[2023-06-08 09:53:38,446] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:53:38,448] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:53:38,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg6af09bea-24c0-465e-8601-796e4380eefb/dqc_reference
[2023-06-08 09:53:41,944] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:53:41,947] [INFO] Task started: Prodigal
[2023-06-08 09:53:41,948] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b5b5590-1220-4169-b82c-0b99ebae9a0a/GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:53:55,229] [INFO] Task succeeded: Prodigal
[2023-06-08 09:53:55,229] [INFO] Task started: HMMsearch
[2023-06-08 09:53:55,229] [INFO] Running command: hmmsearch --tblout GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6af09bea-24c0-465e-8601-796e4380eefb/dqc_reference/reference_markers.hmm GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:53:55,531] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:53:55,533] [INFO] Found 6/6 markers.
[2023-06-08 09:53:55,573] [INFO] Query marker FASTA was written to GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:53:55,573] [INFO] Task started: Blastn
[2023-06-08 09:53:55,574] [INFO] Running command: blastn -query GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6af09bea-24c0-465e-8601-796e4380eefb/dqc_reference/reference_markers.fasta -out GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:53:56,296] [INFO] Task succeeded: Blastn
[2023-06-08 09:53:56,300] [INFO] Selected 26 target genomes.
[2023-06-08 09:53:56,301] [INFO] Target genome list was writen to GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:53:56,304] [INFO] Task started: fastANI
[2023-06-08 09:53:56,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b5b5590-1220-4169-b82c-0b99ebae9a0a/GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:54:12,169] [INFO] Task succeeded: fastANI
[2023-06-08 09:54:12,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6af09bea-24c0-465e-8601-796e4380eefb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:54:12,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6af09bea-24c0-465e-8601-796e4380eefb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:54:12,184] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:54:12,184] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 09:54:12,184] [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_001688845.2	1796646	1796646	type	True	76.9074	68	801	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	76.9074	68	801	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	76.8543	87	801	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	76.8474	68	801	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	76.7993	57	801	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.2231	64	801	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 09:54:12,187] [INFO] DFAST Taxonomy check result was written to GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:54:12,187] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:54:12,187] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:54:12,188] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6af09bea-24c0-465e-8601-796e4380eefb/dqc_reference/checkm_data
[2023-06-08 09:54:12,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:54:12,217] [INFO] Task started: CheckM
[2023-06-08 09:54:12,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:54:53,306] [INFO] Task succeeded: CheckM
[2023-06-08 09:54:53,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:54:53,344] [INFO] ===== Completeness check finished =====
[2023-06-08 09:54:53,344] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:54:53,344] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:54:53,345] [INFO] Task started: Blastn
[2023-06-08 09:54:53,345] [INFO] Running command: blastn -query GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6af09bea-24c0-465e-8601-796e4380eefb/dqc_reference/reference_markers_gtdb.fasta -out GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:54:54,139] [INFO] Task succeeded: Blastn
[2023-06-08 09:54:54,144] [INFO] Selected 23 target genomes.
[2023-06-08 09:54:54,144] [INFO] Target genome list was writen to GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:54:54,155] [INFO] Task started: fastANI
[2023-06-08 09:54:54,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b5b5590-1220-4169-b82c-0b99ebae9a0a/GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:55:04,910] [INFO] Task succeeded: fastANI
[2023-06-08 09:55:04,931] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:55:04,931] [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_910587235.1	s__CAG-873 sp910587235	99.3348	745	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900548975.1	s__CAG-873 sp900548975	77.8322	142	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.98	99.96	0.94	0.89	3	-
GCA_910589055.1	s__CAG-873 sp910589055	77.5649	149	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584905.1	s__CAG-873 sp910584905	77.468	123	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579035.1	s__CAG-873 sp011959565	77.451	110	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.99	96.96	0.89	0.75	5	-
GCA_905193995.1	s__CAG-873 sp905193995	77.3316	57	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002493945.1	s__CAG-873 sp002493945	77.269	127	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.61	97.51	0.95	0.88	8	-
GCA_910583525.1	s__CAG-873 sp910583525	77.2069	142	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578035.1	s__CAG-873 sp910578035	77.1712	116	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009775125.1	s__CAG-873 sp001689665	77.1468	92	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.51	97.14	0.87	0.85	3	-
GCA_014800735.1	s__CAG-873 sp014800735	77.1001	104	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.24	97.04	0.84	0.82	3	-
GCA_910587915.1	s__CAG-873 sp910587915	76.9	117	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905202215.1	s__CAG-873 sp905202215	76.8746	133	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.54	98.54	0.91	0.91	2	-
GCA_014801485.1	s__CAG-873 sp014801485	76.7611	61	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017620635.1	s__CAG-873 sp017620635	76.7459	90	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004552485.1	s__CAG-873 sp004552485	76.7343	87	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.38	99.38	0.89	0.89	2	-
GCA_002491245.1	s__CAG-873 sp002491245	76.7062	77	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.67	97.75	0.93	0.87	9	-
GCA_900551515.1	s__Paramuribaculum sp900551515	76.6781	56	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578095.1	s__CAG-873 sp910578095	76.5385	100	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.96	99.96	0.98	0.98	2	-
GCA_910584365.1	s__UBA7173 sp910584365	76.4829	75	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004102805.1	s__UBA7173 sp004102805	76.4703	65	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	98.86	98.86	0.92	0.89	3	-
GCA_900759865.1	s__UBA3263 sp900759865	76.2318	53	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA3263	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003762875.1	s__Duncaniella sp001689575	76.1959	67	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	97.25	96.19	0.92	0.80	7	-
--------------------------------------------------------------------------------
[2023-06-08 09:55:04,933] [INFO] GTDB search result was written to GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:55:04,933] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:55:04,937] [INFO] DFAST_QC result json was written to GCA_947643855.1_SRR17794294_bin.99_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:55:04,937] [INFO] DFAST_QC completed!
[2023-06-08 09:55:04,938] [INFO] Total running time: 0h1m26s