[2023-06-28 23:25:03,903] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:25:03,905] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:25:03,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg76515a88-de9c-413b-9477-03ca0cb59758/dqc_reference
[2023-06-28 23:25:06,008] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:25:06,009] [INFO] Task started: Prodigal
[2023-06-28 23:25:06,010] [INFO] Running command: gunzip -c /var/lib/cwl/stg56372271-4b58-4ee6-a103-88f514886fdd/GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:25:13,148] [INFO] Task succeeded: Prodigal
[2023-06-28 23:25:13,149] [INFO] Task started: HMMsearch
[2023-06-28 23:25:13,149] [INFO] Running command: hmmsearch --tblout GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76515a88-de9c-413b-9477-03ca0cb59758/dqc_reference/reference_markers.hmm GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:25:13,406] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:25:13,407] [INFO] Found 6/6 markers.
[2023-06-28 23:25:13,443] [INFO] Query marker FASTA was written to GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-28 23:25:13,444] [INFO] Task started: Blastn
[2023-06-28 23:25:13,444] [INFO] Running command: blastn -query GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg76515a88-de9c-413b-9477-03ca0cb59758/dqc_reference/reference_markers.fasta -out GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:25:14,064] [INFO] Task succeeded: Blastn
[2023-06-28 23:25:14,070] [INFO] Selected 28 target genomes.
[2023-06-28 23:25:14,070] [INFO] Target genome list was writen to GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-28 23:25:14,088] [INFO] Task started: fastANI
[2023-06-28 23:25:14,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg56372271-4b58-4ee6-a103-88f514886fdd/GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:25:30,739] [INFO] Task succeeded: fastANI
[2023-06-28 23:25:30,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76515a88-de9c-413b-9477-03ca0cb59758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:25:30,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76515a88-de9c-413b-9477-03ca0cb59758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:25:30,748] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:25:30,748] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:25:30,748] [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
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.2498	126	881	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.1678	60	881	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.1424	122	881	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	75.8573	50	881	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:25:30,750] [INFO] DFAST Taxonomy check result was written to GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-28 23:25:30,751] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:25:30,751] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:25:30,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76515a88-de9c-413b-9477-03ca0cb59758/dqc_reference/checkm_data
[2023-06-28 23:25:30,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:25:30,787] [INFO] Task started: CheckM
[2023-06-28 23:25:30,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-28 23:25:57,695] [INFO] Task succeeded: CheckM
[2023-06-28 23:25:57,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.29%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:25:57,720] [INFO] ===== Completeness check finished =====
[2023-06-28 23:25:57,721] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:25:57,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-28 23:25:57,722] [INFO] Task started: Blastn
[2023-06-28 23:25:57,722] [INFO] Running command: blastn -query GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg76515a88-de9c-413b-9477-03ca0cb59758/dqc_reference/reference_markers_gtdb.fasta -out GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:25:58,657] [INFO] Task succeeded: Blastn
[2023-06-28 23:25:58,664] [INFO] Selected 23 target genomes.
[2023-06-28 23:25:58,665] [INFO] Target genome list was writen to GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:25:58,716] [INFO] Task started: fastANI
[2023-06-28 23:25:58,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg56372271-4b58-4ee6-a103-88f514886fdd/GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:26:12,590] [INFO] Task succeeded: fastANI
[2023-06-28 23:26:12,618] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:26:12,619] [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_910579685.1	s__CAG-95 sp910579685	99.4086	836	881	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	conclusive
GCA_910586025.1	s__CAG-95 sp910586025	84.0692	584	881	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_017622575.1	s__CAG-95 sp017622575	77.7046	166	881	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_017621815.1	s__CAG-95 sp017621815	77.2061	189	881	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_002492465.1	s__CAG-95 sp002492465	77.1854	156	881	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_014803415.1	s__CAG-95 sp014803415	77.1662	148	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	97.80	97.80	0.82	0.82	2	-
GCA_003612395.1	s__CAG-95 sp003612395	77.1237	126	881	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_910577445.1	s__CAG-95 sp910577445	77.0471	158	881	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_017561085.1	s__CAG-95 sp017561085	77.0208	85	881	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_910585075.1	s__CAG-95 sp910585075	76.8989	166	881	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_910577235.1	s__Acetatifactor sp910577235	76.7957	69	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553305.1	s__CAG-95 sp900553305	76.7785	60	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.81	99.81	0.85	0.85	2	-
GCA_910585615.1	s__Acetatifactor sp910585615	76.608	89	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586775.1	s__Acetatifactor sp910586775	76.5627	84	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804285.1	s__CAG-95 sp014804285	76.466	89	881	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_002491905.1	s__UBA3282 sp002491905	76.3675	94	881	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_910587555.1	s__Acetatifactor sp910587555	76.3675	70	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585805.1	s__Acetatifactor sp910585805	76.3471	83	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587935.1	s__MGBC143606 sp910587935	76.2002	75	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MGBC143606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587715.1	s__UBA3282 sp910587715	76.025	96	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:26:12,621] [INFO] GTDB search result was written to GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 23:26:12,621] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:26:12,624] [INFO] DFAST_QC result json was written to GCA_948468345.1_SRR15604503_bin.64_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-28 23:26:12,625] [INFO] DFAST_QC completed!
[2023-06-28 23:26:12,625] [INFO] Total running time: 0h1m9s