[2023-06-13 11:49:44,772] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:49:44,774] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:49:44,775] [INFO] DQC Reference Directory: /var/lib/cwl/stgc432aa34-e649-43ec-a703-2e648eb23470/dqc_reference
[2023-06-13 11:49:47,199] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:49:47,200] [INFO] Task started: Prodigal
[2023-06-13 11:49:47,200] [INFO] Running command: gunzip -c /var/lib/cwl/stg06f03021-62ff-420b-8b19-52ca4b27b86c/GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:50:00,362] [INFO] Task succeeded: Prodigal
[2023-06-13 11:50:00,363] [INFO] Task started: HMMsearch
[2023-06-13 11:50:00,363] [INFO] Running command: hmmsearch --tblout GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc432aa34-e649-43ec-a703-2e648eb23470/dqc_reference/reference_markers.hmm GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:50:00,596] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:50:00,598] [INFO] Found 6/6 markers.
[2023-06-13 11:50:00,622] [INFO] Query marker FASTA was written to GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 11:50:00,623] [INFO] Task started: Blastn
[2023-06-13 11:50:00,623] [INFO] Running command: blastn -query GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc432aa34-e649-43ec-a703-2e648eb23470/dqc_reference/reference_markers.fasta -out GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:50:01,216] [INFO] Task succeeded: Blastn
[2023-06-13 11:50:01,220] [INFO] Selected 25 target genomes.
[2023-06-13 11:50:01,221] [INFO] Target genome list was writen to GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 11:50:01,226] [INFO] Task started: fastANI
[2023-06-13 11:50:01,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg06f03021-62ff-420b-8b19-52ca4b27b86c/GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:50:15,977] [INFO] Task succeeded: fastANI
[2023-06-13 11:50:15,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc432aa34-e649-43ec-a703-2e648eb23470/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:50:15,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc432aa34-e649-43ec-a703-2e648eb23470/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:50:15,988] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:50:15,988] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 11:50:15,988] [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
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	78.7506	62	707	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	78.6432	67	707	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	78.0844	80	707	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	77.8962	55	707	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	77.8328	100	707	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	76.9319	72	707	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:50:15,990] [INFO] DFAST Taxonomy check result was written to GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 11:50:15,991] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:50:15,991] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:50:15,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc432aa34-e649-43ec-a703-2e648eb23470/dqc_reference/checkm_data
[2023-06-13 11:50:15,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:50:16,035] [INFO] Task started: CheckM
[2023-06-13 11:50:16,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 11:50:57,086] [INFO] Task succeeded: CheckM
[2023-06-13 11:50:57,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:50:57,109] [INFO] ===== Completeness check finished =====
[2023-06-13 11:50:57,109] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:50:57,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 11:50:57,110] [INFO] Task started: Blastn
[2023-06-13 11:50:57,110] [INFO] Running command: blastn -query GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc432aa34-e649-43ec-a703-2e648eb23470/dqc_reference/reference_markers_gtdb.fasta -out GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:50:57,989] [INFO] Task succeeded: Blastn
[2023-06-13 11:50:57,994] [INFO] Selected 20 target genomes.
[2023-06-13 11:50:57,995] [INFO] Target genome list was writen to GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:50:58,000] [INFO] Task started: fastANI
[2023-06-13 11:50:58,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg06f03021-62ff-420b-8b19-52ca4b27b86c/GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:51:05,438] [INFO] Task succeeded: fastANI
[2023-06-13 11:51:05,455] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:51:05,455] [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_011959405.1	s__UBA3263 sp001689615	99.0512	463	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	99.21	99.09	0.70	0.66	12	conclusive
GCA_009775265.1	s__CAG-873 sp009775265	82.1229	90	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.34	99.23	0.92	0.92	3	-
GCF_003024805.1	s__Duncaniella muris	77.8328	100	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.34	97.90	0.87	0.80	17	-
GCA_002490725.1	s__UBA3263 sp002490725	77.7425	109	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	99.93	99.92	0.89	0.85	3	-
GCA_014802435.1	s__UBA3263 sp014802435	77.7204	68	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	97.99	97.67	0.88	0.83	9	-
GCA_900759865.1	s__UBA3263 sp900759865	77.6361	107	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001701225.1	s__Duncaniella sp001701225	77.3415	72	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.71	98.22	0.91	0.86	3	-
GCA_014801955.1	s__UBA3263 sp014801955	77.199	93	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	97.82	97.69	0.84	0.82	6	-
GCA_905193485.1	s__Paramuribaculum sp905193485	77.0114	59	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802015.1	s__Duncaniella sp014802015	76.7523	69	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689535.1	s__Paramuribaculum sp001689535	76.749	70	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	98.63	98.52	0.86	0.84	5	-
GCA_014800605.1	s__UBA7173 sp014800605	76.6999	52	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689495.1	s__Duncaniella sp001689495	76.5293	85	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	99.23	99.23	0.93	0.93	2	-
GCA_910588795.1	s__Duncaniella sp910588795	76.5287	52	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	96.60	96.60	0.87	0.87	2	-
GCA_900759915.1	s__Paramuribaculum sp900759915	76.4578	68	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	97.33	97.33	0.87	0.87	2	-
GCA_910586975.1	s__CAG-873 sp910586975	76.3705	62	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:51:05,457] [INFO] GTDB search result was written to GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 11:51:05,458] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:51:05,461] [INFO] DFAST_QC result json was written to GCA_947073445.1_SRR12464018_bin.14_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 11:51:05,461] [INFO] DFAST_QC completed!
[2023-06-13 11:51:05,461] [INFO] Total running time: 0h1m21s