[2023-06-08 09:54:01,136] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:54:01,138] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:54:01,138] [INFO] DQC Reference Directory: /var/lib/cwl/stg3486986a-b2c7-4799-820e-8becb933a63f/dqc_reference
[2023-06-08 09:54:02,473] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:54:02,473] [INFO] Task started: Prodigal
[2023-06-08 09:54:02,474] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4aa1cb5-f1f8-4431-8011-11395c89a0ae/GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:54:06,268] [INFO] Task succeeded: Prodigal
[2023-06-08 09:54:06,269] [INFO] Task started: HMMsearch
[2023-06-08 09:54:06,269] [INFO] Running command: hmmsearch --tblout GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3486986a-b2c7-4799-820e-8becb933a63f/dqc_reference/reference_markers.hmm GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:54:06,476] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:54:06,477] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb4aa1cb5-f1f8-4431-8011-11395c89a0ae/GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 09:54:06,500] [INFO] Query marker FASTA was written to GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:54:06,500] [INFO] Task started: Blastn
[2023-06-08 09:54:06,500] [INFO] Running command: blastn -query GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3486986a-b2c7-4799-820e-8becb933a63f/dqc_reference/reference_markers.fasta -out GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:54:06,981] [INFO] Task succeeded: Blastn
[2023-06-08 09:54:06,985] [INFO] Selected 13 target genomes.
[2023-06-08 09:54:06,986] [INFO] Target genome list was writen to GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:54:06,989] [INFO] Task started: fastANI
[2023-06-08 09:54:06,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4aa1cb5-f1f8-4431-8011-11395c89a0ae/GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:54:13,635] [INFO] Task succeeded: fastANI
[2023-06-08 09:54:13,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3486986a-b2c7-4799-820e-8becb933a63f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:54:13,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3486986a-b2c7-4799-820e-8becb933a63f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:54:13,643] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:54:13,643] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 09:54:13,643] [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
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	75.8201	51	422	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 09:54:13,646] [INFO] DFAST Taxonomy check result was written to GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:54:13,646] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:54:13,647] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:54:13,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3486986a-b2c7-4799-820e-8becb933a63f/dqc_reference/checkm_data
[2023-06-08 09:54:13,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:54:13,668] [INFO] Task started: CheckM
[2023-06-08 09:54:13,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:54:32,410] [INFO] Task succeeded: CheckM
[2023-06-08 09:54:32,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:54:32,438] [INFO] ===== Completeness check finished =====
[2023-06-08 09:54:32,438] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:54:32,439] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:54:32,439] [INFO] Task started: Blastn
[2023-06-08 09:54:32,439] [INFO] Running command: blastn -query GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3486986a-b2c7-4799-820e-8becb933a63f/dqc_reference/reference_markers_gtdb.fasta -out GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:54:32,915] [INFO] Task succeeded: Blastn
[2023-06-08 09:54:32,919] [INFO] Selected 12 target genomes.
[2023-06-08 09:54:32,920] [INFO] Target genome list was writen to GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:54:32,926] [INFO] Task started: fastANI
[2023-06-08 09:54:32,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4aa1cb5-f1f8-4431-8011-11395c89a0ae/GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:54:37,693] [INFO] Task succeeded: fastANI
[2023-06-08 09:54:37,710] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:54:37,710] [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_017622995.1	s__Faecousia sp017622995	98.5824	406	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900547405.1	s__Faecousia sp900547405	81.4761	260	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.15	96.95	0.86	0.86	5	-
GCA_900540635.1	s__Faecousia sp900540635	80.8349	247	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.77	97.74	0.82	0.81	3	-
GCA_900556935.1	s__Faecousia sp900556935	80.4849	226	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918045.1	s__Faecousia sp018918045	80.4775	205	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004562395.1	s__Faecousia sp004562395	79.2796	128	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770015.1	s__Faecousia sp900770015	79.1569	149	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544945.1	s__Faecousia sp900544945	79.1557	168	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.60	96.52	0.82	0.81	4	-
GCA_002436765.1	s__Faecousia sp002436765	78.7065	148	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.53	99.53	0.91	0.91	2	-
GCA_017505505.1	s__Faecousia sp017505505	78.2131	83	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017501695.1	s__Faecousia sp017501695	78.1531	113	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068175.1	s__Faecousia sp015068175	77.9242	92	422	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:54:37,715] [INFO] GTDB search result was written to GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:54:37,721] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:54:37,724] [INFO] DFAST_QC result json was written to GCA_945910135.1_SRR11489776_bin.74_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:54:37,725] [INFO] DFAST_QC completed!
[2023-06-08 09:54:37,725] [INFO] Total running time: 0h0m37s