[2023-06-13 02:19:03,387] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:19:03,420] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:19:03,420] [INFO] DQC Reference Directory: /var/lib/cwl/stgd27eb8ff-46f3-4586-8700-b9d2703730f3/dqc_reference
[2023-06-13 02:19:05,446] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:19:05,448] [INFO] Task started: Prodigal
[2023-06-13 02:19:05,448] [INFO] Running command: gunzip -c /var/lib/cwl/stg626a7ad8-f139-48fe-8452-c83826759705/GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:19:09,219] [INFO] Task succeeded: Prodigal
[2023-06-13 02:19:09,220] [INFO] Task started: HMMsearch
[2023-06-13 02:19:09,220] [INFO] Running command: hmmsearch --tblout GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd27eb8ff-46f3-4586-8700-b9d2703730f3/dqc_reference/reference_markers.hmm GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:19:09,458] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:19:09,460] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg626a7ad8-f139-48fe-8452-c83826759705/GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 02:19:09,482] [INFO] Query marker FASTA was written to GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 02:19:09,483] [INFO] Task started: Blastn
[2023-06-13 02:19:09,483] [INFO] Running command: blastn -query GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd27eb8ff-46f3-4586-8700-b9d2703730f3/dqc_reference/reference_markers.fasta -out GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:19:10,742] [INFO] Task succeeded: Blastn
[2023-06-13 02:19:10,745] [INFO] Selected 13 target genomes.
[2023-06-13 02:19:10,746] [INFO] Target genome list was writen to GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 02:19:10,749] [INFO] Task started: fastANI
[2023-06-13 02:19:10,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg626a7ad8-f139-48fe-8452-c83826759705/GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:19:18,529] [INFO] Task succeeded: fastANI
[2023-06-13 02:19:18,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd27eb8ff-46f3-4586-8700-b9d2703730f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:19:18,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd27eb8ff-46f3-4586-8700-b9d2703730f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:19:18,532] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:19:18,532] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 02:19:18,533] [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 02:19:18,535] [INFO] DFAST Taxonomy check result was written to GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 02:19:18,536] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:19:18,536] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:19:18,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd27eb8ff-46f3-4586-8700-b9d2703730f3/dqc_reference/checkm_data
[2023-06-13 02:19:18,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:19:18,567] [INFO] Task started: CheckM
[2023-06-13 02:19:18,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 02:19:38,669] [INFO] Task succeeded: CheckM
[2023-06-13 02:19:38,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:19:38,691] [INFO] ===== Completeness check finished =====
[2023-06-13 02:19:38,692] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:19:38,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 02:19:38,693] [INFO] Task started: Blastn
[2023-06-13 02:19:38,693] [INFO] Running command: blastn -query GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd27eb8ff-46f3-4586-8700-b9d2703730f3/dqc_reference/reference_markers_gtdb.fasta -out GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:19:39,649] [INFO] Task succeeded: Blastn
[2023-06-13 02:19:39,654] [INFO] Selected 21 target genomes.
[2023-06-13 02:19:39,655] [INFO] Target genome list was writen to GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:19:39,710] [INFO] Task started: fastANI
[2023-06-13 02:19:39,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg626a7ad8-f139-48fe-8452-c83826759705/GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:19:46,976] [INFO] Task succeeded: fastANI
[2023-06-13 02:19:46,979] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 02:19:46,979] [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_905205065.1	s__UMGS911 sp003343545	82.7058	402	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS911	95.0	99.53	99.06	0.87	0.80	4	-
--------------------------------------------------------------------------------
[2023-06-13 02:19:46,981] [INFO] GTDB search result was written to GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 02:19:46,981] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:19:46,983] [INFO] DFAST_QC result json was written to GCA_938048475.1_ERR912125_bin.79_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 02:19:46,983] [INFO] DFAST_QC completed!
[2023-06-13 02:19:46,984] [INFO] Total running time: 0h0m44s