[2023-06-29 15:54:57,987] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:54:57,990] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:54:57,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg138617e6-ddbf-4579-97e7-8a12f8ef3ad6/dqc_reference
[2023-06-29 15:54:59,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:54:59,198] [INFO] Task started: Prodigal
[2023-06-29 15:54:59,199] [INFO] Running command: gunzip -c /var/lib/cwl/stg875f1b2d-80a2-492e-812b-d3a78d1f50e2/GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:55:09,369] [INFO] Task succeeded: Prodigal
[2023-06-29 15:55:09,369] [INFO] Task started: HMMsearch
[2023-06-29 15:55:09,369] [INFO] Running command: hmmsearch --tblout GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg138617e6-ddbf-4579-97e7-8a12f8ef3ad6/dqc_reference/reference_markers.hmm GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:55:09,624] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:55:09,625] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg875f1b2d-80a2-492e-812b-d3a78d1f50e2/GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 15:55:09,666] [INFO] Query marker FASTA was written to GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 15:55:09,667] [INFO] Task started: Blastn
[2023-06-29 15:55:09,667] [INFO] Running command: blastn -query GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg138617e6-ddbf-4579-97e7-8a12f8ef3ad6/dqc_reference/reference_markers.fasta -out GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:55:10,171] [INFO] Task succeeded: Blastn
[2023-06-29 15:55:10,175] [INFO] Selected 0 target genomes.
[2023-06-29 15:55:10,175] [INFO] Target genome list was writen to GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 15:55:10,176] [ERROR] File is empty. [GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt]
[2023-06-29 15:55:10,176] [ERROR] Task failed. No target genome found.
[2023-06-29 15:55:10,176] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:55:10,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg138617e6-ddbf-4579-97e7-8a12f8ef3ad6/dqc_reference/checkm_data
[2023-06-29 15:55:10,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:55:10,205] [INFO] Task started: CheckM
[2023-06-29 15:55:10,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 15:55:46,193] [INFO] Task succeeded: CheckM
[2023-06-29 15:55:46,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.63%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:55:46,220] [INFO] ===== Completeness check finished =====
[2023-06-29 15:55:46,221] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:55:46,221] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 15:55:46,222] [INFO] Task started: Blastn
[2023-06-29 15:55:46,222] [INFO] Running command: blastn -query GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg138617e6-ddbf-4579-97e7-8a12f8ef3ad6/dqc_reference/reference_markers_gtdb.fasta -out GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:55:46,708] [INFO] Task succeeded: Blastn
[2023-06-29 15:55:46,712] [INFO] Selected 9 target genomes.
[2023-06-29 15:55:46,712] [INFO] Target genome list was writen to GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:55:46,767] [INFO] Task started: fastANI
[2023-06-29 15:55:46,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg875f1b2d-80a2-492e-812b-d3a78d1f50e2/GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:55:49,789] [INFO] Task succeeded: fastANI
[2023-06-29 15:55:49,792] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:55:49,793] [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_014729945.1	s__RBG-16-57-9 sp014729945	77.0236	99	523	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__TCS64;f__TCS64;g__RBG-16-57-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:55:49,795] [INFO] GTDB search result was written to GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 15:55:49,796] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:55:49,798] [INFO] DFAST_QC result json was written to GCA_937877765.1_SRR6823441_bin.35_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 15:55:49,799] [INFO] DFAST_QC completed!
[2023-06-29 15:55:49,799] [INFO] Total running time: 0h0m52s