[2023-06-07 18:45:04,973] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:45:04,977] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:45:04,977] [INFO] DQC Reference Directory: /var/lib/cwl/stgfde2ea17-eda4-4709-9606-59e76dddf24f/dqc_reference
[2023-06-07 18:45:06,330] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:45:06,331] [INFO] Task started: Prodigal
[2023-06-07 18:45:06,331] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d7028eb-03ea-4f1d-bf8e-5aa3c4edce66/GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:45:11,750] [INFO] Task succeeded: Prodigal
[2023-06-07 18:45:11,751] [INFO] Task started: HMMsearch
[2023-06-07 18:45:11,751] [INFO] Running command: hmmsearch --tblout GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfde2ea17-eda4-4709-9606-59e76dddf24f/dqc_reference/reference_markers.hmm GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:45:11,978] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:45:11,979] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1d7028eb-03ea-4f1d-bf8e-5aa3c4edce66/GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-07 18:45:12,010] [INFO] Query marker FASTA was written to GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 18:45:12,011] [INFO] Task started: Blastn
[2023-06-07 18:45:12,011] [INFO] Running command: blastn -query GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfde2ea17-eda4-4709-9606-59e76dddf24f/dqc_reference/reference_markers.fasta -out GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:45:12,590] [INFO] Task succeeded: Blastn
[2023-06-07 18:45:12,594] [INFO] Selected 22 target genomes.
[2023-06-07 18:45:12,595] [INFO] Target genome list was writen to GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 18:45:12,597] [INFO] Task started: fastANI
[2023-06-07 18:45:12,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7028eb-03ea-4f1d-bf8e-5aa3c4edce66/GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:45:23,184] [INFO] Task succeeded: fastANI
[2023-06-07 18:45:23,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfde2ea17-eda4-4709-9606-59e76dddf24f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:45:23,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfde2ea17-eda4-4709-9606-59e76dddf24f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:45:23,187] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:45:23,187] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 18:45:23,187] [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
--------------------------------------------------------------------------------
[2023-06-07 18:45:23,189] [INFO] DFAST Taxonomy check result was written to GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 18:45:23,190] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:45:23,190] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:45:23,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfde2ea17-eda4-4709-9606-59e76dddf24f/dqc_reference/checkm_data
[2023-06-07 18:45:23,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:45:23,233] [INFO] Task started: CheckM
[2023-06-07 18:45:23,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 18:45:45,913] [INFO] Task succeeded: CheckM
[2023-06-07 18:45:45,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 18:45:45,940] [INFO] ===== Completeness check finished =====
[2023-06-07 18:45:45,941] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:45:45,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 18:45:45,941] [INFO] Task started: Blastn
[2023-06-07 18:45:45,941] [INFO] Running command: blastn -query GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfde2ea17-eda4-4709-9606-59e76dddf24f/dqc_reference/reference_markers_gtdb.fasta -out GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:45:46,662] [INFO] Task succeeded: Blastn
[2023-06-07 18:45:46,666] [INFO] Selected 10 target genomes.
[2023-06-07 18:45:46,666] [INFO] Target genome list was writen to GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:45:46,670] [INFO] Task started: fastANI
[2023-06-07 18:45:46,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7028eb-03ea-4f1d-bf8e-5aa3c4edce66/GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:45:54,390] [INFO] Task succeeded: fastANI
[2023-06-07 18:45:54,399] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 18:45:54,399] [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_910586205.1	s__Ventrimonas sp910586205	98.9585	634	667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003611875.1	s__Ventrimonas sp003611875	87.5037	580	667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.50	99.24	0.91	0.86	4	-
GCA_910586255.1	s__Ventrimonas sp910586255	79.0991	333	667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009911065.1	s__Ventrimonas sp009911065	78.9898	291	667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	95.78	95.73	0.75	0.73	3	-
GCA_003669055.1	s__Ventrimonas sp003669055	78.9632	263	667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910575255.1	s__Ventrimonas sp910575255	78.8038	288	667	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.31	99.12	0.89	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-07 18:45:54,401] [INFO] GTDB search result was written to GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 18:45:54,401] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:45:54,404] [INFO] DFAST_QC result json was written to GCA_947651445.1_SRR15510233_bin.24_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 18:45:54,404] [INFO] DFAST_QC completed!
[2023-06-07 18:45:54,404] [INFO] Total running time: 0h0m49s