[2023-06-13 06:11:11,215] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:11:11,217] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:11:11,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg629f0130-7955-4840-af01-96058d8129c1/dqc_reference
[2023-06-13 06:11:14,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:11:14,308] [INFO] Task started: Prodigal
[2023-06-13 06:11:14,308] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f27c343-072a-4501-8d7b-c55c36d140a1/GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:11:19,496] [INFO] Task succeeded: Prodigal
[2023-06-13 06:11:19,497] [INFO] Task started: HMMsearch
[2023-06-13 06:11:19,497] [INFO] Running command: hmmsearch --tblout GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg629f0130-7955-4840-af01-96058d8129c1/dqc_reference/reference_markers.hmm GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:11:19,732] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:11:19,733] [INFO] Found 6/6 markers.
[2023-06-13 06:11:19,765] [INFO] Query marker FASTA was written to GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 06:11:19,766] [INFO] Task started: Blastn
[2023-06-13 06:11:19,766] [INFO] Running command: blastn -query GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg629f0130-7955-4840-af01-96058d8129c1/dqc_reference/reference_markers.fasta -out GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:11:20,393] [INFO] Task succeeded: Blastn
[2023-06-13 06:11:20,397] [INFO] Selected 27 target genomes.
[2023-06-13 06:11:20,398] [INFO] Target genome list was writen to GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 06:11:20,405] [INFO] Task started: fastANI
[2023-06-13 06:11:20,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f27c343-072a-4501-8d7b-c55c36d140a1/GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:11:34,170] [INFO] Task succeeded: fastANI
[2023-06-13 06:11:34,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg629f0130-7955-4840-af01-96058d8129c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:11:34,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg629f0130-7955-4840-af01-96058d8129c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:11:34,174] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 06:11:34,174] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 06:11:34,174] [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
--------------------------------------------------------------------------------
[2023-06-13 06:11:34,176] [INFO] DFAST Taxonomy check result was written to GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 06:11:34,177] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:11:34,177] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:11:34,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg629f0130-7955-4840-af01-96058d8129c1/dqc_reference/checkm_data
[2023-06-13 06:11:34,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:11:34,214] [INFO] Task started: CheckM
[2023-06-13 06:11:34,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 06:11:56,364] [INFO] Task succeeded: CheckM
[2023-06-13 06:11:56,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 06:11:56,385] [INFO] ===== Completeness check finished =====
[2023-06-13 06:11:56,385] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:11:56,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 06:11:56,386] [INFO] Task started: Blastn
[2023-06-13 06:11:56,386] [INFO] Running command: blastn -query GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg629f0130-7955-4840-af01-96058d8129c1/dqc_reference/reference_markers_gtdb.fasta -out GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:11:57,425] [INFO] Task succeeded: Blastn
[2023-06-13 06:11:57,429] [INFO] Selected 25 target genomes.
[2023-06-13 06:11:57,430] [INFO] Target genome list was writen to GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:11:57,467] [INFO] Task started: fastANI
[2023-06-13 06:11:57,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f27c343-072a-4501-8d7b-c55c36d140a1/GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:12:07,451] [INFO] Task succeeded: fastANI
[2023-06-13 06:12:07,457] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:12:07,457] [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_900551265.1	s__UMGS1384 sp900551265	99.5679	488	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__UMGS1384	95.0	99.38	99.25	0.80	0.76	3	conclusive
GCA_018384365.1	s__UMGS1384 sp018384365	78.8841	212	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__UMGS1384	95.0	98.09	98.09	0.77	0.77	2	-
GCA_015067705.1	s__UMGS1384 sp015067705	77.5969	82	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__UMGS1384	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 06:12:07,459] [INFO] GTDB search result was written to GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 06:12:07,460] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:12:07,462] [INFO] DFAST_QC result json was written to GCA_938045075.1_SRR5580313_bin.50_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 06:12:07,462] [INFO] DFAST_QC completed!
[2023-06-13 06:12:07,462] [INFO] Total running time: 0h0m56s