[2023-06-28 18:52:32,840] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:52:32,843] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:52:32,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg358e6213-65e1-4a1d-bd19-4e63a24fa5e4/dqc_reference
[2023-06-28 18:52:35,134] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:52:35,135] [INFO] Task started: Prodigal
[2023-06-28 18:52:35,136] [INFO] Running command: gunzip -c /var/lib/cwl/stg48b53111-fdd4-4ee4-b4aa-87f80de8a4ec/GCA_017829155.1_ASM1782915v1_genomic.fna.gz | prodigal -d GCA_017829155.1_ASM1782915v1_genomic.fna/cds.fna -a GCA_017829155.1_ASM1782915v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:52:37,062] [INFO] Task succeeded: Prodigal
[2023-06-28 18:52:37,063] [INFO] Task started: HMMsearch
[2023-06-28 18:52:37,063] [INFO] Running command: hmmsearch --tblout GCA_017829155.1_ASM1782915v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg358e6213-65e1-4a1d-bd19-4e63a24fa5e4/dqc_reference/reference_markers.hmm GCA_017829155.1_ASM1782915v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:52:37,276] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:52:37,278] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg48b53111-fdd4-4ee4-b4aa-87f80de8a4ec/GCA_017829155.1_ASM1782915v1_genomic.fna.gz]
[2023-06-28 18:52:37,293] [INFO] Query marker FASTA was written to GCA_017829155.1_ASM1782915v1_genomic.fna/markers.fasta
[2023-06-28 18:52:37,294] [INFO] Task started: Blastn
[2023-06-28 18:52:37,294] [INFO] Running command: blastn -query GCA_017829155.1_ASM1782915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg358e6213-65e1-4a1d-bd19-4e63a24fa5e4/dqc_reference/reference_markers.fasta -out GCA_017829155.1_ASM1782915v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:52:39,214] [INFO] Task succeeded: Blastn
[2023-06-28 18:52:39,219] [INFO] Selected 19 target genomes.
[2023-06-28 18:52:39,219] [INFO] Target genome list was writen to GCA_017829155.1_ASM1782915v1_genomic.fna/target_genomes.txt
[2023-06-28 18:52:39,222] [INFO] Task started: fastANI
[2023-06-28 18:52:39,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg48b53111-fdd4-4ee4-b4aa-87f80de8a4ec/GCA_017829155.1_ASM1782915v1_genomic.fna.gz --refList GCA_017829155.1_ASM1782915v1_genomic.fna/target_genomes.txt --output GCA_017829155.1_ASM1782915v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:52:47,904] [INFO] Task succeeded: fastANI
[2023-06-28 18:52:47,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg358e6213-65e1-4a1d-bd19-4e63a24fa5e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:52:47,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg358e6213-65e1-4a1d-bd19-4e63a24fa5e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:52:47,907] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:52:47,907] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:52:47,907] [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
--------------------------------------------------------------------------------
[2023-06-28 18:52:47,910] [INFO] DFAST Taxonomy check result was written to GCA_017829155.1_ASM1782915v1_genomic.fna/tc_result.tsv
[2023-06-28 18:52:47,910] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:52:47,911] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:52:47,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg358e6213-65e1-4a1d-bd19-4e63a24fa5e4/dqc_reference/checkm_data
[2023-06-28 18:52:47,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:52:47,932] [INFO] Task started: CheckM
[2023-06-28 18:52:47,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017829155.1_ASM1782915v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017829155.1_ASM1782915v1_genomic.fna/checkm_input GCA_017829155.1_ASM1782915v1_genomic.fna/checkm_result
[2023-06-28 18:53:01,630] [INFO] Task succeeded: CheckM
[2023-06-28 18:53:01,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 34.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:53:01,651] [INFO] ===== Completeness check finished =====
[2023-06-28 18:53:01,652] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:53:01,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017829155.1_ASM1782915v1_genomic.fna/markers.fasta)
[2023-06-28 18:53:01,653] [INFO] Task started: Blastn
[2023-06-28 18:53:01,653] [INFO] Running command: blastn -query GCA_017829155.1_ASM1782915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg358e6213-65e1-4a1d-bd19-4e63a24fa5e4/dqc_reference/reference_markers_gtdb.fasta -out GCA_017829155.1_ASM1782915v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:53:02,487] [INFO] Task succeeded: Blastn
[2023-06-28 18:53:02,492] [INFO] Selected 21 target genomes.
[2023-06-28 18:53:02,493] [INFO] Target genome list was writen to GCA_017829155.1_ASM1782915v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:53:02,497] [INFO] Task started: fastANI
[2023-06-28 18:53:02,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg48b53111-fdd4-4ee4-b4aa-87f80de8a4ec/GCA_017829155.1_ASM1782915v1_genomic.fna.gz --refList GCA_017829155.1_ASM1782915v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017829155.1_ASM1782915v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:53:09,775] [INFO] Task succeeded: fastANI
[2023-06-28 18:53:09,780] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:53:09,781] [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_017847995.1	s__Heteroruminococcus sp017847995	83.5829	63	70	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Heteroruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:53:09,783] [INFO] GTDB search result was written to GCA_017829155.1_ASM1782915v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:53:09,784] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:53:09,786] [INFO] DFAST_QC result json was written to GCA_017829155.1_ASM1782915v1_genomic.fna/dqc_result.json
[2023-06-28 18:53:09,787] [INFO] DFAST_QC completed!
[2023-06-28 18:53:09,787] [INFO] Total running time: 0h0m37s