [INFO] Running command: blastn -query GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b07a0bf-5052-427b-be43-1f45184a81bb/dqc_reference/reference_markers.fasta -out GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:43:48,758] [INFO] Task succeeded: Blastn
[2023-06-08 08:43:48,769] [INFO] Selected 16 target genomes.
[2023-06-08 08:43:48,769] [INFO] Target genome list was writen to GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 08:43:48,771] [INFO] Task started: fastANI
[2023-06-08 08:43:48,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgb45ebc6c-bfa4-4c2f-bc22-31aab3db86f0/GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:43:56,461] [INFO] Task succeeded: fastANI
[2023-06-08 08:43:56,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b07a0bf-5052-427b-be43-1f45184a81bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:43:56,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b07a0bf-5052-427b-be43-1f45184a81bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:43:56,476] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:43:56,477] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:43:56,477] [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
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	77.9239	103	795	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	77.8015	137	795	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	77.6958	111	795	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	77.2052	93	795	95	below_threshold
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	77.1725	73	795	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	76.5747	78	795	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	75.9799	51	795	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	75.9493	52	795	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:43:56,479] [INFO] DFAST Taxonomy check result was written to GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 08:43:56,479] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:43:56,479] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:43:56,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b07a0bf-5052-427b-be43-1f45184a81bb/dqc_reference/checkm_data
[2023-06-08 08:43:56,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:43:56,511] [INFO] Task started: CheckM
[2023-06-08 08:43:56,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 08:44:39,224] [INFO] Task succeeded: CheckM
[2023-06-08 08:44:39,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.65%
Strain heterogeneity: 42.86%
--------------------------------------------------------------------------------
[2023-06-08 08:44:39,257] [INFO] ===== Completeness check finished =====
[2023-06-08 08:44:39,257] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:44:39,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 08:44:39,258] [INFO] Task started: Blastn
[2023-06-08 08:44:39,258] [INFO] Running command: blastn -query GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b07a0bf-5052-427b-be43-1f45184a81bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:44:40,135] [INFO] Task succeeded: Blastn
[2023-06-08 08:44:40,145] [INFO] Selected 16 target genomes.
[2023-06-08 08:44:40,145] [INFO] Target genome list was writen to GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:44:40,146] [INFO] Task started: fastANI
[2023-06-08 08:44:40,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgb45ebc6c-bfa4-4c2f-bc22-31aab3db86f0/GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:44:46,768] [INFO] Task succeeded: fastANI
[2023-06-08 08:44:46,785] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 08:44:46,785] [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_001689535.1	s__Paramuribaculum sp001689535	99.8476	695	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	98.63	98.52	0.86	0.84	5	conclusive
GCA_009775605.1	s__Paramuribaculum sp009775605	90.7668	567	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	99.73	99.73	0.91	0.91	2	-
GCA_003762715.1	s__Paramuribaculum sp001689565	78.142	97	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	98.89	98.71	0.85	0.83	3	-
GCA_900551515.1	s__Paramuribaculum sp900551515	77.9003	143	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014801655.1	s__Paramuribaculum sp014801655	77.7392	137	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	97.33	97.11	0.75	0.73	4	-
GCA_900759915.1	s__Paramuribaculum sp900759915	77.595	134	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	97.33	97.33	0.87	0.87	2	-
GCA_910586665.1	s__Duncaniella sp910586665	77.5541	111	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544535.1	s__Duncaniella sp900544535	77.4795	102	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910587185.1	s__Paramuribaculum sp910587185	77.4394	131	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	96.59	96.53	0.88	0.86	5	-
GCA_910586895.1	s__Paramuribaculum sp910586895	77.4228	135	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546365.1	s__Paramuribaculum sp900546365	77.4206	138	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586565.1	s__UBA7173 sp910586565	77.2924	126	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689445.1	s__M3 sp001689445	77.2675	113	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__M3	95.0	99.97	99.97	0.98	0.98	2	-
GCA_910586475.1	s__Paramuribaculum sp910586475	77.2406	79	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589095.1	s__Paramuribaculum sp910589095	77.1953	96	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587075.1	s__UBA7173 sp910587075	76.8508	112	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 08:44:46,787] [INFO] GTDB search result was written to GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 08:44:46,787] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:44:46,791] [INFO] DFAST_QC result json was written to GCA_947347375.1_SRR14698349_bin.4_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 08:44:46,791] [INFO] DFAST_QC completed!
[2023-06-08 08:44:46,791] [INFO] Total running time: 0h1m14s