[2023-06-08 12:08:20,850] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:08:20,854] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:08:20,855] [INFO] DQC Reference Directory: /var/lib/cwl/stga088f1ab-387d-40c5-a8ff-1c942d637e4b/dqc_reference
[2023-06-08 12:08:23,095] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:08:23,096] [INFO] Task started: Prodigal
[2023-06-08 12:08:23,097] [INFO] Running command: gunzip -c /var/lib/cwl/stgc34c5782-5a38-44bb-a024-430177541fef/GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:08:30,361] [INFO] Task succeeded: Prodigal
[2023-06-08 12:08:30,361] [INFO] Task started: HMMsearch
[2023-06-08 12:08:30,361] [INFO] Running command: hmmsearch --tblout GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga088f1ab-387d-40c5-a8ff-1c942d637e4b/dqc_reference/reference_markers.hmm GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:08:30,626] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:08:30,628] [INFO] Found 6/6 markers.
[2023-06-08 12:08:30,660] [INFO] Query marker FASTA was written to GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:08:30,660] [INFO] Task started: Blastn
[2023-06-08 12:08:30,661] [INFO] Running command: blastn -query GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga088f1ab-387d-40c5-a8ff-1c942d637e4b/dqc_reference/reference_markers.fasta -out GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:08:31,279] [INFO] Task succeeded: Blastn
[2023-06-08 12:08:31,284] [INFO] Selected 16 target genomes.
[2023-06-08 12:08:31,284] [INFO] Target genome list was writen to GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:08:31,287] [INFO] Task started: fastANI
[2023-06-08 12:08:31,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgc34c5782-5a38-44bb-a024-430177541fef/GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:08:38,821] [INFO] Task succeeded: fastANI
[2023-06-08 12:08:38,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga088f1ab-387d-40c5-a8ff-1c942d637e4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:08:38,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga088f1ab-387d-40c5-a8ff-1c942d637e4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:08:38,831] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:08:38,831] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:08:38,831] [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 flavefaciens	strain=ATCC 19208	GCA_000518765.1	1265	1265	suspected-type	True	79.4989	321	1007	95	below_threshold
Ruminococcus bicirculans	strain=80/3	GCA_000723465.1	1160721	1160721	type	True	78.6956	60	1007	95	below_threshold
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	77.3813	125	1007	95	below_threshold
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	77.3437	125	1007	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:08:38,833] [INFO] DFAST Taxonomy check result was written to GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:08:38,834] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:08:38,834] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:08:38,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga088f1ab-387d-40c5-a8ff-1c942d637e4b/dqc_reference/checkm_data
[2023-06-08 12:08:38,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:08:38,875] [INFO] Task started: CheckM
[2023-06-08 12:08:38,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:09:06,802] [INFO] Task succeeded: CheckM
[2023-06-08 12:09:06,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:09:06,825] [INFO] ===== Completeness check finished =====
[2023-06-08 12:09:06,825] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:09:06,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:09:06,826] [INFO] Task started: Blastn
[2023-06-08 12:09:06,826] [INFO] Running command: blastn -query GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga088f1ab-387d-40c5-a8ff-1c942d637e4b/dqc_reference/reference_markers_gtdb.fasta -out GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:09:07,847] [INFO] Task succeeded: Blastn
[2023-06-08 12:09:07,854] [INFO] Selected 12 target genomes.
[2023-06-08 12:09:07,854] [INFO] Target genome list was writen to GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:09:07,864] [INFO] Task started: fastANI
[2023-06-08 12:09:07,866] [INFO] Running command: fastANI --query /var/lib/cwl/stgc34c5782-5a38-44bb-a024-430177541fef/GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:09:16,586] [INFO] Task succeeded: fastANI
[2023-06-08 12:09:16,602] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:09:16,602] [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_016303195.1	s__Ruminococcus sp016303195	98.299	448	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000174895.1	s__Ruminococcus flavefaciens_A	83.9114	603	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	96.87	96.87	0.86	0.86	2	-
GCA_017479805.1	s__Ruminococcus sp017479805	83.7023	451	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792495.1	s__Ruminococcus flavefaciens_Z	83.4249	319	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.07	96.74	0.72	0.58	3	-
GCA_017418765.1	s__Ruminococcus sp017418765	81.3265	234	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116855.1	s__Ruminococcus flavefaciens_R	79.9784	315	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.90	97.16	0.91	0.76	13	-
GCA_902780115.1	s__Ruminococcus flavefaciens_Y	79.9027	214	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002348905.1	s__Ruminococcus flavefaciens_O	79.5469	232	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	99.48	99.48	0.79	0.79	2	-
GCF_000518765.1	s__Ruminococcus flavefaciens	79.539	318	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549005.1	s__Ruminococcus sp017549005	79.4019	314	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290875.1	s__Ruminococcus sp016290875	79.1076	264	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463375.1	s__Ruminococcus sp017463375	78.2652	158	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:09:16,614] [INFO] GTDB search result was written to GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:09:16,615] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:09:16,620] [INFO] DFAST_QC result json was written to GCA_945873175.1_ERR1855550_bin.27_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:09:16,621] [INFO] DFAST_QC completed!
[2023-06-08 12:09:16,621] [INFO] Total running time: 0h0m56s