[2023-06-30 16:53:58,146] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:53:58,148] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:53:58,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dd27770-ca7e-44d9-83a8-2874561c3c61/dqc_reference
[2023-06-30 16:53:59,473] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:53:59,473] [INFO] Task started: Prodigal
[2023-06-30 16:53:59,474] [INFO] Running command: gunzip -c /var/lib/cwl/stg9aaf7203-792a-4511-9be4-c0fd48e9e5e2/GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna.gz | prodigal -d GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/cds.fna -a GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:54:01,479] [INFO] Task succeeded: Prodigal
[2023-06-30 16:54:01,480] [INFO] Task started: HMMsearch
[2023-06-30 16:54:01,480] [INFO] Running command: hmmsearch --tblout GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dd27770-ca7e-44d9-83a8-2874561c3c61/dqc_reference/reference_markers.hmm GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:54:01,696] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:54:01,697] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9aaf7203-792a-4511-9be4-c0fd48e9e5e2/GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna.gz]
[2023-06-30 16:54:01,736] [INFO] Query marker FASTA was written to GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/markers.fasta
[2023-06-30 16:54:01,736] [INFO] Task started: Blastn
[2023-06-30 16:54:01,736] [INFO] Running command: blastn -query GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dd27770-ca7e-44d9-83a8-2874561c3c61/dqc_reference/reference_markers.fasta -out GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:54:02,322] [INFO] Task succeeded: Blastn
[2023-06-30 16:54:02,325] [INFO] Selected 18 target genomes.
[2023-06-30 16:54:02,326] [INFO] Target genome list was writen to GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/target_genomes.txt
[2023-06-30 16:54:02,329] [INFO] Task started: fastANI
[2023-06-30 16:54:02,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aaf7203-792a-4511-9be4-c0fd48e9e5e2/GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna.gz --refList GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/target_genomes.txt --output GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:54:11,146] [INFO] Task succeeded: fastANI
[2023-06-30 16:54:11,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dd27770-ca7e-44d9-83a8-2874561c3c61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:54:11,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dd27770-ca7e-44d9-83a8-2874561c3c61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:54:11,149] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:54:11,149] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 16:54:11,149] [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
--------------------------------------------------------------------------------
[2023-06-30 16:54:11,151] [INFO] DFAST Taxonomy check result was written to GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/tc_result.tsv
[2023-06-30 16:54:11,152] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:54:11,152] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:54:11,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dd27770-ca7e-44d9-83a8-2874561c3c61/dqc_reference/checkm_data
[2023-06-30 16:54:11,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:54:11,173] [INFO] Task started: CheckM
[2023-06-30 16:54:11,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/checkm_input GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/checkm_result
[2023-06-30 16:54:25,543] [INFO] Task succeeded: CheckM
[2023-06-30 16:54:25,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:54:25,567] [INFO] ===== Completeness check finished =====
[2023-06-30 16:54:25,567] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:54:25,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/markers.fasta)
[2023-06-30 16:54:25,568] [INFO] Task started: Blastn
[2023-06-30 16:54:25,568] [INFO] Running command: blastn -query GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dd27770-ca7e-44d9-83a8-2874561c3c61/dqc_reference/reference_markers_gtdb.fasta -out GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:54:26,394] [INFO] Task succeeded: Blastn
[2023-06-30 16:54:26,398] [INFO] Selected 15 target genomes.
[2023-06-30 16:54:26,398] [INFO] Target genome list was writen to GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:54:26,404] [INFO] Task started: fastANI
[2023-06-30 16:54:26,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aaf7203-792a-4511-9be4-c0fd48e9e5e2/GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna.gz --refList GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/target_genomes_gtdb.txt --output GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:54:31,198] [INFO] Task succeeded: fastANI
[2023-06-30 16:54:31,202] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 16:54:31,202] [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_903907935.1	s__UBA6186 sp903907935	98.9993	157	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6186;f__UBA6186;g__UBA6186	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903822055.1	s__UBA6186 sp903822055	78.8023	52	188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6186;f__UBA6186;g__UBA6186	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 16:54:31,204] [INFO] GTDB search result was written to GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/result_gtdb.tsv
[2023-06-30 16:54:31,205] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:54:31,207] [INFO] DFAST_QC result json was written to GCA_903841855.1_freshwater_MAG_---_AM-lipid-01-D5_bin-919_genomic.fna/dqc_result.json
[2023-06-30 16:54:31,207] [INFO] DFAST_QC completed!
[2023-06-30 16:54:31,207] [INFO] Total running time: 0h0m33s