[2023-06-13 03:34:38,138] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:34:38,143] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:34:38,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg271a95e8-ed33-4480-aeb0-82b8ad9649c7/dqc_reference
[2023-06-13 03:34:39,416] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:34:39,417] [INFO] Task started: Prodigal
[2023-06-13 03:34:39,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg15c1cdff-9091-45b3-a32f-1d1a719faf67/GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:34:55,476] [INFO] Task succeeded: Prodigal
[2023-06-13 03:34:55,477] [INFO] Task started: HMMsearch
[2023-06-13 03:34:55,477] [INFO] Running command: hmmsearch --tblout GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg271a95e8-ed33-4480-aeb0-82b8ad9649c7/dqc_reference/reference_markers.hmm GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:34:55,759] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:34:55,760] [INFO] Found 6/6 markers.
[2023-06-13 03:34:55,788] [INFO] Query marker FASTA was written to GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 03:34:55,788] [INFO] Task started: Blastn
[2023-06-13 03:34:55,789] [INFO] Running command: blastn -query GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg271a95e8-ed33-4480-aeb0-82b8ad9649c7/dqc_reference/reference_markers.fasta -out GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:34:56,424] [INFO] Task succeeded: Blastn
[2023-06-13 03:34:56,432] [INFO] Selected 24 target genomes.
[2023-06-13 03:34:56,432] [INFO] Target genome list was writen to GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 03:34:56,438] [INFO] Task started: fastANI
[2023-06-13 03:34:56,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg15c1cdff-9091-45b3-a32f-1d1a719faf67/GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:35:11,825] [INFO] Task succeeded: fastANI
[2023-06-13 03:35:11,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg271a95e8-ed33-4480-aeb0-82b8ad9649c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:35:11,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg271a95e8-ed33-4480-aeb0-82b8ad9649c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:35:11,837] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 03:35:11,837] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 03:35:11,838] [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
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	81.5411	72	926	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	80.847	70	926	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	80.7779	67	926	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	80.5965	72	926	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	78.9164	52	926	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 03:35:11,839] [INFO] DFAST Taxonomy check result was written to GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 03:35:11,840] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:35:11,840] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:35:11,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg271a95e8-ed33-4480-aeb0-82b8ad9649c7/dqc_reference/checkm_data
[2023-06-13 03:35:11,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:35:11,878] [INFO] Task started: CheckM
[2023-06-13 03:35:11,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 03:35:59,065] [INFO] Task succeeded: CheckM
[2023-06-13 03:35:59,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:35:59,085] [INFO] ===== Completeness check finished =====
[2023-06-13 03:35:59,085] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:35:59,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 03:35:59,086] [INFO] Task started: Blastn
[2023-06-13 03:35:59,086] [INFO] Running command: blastn -query GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg271a95e8-ed33-4480-aeb0-82b8ad9649c7/dqc_reference/reference_markers_gtdb.fasta -out GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:35:59,876] [INFO] Task succeeded: Blastn
[2023-06-13 03:35:59,881] [INFO] Selected 16 target genomes.
[2023-06-13 03:35:59,881] [INFO] Target genome list was writen to GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:35:59,889] [INFO] Task started: fastANI
[2023-06-13 03:35:59,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg15c1cdff-9091-45b3-a32f-1d1a719faf67/GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:36:08,311] [INFO] Task succeeded: fastANI
[2023-06-13 03:36:08,338] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 03:36:08,338] [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_003833075.1	s__CAG-485 sp002362485	99.1311	843	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.88	97.97	0.89	0.83	18	conclusive
GCA_910585285.1	s__CAG-485 sp910585285	79.5891	375	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584055.1	s__CAG-485 sp910584055	79.1626	371	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579845.1	s__CAG-485 sp910579845	78.7755	145	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578075.1	s__CAG-485 sp910578075	78.6656	274	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802175.1	s__CAG-485 sp014802175	78.5751	174	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.58	97.46	0.67	0.65	3	-
GCA_910573745.1	s__CAG-485 sp002361215	78.379	87	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.35	98.98	0.93	0.87	9	-
GCA_900549375.1	s__CAG-485 sp900549375	78.2993	167	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	96.66	96.66	0.84	0.84	2	-
GCA_009775355.1	s__CAG-485 sp009775355	77.6735	122	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.73	98.73	0.89	0.89	2	-
GCA_014867205.1	s__CAG-485 sp014867205	77.3351	93	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578385.1	s__CAG-485 sp910578385	77.277	114	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585275.1	s__CAG-485 sp910585275	76.9709	106	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014801585.1	s__CAG-485 sp014801585	76.8021	55	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.82	97.82	0.79	0.79	2	-
GCA_002361155.1	s__CAG-485 sp002361155	76.7374	60	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.36	98.51	0.82	0.74	7	-
GCA_910589425.1	s__CAG-485 sp910589425	76.2869	66	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554845.1	s__CAG-485 sp900554845	75.9417	53	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.47	97.47	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-13 03:36:08,340] [INFO] GTDB search result was written to GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 03:36:08,341] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:36:08,344] [INFO] DFAST_QC result json was written to GCA_947039335.1_ERR8099102_bin.11_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 03:36:08,345] [INFO] DFAST_QC completed!
[2023-06-13 03:36:08,345] [INFO] Total running time: 0h1m30s