[2023-06-29 12:36:07,587] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:36:07,591] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:36:07,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b2d49ad-e391-4d0a-a1ca-cc7a3befebec/dqc_reference
[2023-06-29 12:36:09,973] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:36:09,974] [INFO] Task started: Prodigal
[2023-06-29 12:36:09,974] [INFO] Running command: gunzip -c /var/lib/cwl/stg96db7640-af7f-48de-8ba4-a83d56658458/GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:36:14,417] [INFO] Task succeeded: Prodigal
[2023-06-29 12:36:14,418] [INFO] Task started: HMMsearch
[2023-06-29 12:36:14,418] [INFO] Running command: hmmsearch --tblout GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b2d49ad-e391-4d0a-a1ca-cc7a3befebec/dqc_reference/reference_markers.hmm GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:36:14,599] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:36:14,600] [INFO] Found 6/6 markers.
[2023-06-29 12:36:14,628] [INFO] Query marker FASTA was written to GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 12:36:14,628] [INFO] Task started: Blastn
[2023-06-29 12:36:14,628] [INFO] Running command: blastn -query GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b2d49ad-e391-4d0a-a1ca-cc7a3befebec/dqc_reference/reference_markers.fasta -out GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:36:15,228] [INFO] Task succeeded: Blastn
[2023-06-29 12:36:15,232] [INFO] Selected 20 target genomes.
[2023-06-29 12:36:15,233] [INFO] Target genome list was writen to GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 12:36:15,245] [INFO] Task started: fastANI
[2023-06-29 12:36:15,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg96db7640-af7f-48de-8ba4-a83d56658458/GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:36:27,968] [INFO] Task succeeded: fastANI
[2023-06-29 12:36:27,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b2d49ad-e391-4d0a-a1ca-cc7a3befebec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:36:27,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b2d49ad-e391-4d0a-a1ca-cc7a3befebec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:36:27,971] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:36:27,971] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:36:27,971] [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
--------------------------------------------------------------------------------
[2023-06-29 12:36:27,973] [INFO] DFAST Taxonomy check result was written to GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 12:36:27,974] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:36:27,974] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:36:27,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b2d49ad-e391-4d0a-a1ca-cc7a3befebec/dqc_reference/checkm_data
[2023-06-29 12:36:27,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:36:28,000] [INFO] Task started: CheckM
[2023-06-29 12:36:28,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 12:36:47,539] [INFO] Task succeeded: CheckM
[2023-06-29 12:36:47,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 12:36:47,560] [INFO] ===== Completeness check finished =====
[2023-06-29 12:36:47,560] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:36:47,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 12:36:47,560] [INFO] Task started: Blastn
[2023-06-29 12:36:47,561] [INFO] Running command: blastn -query GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b2d49ad-e391-4d0a-a1ca-cc7a3befebec/dqc_reference/reference_markers_gtdb.fasta -out GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:36:48,500] [INFO] Task succeeded: Blastn
[2023-06-29 12:36:48,504] [INFO] Selected 18 target genomes.
[2023-06-29 12:36:48,504] [INFO] Target genome list was writen to GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:36:48,520] [INFO] Task started: fastANI
[2023-06-29 12:36:48,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg96db7640-af7f-48de-8ba4-a83d56658458/GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:36:55,749] [INFO] Task succeeded: fastANI
[2023-06-29 12:36:55,758] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:36:55,758] [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_910585485.1	s__CAG-41 sp910585485	99.2686	597	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_010206265.1	s__CAG-41 sp010206265	80.9033	280	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	97.79	97.79	0.83	0.83	2	-
GCA_910585795.1	s__CAG-41 sp910585795	80.369	222	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579415.1	s__CAG-41 sp910579415	80.3672	228	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578235.1	s__CAG-41 sp910578235	79.5903	257	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003460745.1	s__CAG-41 sp900066215	78.6612	215	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	97.67	97.16	0.82	0.77	17	-
GCA_001941225.1	s__CAG-41 sp001941225	78.5883	208	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905199755.1	s__UBA4716 sp905199755	76.9445	85	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__UBA4716	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017443895.1	s__12844 sp017443895	76.6636	74	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__12844	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:36:55,760] [INFO] GTDB search result was written to GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 12:36:55,761] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:36:55,764] [INFO] DFAST_QC result json was written to GCA_948439155.1_SRR17684645_bin.26_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 12:36:55,764] [INFO] DFAST_QC completed!
[2023-06-29 12:36:55,764] [INFO] Total running time: 0h0m48s