[2023-06-29 14:42:28,984] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:42:28,986] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:42:28,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f756089-b4f4-4729-a90f-67359ed5ddf7/dqc_reference
[2023-06-29 14:42:30,332] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:42:30,333] [INFO] Task started: Prodigal
[2023-06-29 14:42:30,333] [INFO] Running command: gunzip -c /var/lib/cwl/stgdee8c362-b0d2-4fdc-8afc-d6c9499f31b3/GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:42:34,914] [INFO] Task succeeded: Prodigal
[2023-06-29 14:42:34,915] [INFO] Task started: HMMsearch
[2023-06-29 14:42:34,915] [INFO] Running command: hmmsearch --tblout GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f756089-b4f4-4729-a90f-67359ed5ddf7/dqc_reference/reference_markers.hmm GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:42:35,144] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:42:35,146] [INFO] Found 6/6 markers.
[2023-06-29 14:42:35,170] [INFO] Query marker FASTA was written to GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 14:42:35,171] [INFO] Task started: Blastn
[2023-06-29 14:42:35,171] [INFO] Running command: blastn -query GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f756089-b4f4-4729-a90f-67359ed5ddf7/dqc_reference/reference_markers.fasta -out GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:42:35,834] [INFO] Task succeeded: Blastn
[2023-06-29 14:42:35,838] [INFO] Selected 15 target genomes.
[2023-06-29 14:42:35,838] [INFO] Target genome list was writen to GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 14:42:35,840] [INFO] Task started: fastANI
[2023-06-29 14:42:35,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgdee8c362-b0d2-4fdc-8afc-d6c9499f31b3/GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:42:45,282] [INFO] Task succeeded: fastANI
[2023-06-29 14:42:45,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f756089-b4f4-4729-a90f-67359ed5ddf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:42:45,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f756089-b4f4-4729-a90f-67359ed5ddf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:42:45,284] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:42:45,285] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 14:42:45,285] [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 14:42:45,287] [INFO] DFAST Taxonomy check result was written to GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 14:42:45,288] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:42:45,288] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:42:45,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f756089-b4f4-4729-a90f-67359ed5ddf7/dqc_reference/checkm_data
[2023-06-29 14:42:45,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:42:45,316] [INFO] Task started: CheckM
[2023-06-29 14:42:45,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 14:43:05,748] [INFO] Task succeeded: CheckM
[2023-06-29 14:43:05,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:43:05,769] [INFO] ===== Completeness check finished =====
[2023-06-29 14:43:05,770] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:43:05,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 14:43:05,770] [INFO] Task started: Blastn
[2023-06-29 14:43:05,770] [INFO] Running command: blastn -query GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f756089-b4f4-4729-a90f-67359ed5ddf7/dqc_reference/reference_markers_gtdb.fasta -out GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:43:06,838] [INFO] Task succeeded: Blastn
[2023-06-29 14:43:06,842] [INFO] Selected 6 target genomes.
[2023-06-29 14:43:06,843] [INFO] Target genome list was writen to GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:43:06,844] [INFO] Task started: fastANI
[2023-06-29 14:43:06,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgdee8c362-b0d2-4fdc-8afc-d6c9499f31b3/GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:43:09,541] [INFO] Task succeeded: fastANI
[2023-06-29 14:43:09,549] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:43:09,549] [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_002479075.1	s__CAG-841 sp002479075	99.976	593	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-841	95.0	96.79	96.79	0.89	0.89	2	conclusive
GCA_002405565.1	s__CAG-841 sp002405565	89.6795	387	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-841	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544285.1	s__CAG-841 sp900544285	88.3541	437	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-841	95.0	98.87	98.45	0.89	0.88	4	-
GCA_018383975.1	s__CAG-841 sp018383975	86.1103	370	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-841	95.0	98.92	98.92	0.89	0.89	2	-
GCA_000437375.1	s__CAG-841 sp000437375	81.2058	342	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-841	95.0	99.05	98.81	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2023-06-29 14:43:09,551] [INFO] GTDB search result was written to GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 14:43:09,552] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:43:09,555] [INFO] DFAST_QC result json was written to GCA_937898765.1_SRR1747047_bin.86_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 14:43:09,555] [INFO] DFAST_QC completed!
[2023-06-29 14:43:09,555] [INFO] Total running time: 0h0m41s