[2023-06-07 20:24:52,234] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:24:52,244] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:24:52,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg83dd7959-b962-4ed5-a94e-eaf131b5054e/dqc_reference
[2023-06-07 20:24:54,167] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:24:54,169] [INFO] Task started: Prodigal
[2023-06-07 20:24:54,169] [INFO] Running command: gunzip -c /var/lib/cwl/stg57035ccc-7c94-4e2d-b023-106edd5b9087/GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:25:04,067] [INFO] Task succeeded: Prodigal
[2023-06-07 20:25:04,068] [INFO] Task started: HMMsearch
[2023-06-07 20:25:04,068] [INFO] Running command: hmmsearch --tblout GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83dd7959-b962-4ed5-a94e-eaf131b5054e/dqc_reference/reference_markers.hmm GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:25:04,333] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:25:04,335] [INFO] Found 6/6 markers.
[2023-06-07 20:25:04,375] [INFO] Query marker FASTA was written to GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 20:25:04,375] [INFO] Task started: Blastn
[2023-06-07 20:25:04,375] [INFO] Running command: blastn -query GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg83dd7959-b962-4ed5-a94e-eaf131b5054e/dqc_reference/reference_markers.fasta -out GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:25:05,035] [INFO] Task succeeded: Blastn
[2023-06-07 20:25:05,040] [INFO] Selected 25 target genomes.
[2023-06-07 20:25:05,041] [INFO] Target genome list was writen to GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 20:25:05,042] [INFO] Task started: fastANI
[2023-06-07 20:25:05,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg57035ccc-7c94-4e2d-b023-106edd5b9087/GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:25:20,240] [INFO] Task succeeded: fastANI
[2023-06-07 20:25:20,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83dd7959-b962-4ed5-a94e-eaf131b5054e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:25:20,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83dd7959-b962-4ed5-a94e-eaf131b5054e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:25:20,256] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:25:20,256] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 20:25:20,256] [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
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	78.861	99	1264	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.6438	86	1264	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	76.6509	58	1264	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.6043	77	1264	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.6016	77	1264	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	76.5583	75	1264	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.4745	105	1264	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.4613	63	1264	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.4066	62	1264	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.324	97	1264	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	75.8681	63	1264	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 20:25:20,258] [INFO] DFAST Taxonomy check result was written to GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 20:25:20,259] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:25:20,259] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:25:20,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83dd7959-b962-4ed5-a94e-eaf131b5054e/dqc_reference/checkm_data
[2023-06-07 20:25:20,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:25:20,301] [INFO] Task started: CheckM
[2023-06-07 20:25:20,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 20:25:53,854] [INFO] Task succeeded: CheckM
[2023-06-07 20:25:53,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:25:53,876] [INFO] ===== Completeness check finished =====
[2023-06-07 20:25:53,877] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:25:53,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 20:25:53,877] [INFO] Task started: Blastn
[2023-06-07 20:25:53,878] [INFO] Running command: blastn -query GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg83dd7959-b962-4ed5-a94e-eaf131b5054e/dqc_reference/reference_markers_gtdb.fasta -out GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:25:55,008] [INFO] Task succeeded: Blastn
[2023-06-07 20:25:55,014] [INFO] Selected 10 target genomes.
[2023-06-07 20:25:55,014] [INFO] Target genome list was writen to GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:25:55,016] [INFO] Task started: fastANI
[2023-06-07 20:25:55,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg57035ccc-7c94-4e2d-b023-106edd5b9087/GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:26:03,929] [INFO] Task succeeded: fastANI
[2023-06-07 20:26:03,943] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:26:03,943] [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_910579505.1	s__UBA3282 sp910579505	96.6613	1020	1264	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910586705.1	s__UBA3282 sp910586705	88.1187	917	1264	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003611805.1	s__UBA3282 sp003611805	86.6235	916	1264	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.73	98.68	0.87	0.86	4	-
GCA_910588955.1	s__UBA3282 sp910588955	86.1708	882	1264	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584725.1	s__UBA3282 sp910584725	85.5983	872	1264	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774215.1	s__UBA3282 sp009774215	84.9728	738	1264	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.90	98.90	0.87	0.87	2	-
GCA_910575775.1	s__UBA3282 sp910575775	84.0818	869	1264	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.26	98.26	0.81	0.81	2	-
GCA_910579285.1	s__UBA3282 sp910579285	83.6841	818	1264	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002491905.1	s__UBA3282 sp002491905	83.0579	750	1264	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587095.1	s__UBA3282 sp910587095	81.6049	624	1264	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 20:26:03,945] [INFO] GTDB search result was written to GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 20:26:03,946] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:26:03,949] [INFO] DFAST_QC result json was written to GCA_947072915.1_SRR12464014_bin.21_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 20:26:03,949] [INFO] DFAST_QC completed!
[2023-06-07 20:26:03,949] [INFO] Total running time: 0h1m12s