[2023-06-28 12:00:30,558] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:00:30,561] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:00:30,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c73b5d0-50a1-4244-a7b9-916abb9c72b1/dqc_reference
[2023-06-28 12:00:31,772] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:00:31,773] [INFO] Task started: Prodigal
[2023-06-28 12:00:31,773] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b2e591d-13d5-44cc-8203-b6378d058466/GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:00:40,320] [INFO] Task succeeded: Prodigal
[2023-06-28 12:00:40,320] [INFO] Task started: HMMsearch
[2023-06-28 12:00:40,320] [INFO] Running command: hmmsearch --tblout GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c73b5d0-50a1-4244-a7b9-916abb9c72b1/dqc_reference/reference_markers.hmm GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:00:40,574] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:00:40,576] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9b2e591d-13d5-44cc-8203-b6378d058466/GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-28 12:00:40,612] [INFO] Query marker FASTA was written to GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-28 12:00:40,613] [INFO] Task started: Blastn
[2023-06-28 12:00:40,613] [INFO] Running command: blastn -query GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c73b5d0-50a1-4244-a7b9-916abb9c72b1/dqc_reference/reference_markers.fasta -out GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:00:41,272] [INFO] Task succeeded: Blastn
[2023-06-28 12:00:41,275] [INFO] Selected 29 target genomes.
[2023-06-28 12:00:41,276] [INFO] Target genome list was writen to GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-28 12:00:41,277] [INFO] Task started: fastANI
[2023-06-28 12:00:41,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b2e591d-13d5-44cc-8203-b6378d058466/GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:00:59,613] [INFO] Task succeeded: fastANI
[2023-06-28 12:00:59,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c73b5d0-50a1-4244-a7b9-916abb9c72b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:00:59,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c73b5d0-50a1-4244-a7b9-916abb9c72b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:00:59,620] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:00:59,620] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:00:59,620] [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
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	76.7735	53	1095	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.3737	51	1095	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	75.9967	55	1095	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	75.8373	55	1095	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:00:59,622] [INFO] DFAST Taxonomy check result was written to GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-28 12:00:59,622] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:00:59,623] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:00:59,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c73b5d0-50a1-4244-a7b9-916abb9c72b1/dqc_reference/checkm_data
[2023-06-28 12:00:59,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:00:59,660] [INFO] Task started: CheckM
[2023-06-28 12:00:59,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-28 12:01:31,369] [INFO] Task succeeded: CheckM
[2023-06-28 12:01:31,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:01:31,392] [INFO] ===== Completeness check finished =====
[2023-06-28 12:01:31,392] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:01:31,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-28 12:01:31,393] [INFO] Task started: Blastn
[2023-06-28 12:01:31,394] [INFO] Running command: blastn -query GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c73b5d0-50a1-4244-a7b9-916abb9c72b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:32,517] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:32,524] [INFO] Selected 14 target genomes.
[2023-06-28 12:01:32,524] [INFO] Target genome list was writen to GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:01:32,572] [INFO] Task started: fastANI
[2023-06-28 12:01:32,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b2e591d-13d5-44cc-8203-b6378d058466/GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:01:41,559] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:41,570] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:01:41,570] [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_000403335.2	s__COE1 sp000403335	98.8471	1028	1095	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.29	97.29	0.83	0.75	4	conclusive
GCA_910586715.1	s__COE1 sp910586715	94.0654	864	1095	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578795.1	s__COE1 sp910578795	86.5426	749	1095	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577115.1	s__COE1 sp910577115	82.5729	696	1095	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002492295.1	s__COE1 sp002492295	82.0915	646	1095	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804225.1	s__COE1 sp014804225	79.2527	296	1095	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804345.1	s__COE1 sp014804345	79.2352	311	1095	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774345.1	s__COE1 sp009774345	77.5424	218	1095	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.29	99.29	0.85	0.85	2	-
GCA_002358575.1	s__COE1 sp002358575	77.3768	191	1095	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.93	98.87	0.85	0.82	4	-
GCF_003612565.1	s__1XD42-69 sp003612565	77.3433	55	1095	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	99.22	99.22	0.93	0.93	2	-
GCA_017391545.1	s__COE1 sp017391545	76.4612	89	1095	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:01:41,572] [INFO] GTDB search result was written to GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 12:01:41,573] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:01:41,576] [INFO] DFAST_QC result json was written to GCA_948438855.1_SRR17684628_bin.41_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-28 12:01:41,576] [INFO] DFAST_QC completed!
[2023-06-28 12:01:41,576] [INFO] Total running time: 0h1m11s