[2023-06-05 23:02:12,263] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:02:12,267] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:02:12,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg216b8c47-96cf-4f29-b3fb-617a7b143a9e/dqc_reference
[2023-06-05 23:02:15,203] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:02:15,207] [INFO] Task started: Prodigal
[2023-06-05 23:02:15,207] [INFO] Running command: gunzip -c /var/lib/cwl/stgac237a8c-5b42-4547-a621-2f097b83f9a0/GCA_934148875.1_ERR7746349_bin.202_genomic.fna.gz | prodigal -d GCA_934148875.1_ERR7746349_bin.202_genomic.fna/cds.fna -a GCA_934148875.1_ERR7746349_bin.202_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:02:17,757] [INFO] Task succeeded: Prodigal
[2023-06-05 23:02:17,757] [INFO] Task started: HMMsearch
[2023-06-05 23:02:17,757] [INFO] Running command: hmmsearch --tblout GCA_934148875.1_ERR7746349_bin.202_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg216b8c47-96cf-4f29-b3fb-617a7b143a9e/dqc_reference/reference_markers.hmm GCA_934148875.1_ERR7746349_bin.202_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:02:18,146] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:02:18,147] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgac237a8c-5b42-4547-a621-2f097b83f9a0/GCA_934148875.1_ERR7746349_bin.202_genomic.fna.gz]
[2023-06-05 23:02:18,180] [INFO] Query marker FASTA was written to GCA_934148875.1_ERR7746349_bin.202_genomic.fna/markers.fasta
[2023-06-05 23:02:18,181] [INFO] Task started: Blastn
[2023-06-05 23:02:18,181] [INFO] Running command: blastn -query GCA_934148875.1_ERR7746349_bin.202_genomic.fna/markers.fasta -db /var/lib/cwl/stg216b8c47-96cf-4f29-b3fb-617a7b143a9e/dqc_reference/reference_markers.fasta -out GCA_934148875.1_ERR7746349_bin.202_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:02:20,802] [INFO] Task succeeded: Blastn
[2023-06-05 23:02:20,807] [INFO] Selected 30 target genomes.
[2023-06-05 23:02:20,807] [INFO] Target genome list was writen to GCA_934148875.1_ERR7746349_bin.202_genomic.fna/target_genomes.txt
[2023-06-05 23:02:20,879] [INFO] Task started: fastANI
[2023-06-05 23:02:20,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgac237a8c-5b42-4547-a621-2f097b83f9a0/GCA_934148875.1_ERR7746349_bin.202_genomic.fna.gz --refList GCA_934148875.1_ERR7746349_bin.202_genomic.fna/target_genomes.txt --output GCA_934148875.1_ERR7746349_bin.202_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:02:39,720] [INFO] Task succeeded: fastANI
[2023-06-05 23:02:39,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg216b8c47-96cf-4f29-b3fb-617a7b143a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:02:39,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg216b8c47-96cf-4f29-b3fb-617a7b143a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:02:39,723] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 23:02:39,724] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 23:02:39,724] [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
--------------------------------------------------------------------------------
[2023-06-05 23:02:39,727] [INFO] DFAST Taxonomy check result was written to GCA_934148875.1_ERR7746349_bin.202_genomic.fna/tc_result.tsv
[2023-06-05 23:02:39,728] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:02:39,728] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:02:39,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg216b8c47-96cf-4f29-b3fb-617a7b143a9e/dqc_reference/checkm_data
[2023-06-05 23:02:39,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:02:39,783] [INFO] Task started: CheckM
[2023-06-05 23:02:39,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934148875.1_ERR7746349_bin.202_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934148875.1_ERR7746349_bin.202_genomic.fna/checkm_input GCA_934148875.1_ERR7746349_bin.202_genomic.fna/checkm_result
[2023-06-05 23:03:01,253] [INFO] Task succeeded: CheckM
[2023-06-05 23:03:01,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.64%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 23:03:01,313] [INFO] ===== Completeness check finished =====
[2023-06-05 23:03:01,314] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:03:01,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934148875.1_ERR7746349_bin.202_genomic.fna/markers.fasta)
[2023-06-05 23:03:01,314] [INFO] Task started: Blastn
[2023-06-05 23:03:01,315] [INFO] Running command: blastn -query GCA_934148875.1_ERR7746349_bin.202_genomic.fna/markers.fasta -db /var/lib/cwl/stg216b8c47-96cf-4f29-b3fb-617a7b143a9e/dqc_reference/reference_markers_gtdb.fasta -out GCA_934148875.1_ERR7746349_bin.202_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:03:02,449] [INFO] Task succeeded: Blastn
[2023-06-05 23:03:02,458] [INFO] Selected 26 target genomes.
[2023-06-05 23:03:02,459] [INFO] Target genome list was writen to GCA_934148875.1_ERR7746349_bin.202_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:03:02,508] [INFO] Task started: fastANI
[2023-06-05 23:03:02,508] [INFO] Running command: fastANI --query /var/lib/cwl/stgac237a8c-5b42-4547-a621-2f097b83f9a0/GCA_934148875.1_ERR7746349_bin.202_genomic.fna.gz --refList GCA_934148875.1_ERR7746349_bin.202_genomic.fna/target_genomes_gtdb.txt --output GCA_934148875.1_ERR7746349_bin.202_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:03:11,003] [INFO] Task succeeded: fastANI
[2023-06-05 23:03:11,011] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 23:03:11,011] [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_900542735.1	s__Scybalousia sp900542735	81.2622	210	446	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	98.00	97.98	0.84	0.82	4	-
GCA_910584255.1	s__Scybalousia sp910584255	76.8011	72	446	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801525.1	s__RUG14670 sp902801525	76.5419	55	446	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14670	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059405.1	s__RUG11788 sp015059405	76.5235	71	446	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11788	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002369415.1	s__UBA3789 sp002369415	76.513	53	446	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017416535.1	s__CAG-877 sp017416535	76.4221	52	446	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477275.1	s__CAG-417 sp002477275	76.3226	50	446	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-417	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 23:03:11,014] [INFO] GTDB search result was written to GCA_934148875.1_ERR7746349_bin.202_genomic.fna/result_gtdb.tsv
[2023-06-05 23:03:11,014] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:03:11,017] [INFO] DFAST_QC result json was written to GCA_934148875.1_ERR7746349_bin.202_genomic.fna/dqc_result.json
[2023-06-05 23:03:11,018] [INFO] DFAST_QC completed!
[2023-06-05 23:03:11,018] [INFO] Total running time: 0h0m59s