[2023-06-28 16:14:08,455] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:14:08,457] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:14:08,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgf70ad2e6-3818-4809-8abf-97b23d4d55be/dqc_reference
[2023-06-28 16:14:09,653] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:14:09,654] [INFO] Task started: Prodigal
[2023-06-28 16:14:09,654] [INFO] Running command: gunzip -c /var/lib/cwl/stgddb62f36-204f-4ab0-8d0c-38a41804b9f4/GCA_944376795.1_E14_bin269_genomic.fna.gz | prodigal -d GCA_944376795.1_E14_bin269_genomic.fna/cds.fna -a GCA_944376795.1_E14_bin269_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:14:17,263] [INFO] Task succeeded: Prodigal
[2023-06-28 16:14:17,263] [INFO] Task started: HMMsearch
[2023-06-28 16:14:17,263] [INFO] Running command: hmmsearch --tblout GCA_944376795.1_E14_bin269_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf70ad2e6-3818-4809-8abf-97b23d4d55be/dqc_reference/reference_markers.hmm GCA_944376795.1_E14_bin269_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:14:17,456] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:14:17,457] [INFO] Found 6/6 markers.
[2023-06-28 16:14:17,481] [INFO] Query marker FASTA was written to GCA_944376795.1_E14_bin269_genomic.fna/markers.fasta
[2023-06-28 16:14:17,481] [INFO] Task started: Blastn
[2023-06-28 16:14:17,481] [INFO] Running command: blastn -query GCA_944376795.1_E14_bin269_genomic.fna/markers.fasta -db /var/lib/cwl/stgf70ad2e6-3818-4809-8abf-97b23d4d55be/dqc_reference/reference_markers.fasta -out GCA_944376795.1_E14_bin269_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:14:18,066] [INFO] Task succeeded: Blastn
[2023-06-28 16:14:18,069] [INFO] Selected 27 target genomes.
[2023-06-28 16:14:18,069] [INFO] Target genome list was writen to GCA_944376795.1_E14_bin269_genomic.fna/target_genomes.txt
[2023-06-28 16:14:18,070] [INFO] Task started: fastANI
[2023-06-28 16:14:18,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgddb62f36-204f-4ab0-8d0c-38a41804b9f4/GCA_944376795.1_E14_bin269_genomic.fna.gz --refList GCA_944376795.1_E14_bin269_genomic.fna/target_genomes.txt --output GCA_944376795.1_E14_bin269_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:14:32,511] [INFO] Task succeeded: fastANI
[2023-06-28 16:14:32,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf70ad2e6-3818-4809-8abf-97b23d4d55be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:14:32,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf70ad2e6-3818-4809-8abf-97b23d4d55be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:14:32,513] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:14:32,513] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:14:32,513] [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 16:14:32,515] [INFO] DFAST Taxonomy check result was written to GCA_944376795.1_E14_bin269_genomic.fna/tc_result.tsv
[2023-06-28 16:14:32,516] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:14:32,516] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:14:32,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf70ad2e6-3818-4809-8abf-97b23d4d55be/dqc_reference/checkm_data
[2023-06-28 16:14:32,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:14:32,546] [INFO] Task started: CheckM
[2023-06-28 16:14:32,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944376795.1_E14_bin269_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944376795.1_E14_bin269_genomic.fna/checkm_input GCA_944376795.1_E14_bin269_genomic.fna/checkm_result
[2023-06-28 16:14:58,691] [INFO] Task succeeded: CheckM
[2023-06-28 16:14:58,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:14:58,713] [INFO] ===== Completeness check finished =====
[2023-06-28 16:14:58,713] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:14:58,714] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944376795.1_E14_bin269_genomic.fna/markers.fasta)
[2023-06-28 16:14:58,714] [INFO] Task started: Blastn
[2023-06-28 16:14:58,714] [INFO] Running command: blastn -query GCA_944376795.1_E14_bin269_genomic.fna/markers.fasta -db /var/lib/cwl/stgf70ad2e6-3818-4809-8abf-97b23d4d55be/dqc_reference/reference_markers_gtdb.fasta -out GCA_944376795.1_E14_bin269_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:14:59,569] [INFO] Task succeeded: Blastn
[2023-06-28 16:14:59,575] [INFO] Selected 30 target genomes.
[2023-06-28 16:14:59,575] [INFO] Target genome list was writen to GCA_944376795.1_E14_bin269_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:14:59,582] [INFO] Task started: fastANI
[2023-06-28 16:14:59,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgddb62f36-204f-4ab0-8d0c-38a41804b9f4/GCA_944376795.1_E14_bin269_genomic.fna.gz --refList GCA_944376795.1_E14_bin269_genomic.fna/target_genomes_gtdb.txt --output GCA_944376795.1_E14_bin269_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:15:12,959] [INFO] Task succeeded: fastANI
[2023-06-28 16:15:12,964] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:15:12,964] [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_900542005.1	s__Parachristensenella sp900542005	76.8886	85	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UMGS416;g__Parachristensenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004563405.1	s__SFTH01 sp004563405	76.6027	50	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFTH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017534885.1	s__RUG11272 sp017534885	76.3409	54	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG11272	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716505.1	s__Faecaligallichristensenella faecipullorum	76.3368	66	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Faecaligallichristensenella	95.0	98.68	98.68	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-28 16:15:12,966] [INFO] GTDB search result was written to GCA_944376795.1_E14_bin269_genomic.fna/result_gtdb.tsv
[2023-06-28 16:15:12,967] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:15:12,970] [INFO] DFAST_QC result json was written to GCA_944376795.1_E14_bin269_genomic.fna/dqc_result.json
[2023-06-28 16:15:12,970] [INFO] DFAST_QC completed!
[2023-06-28 16:15:12,970] [INFO] Total running time: 0h1m5s