[2024-01-24 12:44:43,001] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,005] [INFO] DQC Reference Directory: /var/lib/cwl/stgc96336e6-eee9-4fe6-9faf-20c81aee30f3/dqc_reference
[2024-01-24 12:44:44,461] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:44,462] [INFO] Task started: Prodigal
[2024-01-24 12:44:44,462] [INFO] Running command: gunzip -c /var/lib/cwl/stg70458824-a06c-42d0-bf48-8a1d9407ab63/GCF_900199515.1_PRJEB21311_genomic.fna.gz | prodigal -d GCF_900199515.1_PRJEB21311_genomic.fna/cds.fna -a GCF_900199515.1_PRJEB21311_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:51,437] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:51,437] [INFO] Task started: HMMsearch
[2024-01-24 12:44:51,437] [INFO] Running command: hmmsearch --tblout GCF_900199515.1_PRJEB21311_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc96336e6-eee9-4fe6-9faf-20c81aee30f3/dqc_reference/reference_markers.hmm GCF_900199515.1_PRJEB21311_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:51,710] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:51,712] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg70458824-a06c-42d0-bf48-8a1d9407ab63/GCF_900199515.1_PRJEB21311_genomic.fna.gz]
[2024-01-24 12:44:51,735] [INFO] Query marker FASTA was written to GCF_900199515.1_PRJEB21311_genomic.fna/markers.fasta
[2024-01-24 12:44:51,735] [INFO] Task started: Blastn
[2024-01-24 12:44:51,736] [INFO] Running command: blastn -query GCF_900199515.1_PRJEB21311_genomic.fna/markers.fasta -db /var/lib/cwl/stgc96336e6-eee9-4fe6-9faf-20c81aee30f3/dqc_reference/reference_markers.fasta -out GCF_900199515.1_PRJEB21311_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:52,363] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:52,367] [INFO] Selected 24 target genomes.
[2024-01-24 12:44:52,367] [INFO] Target genome list was writen to GCF_900199515.1_PRJEB21311_genomic.fna/target_genomes.txt
[2024-01-24 12:44:52,380] [INFO] Task started: fastANI
[2024-01-24 12:44:52,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg70458824-a06c-42d0-bf48-8a1d9407ab63/GCF_900199515.1_PRJEB21311_genomic.fna.gz --refList GCF_900199515.1_PRJEB21311_genomic.fna/target_genomes.txt --output GCF_900199515.1_PRJEB21311_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:06,283] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:06,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc96336e6-eee9-4fe6-9faf-20c81aee30f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:06,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc96336e6-eee9-4fe6-9faf-20c81aee30f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:06,287] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:06,288] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:06,288] [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
Massilicoli timonensis	strain=Marseille-P3755	GCA_900199515.1	2015901	2015901	type	True	100.0	834	834	95	conclusive
Copranaerobaculum intestinale	strain=DONG20-135	GCA_009831105.1	2692629	2692629	type	True	77.3799	85	834	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:06,289] [INFO] DFAST Taxonomy check result was written to GCF_900199515.1_PRJEB21311_genomic.fna/tc_result.tsv
[2024-01-24 12:45:06,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:06,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:06,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc96336e6-eee9-4fe6-9faf-20c81aee30f3/dqc_reference/checkm_data
[2024-01-24 12:45:06,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:06,326] [INFO] Task started: CheckM
[2024-01-24 12:45:06,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900199515.1_PRJEB21311_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900199515.1_PRJEB21311_genomic.fna/checkm_input GCF_900199515.1_PRJEB21311_genomic.fna/checkm_result
[2024-01-24 12:45:33,482] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:33,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:33,503] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:33,503] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:33,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900199515.1_PRJEB21311_genomic.fna/markers.fasta)
[2024-01-24 12:45:33,504] [INFO] Task started: Blastn
[2024-01-24 12:45:33,504] [INFO] Running command: blastn -query GCF_900199515.1_PRJEB21311_genomic.fna/markers.fasta -db /var/lib/cwl/stgc96336e6-eee9-4fe6-9faf-20c81aee30f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900199515.1_PRJEB21311_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:34,407] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:34,414] [INFO] Selected 21 target genomes.
[2024-01-24 12:45:34,414] [INFO] Target genome list was writen to GCF_900199515.1_PRJEB21311_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:34,450] [INFO] Task started: fastANI
[2024-01-24 12:45:34,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg70458824-a06c-42d0-bf48-8a1d9407ab63/GCF_900199515.1_PRJEB21311_genomic.fna.gz --refList GCF_900199515.1_PRJEB21311_genomic.fna/target_genomes_gtdb.txt --output GCF_900199515.1_PRJEB21311_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:43,425] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:43,438] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:43,439] [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
GCF_900199515.1	s__Massilicoli timonensis	100.0	834	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Massilicoli	95.0	98.84	98.66	0.94	0.87	5	conclusive
GCA_017161075.1	s__Clostridium_AQ sp000165065	80.6938	67	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	97.84	97.80	0.84	0.80	7	-
GCF_010537335.1	s__Amedibacterium intestinale	78.3071	60	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	98.96	98.46	0.86	0.72	14	-
GCA_910575705.1	s__CAJTFG01 sp910575705	77.923	50	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__CAJTFG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543035.1	s__Merdibacter merdipullorum	77.6912	53	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Merdibacter	95.0	99.07	98.57	0.95	0.92	4	-
GCA_009831105.1	s__DONG20-135 sp009831105	77.3799	85	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__DONG20-135	95.0	98.89	98.89	0.93	0.93	2	-
GCA_900759455.1	s__Merdibacter sp900759455	77.029	50	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Merdibacter	95.0	98.55	98.55	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:43,442] [INFO] GTDB search result was written to GCF_900199515.1_PRJEB21311_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:43,443] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:43,447] [INFO] DFAST_QC result json was written to GCF_900199515.1_PRJEB21311_genomic.fna/dqc_result.json
[2024-01-24 12:45:43,448] [INFO] DFAST_QC completed!
[2024-01-24 12:45:43,448] [INFO] Total running time: 0h1m0s