[2023-06-28 00:49:35,116] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:49:35,120] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:49:35,120] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b0c7504-58df-4808-aad5-5b8ca77c502b/dqc_reference
[2023-06-28 00:49:37,642] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:49:37,643] [INFO] Task started: Prodigal
[2023-06-28 00:49:37,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b61c65d-b0e0-4968-bac0-d6605338ae61/GCA_002492415.1_ASM249241v1_genomic.fna.gz | prodigal -d GCA_002492415.1_ASM249241v1_genomic.fna/cds.fna -a GCA_002492415.1_ASM249241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:49:45,142] [INFO] Task succeeded: Prodigal
[2023-06-28 00:49:45,142] [INFO] Task started: HMMsearch
[2023-06-28 00:49:45,142] [INFO] Running command: hmmsearch --tblout GCA_002492415.1_ASM249241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b0c7504-58df-4808-aad5-5b8ca77c502b/dqc_reference/reference_markers.hmm GCA_002492415.1_ASM249241v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:49:45,384] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:49:45,385] [INFO] Found 6/6 markers.
[2023-06-28 00:49:45,420] [INFO] Query marker FASTA was written to GCA_002492415.1_ASM249241v1_genomic.fna/markers.fasta
[2023-06-28 00:49:45,420] [INFO] Task started: Blastn
[2023-06-28 00:49:45,420] [INFO] Running command: blastn -query GCA_002492415.1_ASM249241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b0c7504-58df-4808-aad5-5b8ca77c502b/dqc_reference/reference_markers.fasta -out GCA_002492415.1_ASM249241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:49:46,016] [INFO] Task succeeded: Blastn
[2023-06-28 00:49:46,021] [INFO] Selected 28 target genomes.
[2023-06-28 00:49:46,022] [INFO] Target genome list was writen to GCA_002492415.1_ASM249241v1_genomic.fna/target_genomes.txt
[2023-06-28 00:49:46,031] [INFO] Task started: fastANI
[2023-06-28 00:49:46,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b61c65d-b0e0-4968-bac0-d6605338ae61/GCA_002492415.1_ASM249241v1_genomic.fna.gz --refList GCA_002492415.1_ASM249241v1_genomic.fna/target_genomes.txt --output GCA_002492415.1_ASM249241v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:50:01,387] [INFO] Task succeeded: fastANI
[2023-06-28 00:50:01,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b0c7504-58df-4808-aad5-5b8ca77c502b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:50:01,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b0c7504-58df-4808-aad5-5b8ca77c502b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:50:01,389] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:50:01,389] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:50:01,389] [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 00:50:01,391] [INFO] DFAST Taxonomy check result was written to GCA_002492415.1_ASM249241v1_genomic.fna/tc_result.tsv
[2023-06-28 00:50:01,391] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:50:01,391] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:50:01,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b0c7504-58df-4808-aad5-5b8ca77c502b/dqc_reference/checkm_data
[2023-06-28 00:50:01,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:50:01,430] [INFO] Task started: CheckM
[2023-06-28 00:50:01,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002492415.1_ASM249241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002492415.1_ASM249241v1_genomic.fna/checkm_input GCA_002492415.1_ASM249241v1_genomic.fna/checkm_result
[2023-06-28 00:50:27,805] [INFO] Task succeeded: CheckM
[2023-06-28 00:50:27,807] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:50:27,826] [INFO] ===== Completeness check finished =====
[2023-06-28 00:50:27,827] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:50:27,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002492415.1_ASM249241v1_genomic.fna/markers.fasta)
[2023-06-28 00:50:27,828] [INFO] Task started: Blastn
[2023-06-28 00:50:27,828] [INFO] Running command: blastn -query GCA_002492415.1_ASM249241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b0c7504-58df-4808-aad5-5b8ca77c502b/dqc_reference/reference_markers_gtdb.fasta -out GCA_002492415.1_ASM249241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:50:28,693] [INFO] Task succeeded: Blastn
[2023-06-28 00:50:28,698] [INFO] Selected 12 target genomes.
[2023-06-28 00:50:28,698] [INFO] Target genome list was writen to GCA_002492415.1_ASM249241v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:50:28,703] [INFO] Task started: fastANI
[2023-06-28 00:50:28,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b61c65d-b0e0-4968-bac0-d6605338ae61/GCA_002492415.1_ASM249241v1_genomic.fna.gz --refList GCA_002492415.1_ASM249241v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002492415.1_ASM249241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:50:34,732] [INFO] Task succeeded: fastANI
[2023-06-28 00:50:34,747] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:50:34,747] [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_002492415.1	s__Spyradocola sp002492415	99.9999	790	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1750;g__Spyradocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_904393115.1	s__Spyradocola merdavium	80.1258	407	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1750;g__Spyradocola	95.0	98.74	98.61	0.95	0.94	8	-
GCA_905193155.1	s__Spyradocola sp905193155	79.6441	362	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1750;g__Spyradocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002315655.1	s__Spyradocola sp002315655	77.9753	200	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1750;g__Spyradocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936765.1	s__UBA11524 sp017936765	77.0352	52	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	96.73	96.73	0.86	0.86	2	-
GCA_018713325.1	s__Onthenecus intestinigallinarum	76.9669	94	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Onthenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553265.1	s__Faecivicinus sp900553265	76.9202	86	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Faecivicinus	95.0	98.26	98.26	0.81	0.81	2	-
GCA_004557125.1	s__SFTH01 sp004557125	76.8771	99	800	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_017399225.1	s__UBA11524 sp017399225	76.6599	59	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555535.1	s__Ventricola sp004555535	76.544	71	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540045.1	s__Limiplasma merdipullorum	76.4005	74	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	97.42	97.19	0.80	0.74	6	-
GCA_902790345.1	s__Firm-10 sp902790345	76.2858	86	800	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Firm-10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:50:34,751] [INFO] GTDB search result was written to GCA_002492415.1_ASM249241v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:50:34,751] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:50:34,754] [INFO] DFAST_QC result json was written to GCA_002492415.1_ASM249241v1_genomic.fna/dqc_result.json
[2023-06-28 00:50:34,755] [INFO] DFAST_QC completed!
[2023-06-28 00:50:34,755] [INFO] Total running time: 0h0m60s