[2023-06-30 17:00:13,403] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:00:13,406] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:00:13,406] [INFO] DQC Reference Directory: /var/lib/cwl/stge726adf9-5097-456e-a0b4-081fc40338c0/dqc_reference
[2023-06-30 17:00:14,722] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:00:14,723] [INFO] Task started: Prodigal
[2023-06-30 17:00:14,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg71bdc3f1-07c3-4830-896f-3ce90f14f881/GCA_900768685.1_SRS476152_7_genomic.fna.gz | prodigal -d GCA_900768685.1_SRS476152_7_genomic.fna/cds.fna -a GCA_900768685.1_SRS476152_7_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:00:25,194] [INFO] Task succeeded: Prodigal
[2023-06-30 17:00:25,195] [INFO] Task started: HMMsearch
[2023-06-30 17:00:25,195] [INFO] Running command: hmmsearch --tblout GCA_900768685.1_SRS476152_7_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge726adf9-5097-456e-a0b4-081fc40338c0/dqc_reference/reference_markers.hmm GCA_900768685.1_SRS476152_7_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:00:25,431] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:00:25,433] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg71bdc3f1-07c3-4830-896f-3ce90f14f881/GCA_900768685.1_SRS476152_7_genomic.fna.gz]
[2023-06-30 17:00:25,461] [INFO] Query marker FASTA was written to GCA_900768685.1_SRS476152_7_genomic.fna/markers.fasta
[2023-06-30 17:00:25,462] [INFO] Task started: Blastn
[2023-06-30 17:00:25,462] [INFO] Running command: blastn -query GCA_900768685.1_SRS476152_7_genomic.fna/markers.fasta -db /var/lib/cwl/stge726adf9-5097-456e-a0b4-081fc40338c0/dqc_reference/reference_markers.fasta -out GCA_900768685.1_SRS476152_7_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:00:26,060] [INFO] Task succeeded: Blastn
[2023-06-30 17:00:26,064] [INFO] Selected 20 target genomes.
[2023-06-30 17:00:26,064] [INFO] Target genome list was writen to GCA_900768685.1_SRS476152_7_genomic.fna/target_genomes.txt
[2023-06-30 17:00:26,068] [INFO] Task started: fastANI
[2023-06-30 17:00:26,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg71bdc3f1-07c3-4830-896f-3ce90f14f881/GCA_900768685.1_SRS476152_7_genomic.fna.gz --refList GCA_900768685.1_SRS476152_7_genomic.fna/target_genomes.txt --output GCA_900768685.1_SRS476152_7_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:00:36,799] [INFO] Task succeeded: fastANI
[2023-06-30 17:00:36,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge726adf9-5097-456e-a0b4-081fc40338c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:00:36,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge726adf9-5097-456e-a0b4-081fc40338c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:00:36,801] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:00:36,801] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 17:00:36,801] [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 17:00:36,803] [INFO] DFAST Taxonomy check result was written to GCA_900768685.1_SRS476152_7_genomic.fna/tc_result.tsv
[2023-06-30 17:00:36,804] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:00:36,804] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:00:36,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge726adf9-5097-456e-a0b4-081fc40338c0/dqc_reference/checkm_data
[2023-06-30 17:00:36,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:00:36,834] [INFO] Task started: CheckM
[2023-06-30 17:00:36,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900768685.1_SRS476152_7_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900768685.1_SRS476152_7_genomic.fna/checkm_input GCA_900768685.1_SRS476152_7_genomic.fna/checkm_result
[2023-06-30 17:01:11,760] [INFO] Task succeeded: CheckM
[2023-06-30 17:01:11,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 17:01:11,782] [INFO] ===== Completeness check finished =====
[2023-06-30 17:01:11,782] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:01:11,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900768685.1_SRS476152_7_genomic.fna/markers.fasta)
[2023-06-30 17:01:11,783] [INFO] Task started: Blastn
[2023-06-30 17:01:11,783] [INFO] Running command: blastn -query GCA_900768685.1_SRS476152_7_genomic.fna/markers.fasta -db /var/lib/cwl/stge726adf9-5097-456e-a0b4-081fc40338c0/dqc_reference/reference_markers_gtdb.fasta -out GCA_900768685.1_SRS476152_7_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:01:12,613] [INFO] Task succeeded: Blastn
[2023-06-30 17:01:12,618] [INFO] Selected 22 target genomes.
[2023-06-30 17:01:12,618] [INFO] Target genome list was writen to GCA_900768685.1_SRS476152_7_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:01:12,630] [INFO] Task started: fastANI
[2023-06-30 17:01:12,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg71bdc3f1-07c3-4830-896f-3ce90f14f881/GCA_900768685.1_SRS476152_7_genomic.fna.gz --refList GCA_900768685.1_SRS476152_7_genomic.fna/target_genomes_gtdb.txt --output GCA_900768685.1_SRS476152_7_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:01:21,855] [INFO] Task succeeded: fastANI
[2023-06-30 17:01:21,861] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 17:01:21,861] [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_900768685.1	s__UBA7173 sp900768685	100.0	652	653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017399915.1	s__RGIG4079 sp017399915	77.1487	54	653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__RGIG4079	95.0	97.38	97.02	0.81	0.80	4	-
--------------------------------------------------------------------------------
[2023-06-30 17:01:21,863] [INFO] GTDB search result was written to GCA_900768685.1_SRS476152_7_genomic.fna/result_gtdb.tsv
[2023-06-30 17:01:21,864] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:01:21,866] [INFO] DFAST_QC result json was written to GCA_900768685.1_SRS476152_7_genomic.fna/dqc_result.json
[2023-06-30 17:01:21,866] [INFO] DFAST_QC completed!
[2023-06-30 17:01:21,866] [INFO] Total running time: 0h1m8s