[2023-06-29 17:08:00,755] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:08:00,757] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:08:00,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg8df795cc-9d12-45a2-87c8-9bfa45a53141/dqc_reference
[2023-06-29 17:08:04,520] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:08:04,522] [INFO] Task started: Prodigal
[2023-06-29 17:08:04,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg53b06c17-378b-4c11-b620-72f94fe10676/GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:08:08,504] [INFO] Task succeeded: Prodigal
[2023-06-29 17:08:08,505] [INFO] Task started: HMMsearch
[2023-06-29 17:08:08,505] [INFO] Running command: hmmsearch --tblout GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8df795cc-9d12-45a2-87c8-9bfa45a53141/dqc_reference/reference_markers.hmm GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:08:08,725] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:08:08,727] [INFO] Found 6/6 markers.
[2023-06-29 17:08:08,753] [INFO] Query marker FASTA was written to GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 17:08:08,753] [INFO] Task started: Blastn
[2023-06-29 17:08:08,754] [INFO] Running command: blastn -query GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8df795cc-9d12-45a2-87c8-9bfa45a53141/dqc_reference/reference_markers.fasta -out GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:08:11,136] [INFO] Task succeeded: Blastn
[2023-06-29 17:08:11,148] [INFO] Selected 29 target genomes.
[2023-06-29 17:08:11,148] [INFO] Target genome list was writen to GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 17:08:11,151] [INFO] Task started: fastANI
[2023-06-29 17:08:11,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b06c17-378b-4c11-b620-72f94fe10676/GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:08:28,414] [INFO] Task succeeded: fastANI
[2023-06-29 17:08:28,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8df795cc-9d12-45a2-87c8-9bfa45a53141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:08:28,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8df795cc-9d12-45a2-87c8-9bfa45a53141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:08:28,417] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 17:08:28,417] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 17:08:28,417] [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 17:08:28,422] [INFO] DFAST Taxonomy check result was written to GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 17:08:28,423] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:08:28,423] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:08:28,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8df795cc-9d12-45a2-87c8-9bfa45a53141/dqc_reference/checkm_data
[2023-06-29 17:08:28,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:08:28,453] [INFO] Task started: CheckM
[2023-06-29 17:08:28,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 17:08:48,941] [INFO] Task succeeded: CheckM
[2023-06-29 17:08:48,943] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 17:08:48,967] [INFO] ===== Completeness check finished =====
[2023-06-29 17:08:48,967] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:08:48,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 17:08:48,968] [INFO] Task started: Blastn
[2023-06-29 17:08:48,968] [INFO] Running command: blastn -query GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8df795cc-9d12-45a2-87c8-9bfa45a53141/dqc_reference/reference_markers_gtdb.fasta -out GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:08:49,994] [INFO] Task succeeded: Blastn
[2023-06-29 17:08:49,999] [INFO] Selected 27 target genomes.
[2023-06-29 17:08:49,999] [INFO] Target genome list was writen to GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:08:50,013] [INFO] Task started: fastANI
[2023-06-29 17:08:50,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b06c17-378b-4c11-b620-72f94fe10676/GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:09:00,548] [INFO] Task succeeded: fastANI
[2023-06-29 17:09:00,552] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 17:09:00,553] [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_002699085.1	s__UBA9664 sp002699085	99.9946	536	551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__UBA9664	95.0	99.97	99.97	0.97	0.97	2	conclusive
--------------------------------------------------------------------------------
[2023-06-29 17:09:00,555] [INFO] GTDB search result was written to GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 17:09:00,555] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:09:00,557] [INFO] DFAST_QC result json was written to GCA_937892175.1_ERR598996_bin.8_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 17:09:00,558] [INFO] DFAST_QC completed!
[2023-06-29 17:09:00,558] [INFO] Total running time: 0h0m60s