[2023-06-08 20:36:19,798] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:36:19,800] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:36:19,801] [INFO] DQC Reference Directory: /var/lib/cwl/stgc00cb5c6-c3f2-4476-946d-6c731015a4b3/dqc_reference
[2023-06-08 20:36:21,200] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:36:21,201] [INFO] Task started: Prodigal
[2023-06-08 20:36:21,201] [INFO] Running command: gunzip -c /var/lib/cwl/stgf100c393-c409-40e0-b1aa-5cdeba5de3c8/GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:36:25,967] [INFO] Task succeeded: Prodigal
[2023-06-08 20:36:25,968] [INFO] Task started: HMMsearch
[2023-06-08 20:36:25,968] [INFO] Running command: hmmsearch --tblout GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc00cb5c6-c3f2-4476-946d-6c731015a4b3/dqc_reference/reference_markers.hmm GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:36:26,220] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:36:26,221] [INFO] Found 6/6 markers.
[2023-06-08 20:36:26,243] [INFO] Query marker FASTA was written to GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 20:36:26,244] [INFO] Task started: Blastn
[2023-06-08 20:36:26,244] [INFO] Running command: blastn -query GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc00cb5c6-c3f2-4476-946d-6c731015a4b3/dqc_reference/reference_markers.fasta -out GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:26,895] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:26,901] [INFO] Selected 24 target genomes.
[2023-06-08 20:36:26,901] [INFO] Target genome list was writen to GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 20:36:26,905] [INFO] Task started: fastANI
[2023-06-08 20:36:26,905] [INFO] Running command: fastANI --query /var/lib/cwl/stgf100c393-c409-40e0-b1aa-5cdeba5de3c8/GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:36:41,182] [INFO] Task succeeded: fastANI
[2023-06-08 20:36:41,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc00cb5c6-c3f2-4476-946d-6c731015a4b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:36:41,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc00cb5c6-c3f2-4476-946d-6c731015a4b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:36:41,187] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:36:41,188] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:36:41,188] [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
Eubacterium coprostanoligenes	strain=ATCC 51222	GCA_900167205.1	290054	290054	type	True	77.4782	128	687	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:36:41,190] [INFO] DFAST Taxonomy check result was written to GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 20:36:41,190] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:36:41,190] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:36:41,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc00cb5c6-c3f2-4476-946d-6c731015a4b3/dqc_reference/checkm_data
[2023-06-08 20:36:41,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:36:41,221] [INFO] Task started: CheckM
[2023-06-08 20:36:41,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 20:37:02,886] [INFO] Task succeeded: CheckM
[2023-06-08 20:37:02,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:37:02,909] [INFO] ===== Completeness check finished =====
[2023-06-08 20:37:02,909] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:37:02,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 20:37:02,910] [INFO] Task started: Blastn
[2023-06-08 20:37:02,910] [INFO] Running command: blastn -query GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc00cb5c6-c3f2-4476-946d-6c731015a4b3/dqc_reference/reference_markers_gtdb.fasta -out GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:37:03,914] [INFO] Task succeeded: Blastn
[2023-06-08 20:37:03,919] [INFO] Selected 9 target genomes.
[2023-06-08 20:37:03,920] [INFO] Target genome list was writen to GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:37:03,927] [INFO] Task started: fastANI
[2023-06-08 20:37:03,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgf100c393-c409-40e0-b1aa-5cdeba5de3c8/GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:37:07,445] [INFO] Task succeeded: fastANI
[2023-06-08 20:37:07,460] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:37:07,460] [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_009774735.1	s__Eubacterium_R sp009774735	98.3893	406	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.57	98.57	0.83	0.83	2	conclusive
GCA_002493325.1	s__Eubacterium_R sp002493325	87.2676	481	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.54	97.36	0.89	0.85	3	-
GCA_910577195.1	s__Eubacterium_R sp910577195	80.121	311	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	96.35	96.35	0.82	0.82	2	-
GCA_900544515.1	s__Eubacterium_R sp900544515	79.9476	238	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900767025.1	s__Eubacterium_R sp900767025	79.4129	304	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002493595.1	s__Eubacterium_R sp002493595	78.9128	232	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436835.1	s__Eubacterium_R sp000436835	78.5641	195	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.32	97.52	0.92	0.86	14	-
GCA_014465955.1	s__Eubacterium_R sp014465955	78.4529	186	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002494125.1	s__Eubacterium_R sp002494125	77.3096	125	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.97	97.69	0.80	0.75	3	-
--------------------------------------------------------------------------------
[2023-06-08 20:37:07,462] [INFO] GTDB search result was written to GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 20:37:07,462] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:37:07,465] [INFO] DFAST_QC result json was written to GCA_947562005.1_SRR12272184_bin.1_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 20:37:07,465] [INFO] DFAST_QC completed!
[2023-06-08 20:37:07,466] [INFO] Total running time: 0h0m48s