[2023-06-08 07:43:03,625] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:43:03,627] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:43:03,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg57e40906-f7ab-49c9-9e07-ac4363cdff1f/dqc_reference
[2023-06-08 07:43:05,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:43:05,650] [INFO] Task started: Prodigal
[2023-06-08 07:43:05,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg282cc076-af4b-48fa-a302-7e8d87bbb474/GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:43:13,220] [INFO] Task succeeded: Prodigal
[2023-06-08 07:43:13,221] [INFO] Task started: HMMsearch
[2023-06-08 07:43:13,221] [INFO] Running command: hmmsearch --tblout GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57e40906-f7ab-49c9-9e07-ac4363cdff1f/dqc_reference/reference_markers.hmm GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:43:13,493] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:43:13,494] [INFO] Found 6/6 markers.
[2023-06-08 07:43:13,535] [INFO] Query marker FASTA was written to GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 07:43:13,535] [INFO] Task started: Blastn
[2023-06-08 07:43:13,535] [INFO] Running command: blastn -query GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e40906-f7ab-49c9-9e07-ac4363cdff1f/dqc_reference/reference_markers.fasta -out GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:43:14,212] [INFO] Task succeeded: Blastn
[2023-06-08 07:43:14,217] [INFO] Selected 27 target genomes.
[2023-06-08 07:43:14,218] [INFO] Target genome list was writen to GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 07:43:14,223] [INFO] Task started: fastANI
[2023-06-08 07:43:14,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg282cc076-af4b-48fa-a302-7e8d87bbb474/GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:43:30,162] [INFO] Task succeeded: fastANI
[2023-06-08 07:43:30,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57e40906-f7ab-49c9-9e07-ac4363cdff1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:43:30,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57e40906-f7ab-49c9-9e07-ac4363cdff1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:43:30,175] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:43:30,175] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 07:43:30,175] [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
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.8745	86	1040	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.7384	86	1040	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.3925	95	1040	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.2448	96	1040	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.2373	91	1040	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.2083	85	1040	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:43:30,177] [INFO] DFAST Taxonomy check result was written to GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 07:43:30,178] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:43:30,178] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:43:30,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57e40906-f7ab-49c9-9e07-ac4363cdff1f/dqc_reference/checkm_data
[2023-06-08 07:43:30,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:43:30,221] [INFO] Task started: CheckM
[2023-06-08 07:43:30,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 07:43:58,590] [INFO] Task succeeded: CheckM
[2023-06-08 07:43:58,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:43:58,612] [INFO] ===== Completeness check finished =====
[2023-06-08 07:43:58,612] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:43:58,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 07:43:58,613] [INFO] Task started: Blastn
[2023-06-08 07:43:58,613] [INFO] Running command: blastn -query GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e40906-f7ab-49c9-9e07-ac4363cdff1f/dqc_reference/reference_markers_gtdb.fasta -out GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:43:59,771] [INFO] Task succeeded: Blastn
[2023-06-08 07:43:59,776] [INFO] Selected 12 target genomes.
[2023-06-08 07:43:59,776] [INFO] Target genome list was writen to GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:43:59,782] [INFO] Task started: fastANI
[2023-06-08 07:43:59,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg282cc076-af4b-48fa-a302-7e8d87bbb474/GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:44:07,580] [INFO] Task succeeded: fastANI
[2023-06-08 07:44:07,593] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:44:07,593] [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_910584965.1	s__UBA3282 sp910584965	99.1986	966	1040	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_910578475.1	s__UBA3282 sp910578475	82.6526	751	1040	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_910578715.1	s__UBA3282 sp910578715	82.1553	747	1040	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_910579395.1	s__UBA3282 sp910579395	80.8238	633	1040	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_910579735.1	s__UBA3282 sp910579735	78.3597	378	1040	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_017626325.1	s__UBA3282 sp017626325	76.8992	169	1040	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_009774175.1	s__UBA3282 sp009774175	76.8951	153	1040	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.14	99.14	0.87	0.87	2	-
GCA_009774655.1	s__UBA3282 sp009774655	76.7672	162	1040	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.36	98.36	0.78	0.78	2	-
GCF_018917935.1	s__CAG-194 sp018917935	76.5625	61	1040	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-194	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550285.1	s__Eisenbergiella sp900550285	76.5619	63	1040	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	99.00	98.94	0.88	0.81	4	-
GCA_002492525.1	s__UBA3282 sp002492525	76.5132	147	1040	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.83	99.82	0.86	0.82	3	-
--------------------------------------------------------------------------------
[2023-06-08 07:44:07,601] [INFO] GTDB search result was written to GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 07:44:07,601] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:44:07,605] [INFO] DFAST_QC result json was written to GCA_947088375.1_SRR14038235_bin.29_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 07:44:07,605] [INFO] DFAST_QC completed!
[2023-06-08 07:44:07,606] [INFO] Total running time: 0h1m4s