[2023-06-28 10:22:07,850] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:22:07,862] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:22:07,863] [INFO] DQC Reference Directory: /var/lib/cwl/stge29e4867-a145-4b33-92d6-5b043d49a087/dqc_reference
[2023-06-28 10:22:10,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:22:10,405] [INFO] Task started: Prodigal
[2023-06-28 10:22:10,406] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9baf33f-e583-4cca-9c87-c9a3735b81fa/GCA_017481885.1_ASM1748188v1_genomic.fna.gz | prodigal -d GCA_017481885.1_ASM1748188v1_genomic.fna/cds.fna -a GCA_017481885.1_ASM1748188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:22:14,729] [INFO] Task succeeded: Prodigal
[2023-06-28 10:22:14,729] [INFO] Task started: HMMsearch
[2023-06-28 10:22:14,729] [INFO] Running command: hmmsearch --tblout GCA_017481885.1_ASM1748188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge29e4867-a145-4b33-92d6-5b043d49a087/dqc_reference/reference_markers.hmm GCA_017481885.1_ASM1748188v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:22:14,993] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:22:14,994] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb9baf33f-e583-4cca-9c87-c9a3735b81fa/GCA_017481885.1_ASM1748188v1_genomic.fna.gz]
[2023-06-28 10:22:15,016] [INFO] Query marker FASTA was written to GCA_017481885.1_ASM1748188v1_genomic.fna/markers.fasta
[2023-06-28 10:22:15,017] [INFO] Task started: Blastn
[2023-06-28 10:22:15,017] [INFO] Running command: blastn -query GCA_017481885.1_ASM1748188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge29e4867-a145-4b33-92d6-5b043d49a087/dqc_reference/reference_markers.fasta -out GCA_017481885.1_ASM1748188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:22:15,669] [INFO] Task succeeded: Blastn
[2023-06-28 10:22:15,685] [INFO] Selected 17 target genomes.
[2023-06-28 10:22:15,685] [INFO] Target genome list was writen to GCA_017481885.1_ASM1748188v1_genomic.fna/target_genomes.txt
[2023-06-28 10:22:15,688] [INFO] Task started: fastANI
[2023-06-28 10:22:15,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9baf33f-e583-4cca-9c87-c9a3735b81fa/GCA_017481885.1_ASM1748188v1_genomic.fna.gz --refList GCA_017481885.1_ASM1748188v1_genomic.fna/target_genomes.txt --output GCA_017481885.1_ASM1748188v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:22:27,958] [INFO] Task succeeded: fastANI
[2023-06-28 10:22:27,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge29e4867-a145-4b33-92d6-5b043d49a087/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:22:27,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge29e4867-a145-4b33-92d6-5b043d49a087/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:22:27,963] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:22:27,963] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:22:27,963] [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
Ruminococcus bromii	strain=ATCC 27255	GCA_002834225.1	40518	40518	suspected-type	True	77.022	55	590	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:22:27,966] [INFO] DFAST Taxonomy check result was written to GCA_017481885.1_ASM1748188v1_genomic.fna/tc_result.tsv
[2023-06-28 10:22:27,967] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:22:27,967] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:22:27,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge29e4867-a145-4b33-92d6-5b043d49a087/dqc_reference/checkm_data
[2023-06-28 10:22:27,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:22:28,029] [INFO] Task started: CheckM
[2023-06-28 10:22:28,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017481885.1_ASM1748188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017481885.1_ASM1748188v1_genomic.fna/checkm_input GCA_017481885.1_ASM1748188v1_genomic.fna/checkm_result
[2023-06-28 10:22:49,501] [INFO] Task succeeded: CheckM
[2023-06-28 10:22:49,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:22:49,529] [INFO] ===== Completeness check finished =====
[2023-06-28 10:22:49,529] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:22:49,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017481885.1_ASM1748188v1_genomic.fna/markers.fasta)
[2023-06-28 10:22:49,530] [INFO] Task started: Blastn
[2023-06-28 10:22:49,530] [INFO] Running command: blastn -query GCA_017481885.1_ASM1748188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge29e4867-a145-4b33-92d6-5b043d49a087/dqc_reference/reference_markers_gtdb.fasta -out GCA_017481885.1_ASM1748188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:22:50,479] [INFO] Task succeeded: Blastn
[2023-06-28 10:22:50,499] [INFO] Selected 8 target genomes.
[2023-06-28 10:22:50,499] [INFO] Target genome list was writen to GCA_017481885.1_ASM1748188v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:22:50,509] [INFO] Task started: fastANI
[2023-06-28 10:22:50,509] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9baf33f-e583-4cca-9c87-c9a3735b81fa/GCA_017481885.1_ASM1748188v1_genomic.fna.gz --refList GCA_017481885.1_ASM1748188v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017481885.1_ASM1748188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:22:53,662] [INFO] Task succeeded: fastANI
[2023-06-28 10:22:53,678] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:22:53,678] [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_017481885.1	s__Ruminococcus_E sp017481885	100.0	585	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017473555.1	s__Ruminococcus_E sp017473555	84.1667	365	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017473955.1	s__Ruminococcus_E sp017473955	83.2665	303	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410265.1	s__Ruminococcus_E sp017410265	81.5411	290	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.82	97.82	0.84	0.84	2	-
GCA_017464765.1	s__Ruminococcus_E sp017464765	81.5263	228	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017380355.1	s__Ruminococcus_E sp017380355	80.8196	214	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017411835.1	s__Ruminococcus_E sp017411835	80.3155	251	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015066595.1	s__Ruminococcus_E sp015066595	79.8404	242	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:22:53,681] [INFO] GTDB search result was written to GCA_017481885.1_ASM1748188v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:22:53,683] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:22:53,687] [INFO] DFAST_QC result json was written to GCA_017481885.1_ASM1748188v1_genomic.fna/dqc_result.json
[2023-06-28 10:22:53,687] [INFO] DFAST_QC completed!
[2023-06-28 10:22:53,687] [INFO] Total running time: 0h0m46s