[2023-06-14 01:00:04,977] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:00:04,982] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:00:04,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg91079de0-e5e4-4da4-aa34-e5b61c7b2219/dqc_reference
[2023-06-14 01:00:06,844] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:00:06,845] [INFO] Task started: Prodigal
[2023-06-14 01:00:06,846] [INFO] Running command: gunzip -c /var/lib/cwl/stg0df50484-752a-49bc-bddb-b3019117ddbd/GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:00:13,017] [INFO] Task succeeded: Prodigal
[2023-06-14 01:00:13,017] [INFO] Task started: HMMsearch
[2023-06-14 01:00:13,017] [INFO] Running command: hmmsearch --tblout GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91079de0-e5e4-4da4-aa34-e5b61c7b2219/dqc_reference/reference_markers.hmm GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:00:13,245] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:00:13,247] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0df50484-752a-49bc-bddb-b3019117ddbd/GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-14 01:00:13,279] [INFO] Query marker FASTA was written to GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-14 01:00:13,279] [INFO] Task started: Blastn
[2023-06-14 01:00:13,279] [INFO] Running command: blastn -query GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg91079de0-e5e4-4da4-aa34-e5b61c7b2219/dqc_reference/reference_markers.fasta -out GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:00:13,865] [INFO] Task succeeded: Blastn
[2023-06-14 01:00:13,869] [INFO] Selected 18 target genomes.
[2023-06-14 01:00:13,869] [INFO] Target genome list was writen to GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-14 01:00:13,875] [INFO] Task started: fastANI
[2023-06-14 01:00:13,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg0df50484-752a-49bc-bddb-b3019117ddbd/GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:00:26,948] [INFO] Task succeeded: fastANI
[2023-06-14 01:00:26,949] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91079de0-e5e4-4da4-aa34-e5b61c7b2219/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:00:26,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91079de0-e5e4-4da4-aa34-e5b61c7b2219/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:00:26,959] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:00:26,959] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 01:00:26,959] [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
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.0311	51	717	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	75.9334	54	717	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	75.8684	51	717	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	75.7476	53	717	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:00:26,961] [INFO] DFAST Taxonomy check result was written to GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-14 01:00:26,961] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:00:26,961] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:00:26,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91079de0-e5e4-4da4-aa34-e5b61c7b2219/dqc_reference/checkm_data
[2023-06-14 01:00:26,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:00:26,997] [INFO] Task started: CheckM
[2023-06-14 01:00:26,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-14 01:00:52,559] [INFO] Task succeeded: CheckM
[2023-06-14 01:00:52,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:00:52,583] [INFO] ===== Completeness check finished =====
[2023-06-14 01:00:52,584] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:00:52,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-14 01:00:52,584] [INFO] Task started: Blastn
[2023-06-14 01:00:52,585] [INFO] Running command: blastn -query GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg91079de0-e5e4-4da4-aa34-e5b61c7b2219/dqc_reference/reference_markers_gtdb.fasta -out GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:00:53,369] [INFO] Task succeeded: Blastn
[2023-06-14 01:00:53,374] [INFO] Selected 23 target genomes.
[2023-06-14 01:00:53,374] [INFO] Target genome list was writen to GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:00:53,419] [INFO] Task started: fastANI
[2023-06-14 01:00:53,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg0df50484-752a-49bc-bddb-b3019117ddbd/GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:01:08,252] [INFO] Task succeeded: fastANI
[2023-06-14 01:01:08,267] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:01:08,267] [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_910575255.1	s__Ventrimonas sp910575255	99.3062	626	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.31	99.12	0.89	0.88	4	conclusive
GCA_910586025.1	s__CAG-95 sp910586025	85.3827	52	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588875.1	s__Ventrimonas sp910588875	82.472	317	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669055.1	s__Ventrimonas sp003669055	80.0747	308	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910586255.1	s__Ventrimonas sp910586255	80.0499	309	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003611875.1	s__Ventrimonas sp003611875	78.9555	261	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.50	99.24	0.91	0.86	4	-
GCA_910586205.1	s__Ventrimonas sp910586205	78.6936	239	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009911065.1	s__Ventrimonas sp009911065	77.6738	177	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	95.78	95.73	0.75	0.73	3	-
GCA_018715565.1	s__Ventrimonas merdavium	77.211	101	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCA_910577655.1	s__Ventrimonas sp910577655	77.1924	120	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540335.1	s__Ventrimonas sp900540335	76.6697	95	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.37	99.36	0.86	0.81	3	-
GCA_004554205.1	s__Ventrimonas sp004554205	76.6387	63	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900538475.1	s__Ventrimonas sp900538475	76.4217	91	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.39	99.20	0.94	0.93	3	-
GCA_018715905.1	s__Caccovicinus merdipullorum	76.0401	52	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	98.94	98.69	0.87	0.79	3	-
GCF_000158075.1	s__Enterocloster asparagiformis	75.7724	52	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.72	98.33	0.90	0.88	5	-
--------------------------------------------------------------------------------
[2023-06-14 01:01:08,269] [INFO] GTDB search result was written to GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-14 01:01:08,270] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:01:08,274] [INFO] DFAST_QC result json was written to GCA_947039305.1_ERR8099099_bin.15_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-14 01:01:08,275] [INFO] DFAST_QC completed!
[2023-06-14 01:01:08,275] [INFO] Total running time: 0h1m3s