[2023-06-08 08:35:21,337] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:35:21,342] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:35:21,342] [INFO] DQC Reference Directory: /var/lib/cwl/stg28e1c097-0800-4c61-8cf6-e4b481f90aa8/dqc_reference
[2023-06-08 08:35:23,619] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:35:23,620] [INFO] Task started: Prodigal
[2023-06-08 08:35:23,621] [INFO] Running command: gunzip -c /var/lib/cwl/stgd107b9d2-7176-40f5-ad14-a6c529b648fd/GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:35:26,162] [INFO] Task succeeded: Prodigal
[2023-06-08 08:35:26,163] [INFO] Task started: HMMsearch
[2023-06-08 08:35:26,163] [INFO] Running command: hmmsearch --tblout GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28e1c097-0800-4c61-8cf6-e4b481f90aa8/dqc_reference/reference_markers.hmm GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:35:26,386] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:35:26,393] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd107b9d2-7176-40f5-ad14-a6c529b648fd/GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 08:35:26,416] [INFO] Query marker FASTA was written to GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 08:35:26,417] [INFO] Task started: Blastn
[2023-06-08 08:35:26,417] [INFO] Running command: blastn -query GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg28e1c097-0800-4c61-8cf6-e4b481f90aa8/dqc_reference/reference_markers.fasta -out GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:35:27,696] [INFO] Task succeeded: Blastn
[2023-06-08 08:35:27,700] [INFO] Selected 18 target genomes.
[2023-06-08 08:35:27,701] [INFO] Target genome list was writen to GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 08:35:27,715] [INFO] Task started: fastANI
[2023-06-08 08:35:27,716] [INFO] Running command: fastANI --query /var/lib/cwl/stgd107b9d2-7176-40f5-ad14-a6c529b648fd/GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:35:38,048] [INFO] Task succeeded: fastANI
[2023-06-08 08:35:38,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28e1c097-0800-4c61-8cf6-e4b481f90aa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:35:38,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28e1c097-0800-4c61-8cf6-e4b481f90aa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:35:38,054] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:35:38,054] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:35:38,054] [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
Ruminococcus bromii	strain=ATCC 27255	GCA_002834225.1	40518	40518	suspected-type	True	78.9706	129	306	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:35:38,059] [INFO] DFAST Taxonomy check result was written to GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 08:35:38,065] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:35:38,065] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:35:38,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28e1c097-0800-4c61-8cf6-e4b481f90aa8/dqc_reference/checkm_data
[2023-06-08 08:35:38,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:35:38,095] [INFO] Task started: CheckM
[2023-06-08 08:35:38,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 08:35:56,042] [INFO] Task succeeded: CheckM
[2023-06-08 08:35:56,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 08:35:56,066] [INFO] ===== Completeness check finished =====
[2023-06-08 08:35:56,067] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:35:56,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 08:35:56,067] [INFO] Task started: Blastn
[2023-06-08 08:35:56,068] [INFO] Running command: blastn -query GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg28e1c097-0800-4c61-8cf6-e4b481f90aa8/dqc_reference/reference_markers_gtdb.fasta -out GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:35:56,851] [INFO] Task succeeded: Blastn
[2023-06-08 08:35:56,856] [INFO] Selected 13 target genomes.
[2023-06-08 08:35:56,856] [INFO] Target genome list was writen to GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:35:56,865] [INFO] Task started: fastANI
[2023-06-08 08:35:56,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgd107b9d2-7176-40f5-ad14-a6c529b648fd/GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:36:01,460] [INFO] Task succeeded: fastANI
[2023-06-08 08:36:01,476] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 08:36:01,476] [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_003521625.1	s__Ruminococcus_E sp003521625	81.9138	212	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002491825.1	s__Ruminococcus_E sp002491825	81.6964	152	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766885.1	s__Ruminococcus_E sp902766885	81.3072	208	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215855.1	s__Ruminococcus_E sp905215855	79.239	121	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.72	97.72	0.86	0.84	4	-
GCF_002834225.1	s__Ruminococcus_E bromii	78.9706	129	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.59	98.08	0.94	0.90	6	-
GCF_002834235.1	s__Ruminococcus_E bromii_B	78.9571	133	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.64	96.93	0.86	0.80	74	-
GCA_900543095.1	s__Ruminococcus_E sp900543095	78.3004	97	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.93	99.93	0.91	0.91	2	-
GCA_902771755.1	s__Ruminococcus_E sp902771755	78.1331	109	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002493635.1	s__Ruminococcus_E sp002493635	78.1008	101	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.92	97.46	0.88	0.85	4	-
GCF_900101355.1	s__Ruminococcus_E bromii_A	78.0965	106	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.01	98.16	0.84	0.65	5	-
GCF_003438075.1	s__Ruminococcus_E sp003438075	78.0632	113	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.49	97.62	0.94	0.88	5	-
GCA_900315085.1	s__Ruminococcus_E sp900315085	77.5396	69	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.46	97.96	0.77	0.69	11	-
GCA_900315195.1	s__Ruminococcus_E sp900315195	77.0651	63	306	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.59	99.19	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-08 08:36:01,479] [INFO] GTDB search result was written to GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 08:36:01,479] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:36:01,484] [INFO] DFAST_QC result json was written to GCA_945875355.1_ERR1855545_bin.50_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 08:36:01,485] [INFO] DFAST_QC completed!
[2023-06-08 08:36:01,485] [INFO] Total running time: 0h0m40s