[2023-06-18 23:32:26,580] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:32:26,583] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:32:26,583] [INFO] DQC Reference Directory: /var/lib/cwl/stgeecfd3fd-bec0-42db-9c0a-ffffb54cda59/dqc_reference
[2023-06-18 23:32:28,896] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:32:28,897] [INFO] Task started: Prodigal
[2023-06-18 23:32:28,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg825f517c-9842-4bc2-b8bc-a57c251b8319/GCA_018714445.1_ASM1871444v1_genomic.fna.gz | prodigal -d GCA_018714445.1_ASM1871444v1_genomic.fna/cds.fna -a GCA_018714445.1_ASM1871444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:32:36,624] [INFO] Task succeeded: Prodigal
[2023-06-18 23:32:36,624] [INFO] Task started: HMMsearch
[2023-06-18 23:32:36,625] [INFO] Running command: hmmsearch --tblout GCA_018714445.1_ASM1871444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeecfd3fd-bec0-42db-9c0a-ffffb54cda59/dqc_reference/reference_markers.hmm GCA_018714445.1_ASM1871444v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:32:36,844] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:32:36,845] [INFO] Found 6/6 markers.
[2023-06-18 23:32:36,879] [INFO] Query marker FASTA was written to GCA_018714445.1_ASM1871444v1_genomic.fna/markers.fasta
[2023-06-18 23:32:36,879] [INFO] Task started: Blastn
[2023-06-18 23:32:36,879] [INFO] Running command: blastn -query GCA_018714445.1_ASM1871444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeecfd3fd-bec0-42db-9c0a-ffffb54cda59/dqc_reference/reference_markers.fasta -out GCA_018714445.1_ASM1871444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:32:37,482] [INFO] Task succeeded: Blastn
[2023-06-18 23:32:37,491] [INFO] Selected 26 target genomes.
[2023-06-18 23:32:37,492] [INFO] Target genome list was writen to GCA_018714445.1_ASM1871444v1_genomic.fna/target_genomes.txt
[2023-06-18 23:32:37,496] [INFO] Task started: fastANI
[2023-06-18 23:32:37,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg825f517c-9842-4bc2-b8bc-a57c251b8319/GCA_018714445.1_ASM1871444v1_genomic.fna.gz --refList GCA_018714445.1_ASM1871444v1_genomic.fna/target_genomes.txt --output GCA_018714445.1_ASM1871444v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:32:53,042] [INFO] Task succeeded: fastANI
[2023-06-18 23:32:53,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeecfd3fd-bec0-42db-9c0a-ffffb54cda59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:32:53,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeecfd3fd-bec0-42db-9c0a-ffffb54cda59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:32:53,045] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:32:53,045] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 23:32:53,045] [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
--------------------------------------------------------------------------------
[2023-06-18 23:32:53,048] [INFO] DFAST Taxonomy check result was written to GCA_018714445.1_ASM1871444v1_genomic.fna/tc_result.tsv
[2023-06-18 23:32:53,049] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:32:53,049] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:32:53,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeecfd3fd-bec0-42db-9c0a-ffffb54cda59/dqc_reference/checkm_data
[2023-06-18 23:32:53,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:32:53,082] [INFO] Task started: CheckM
[2023-06-18 23:32:53,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018714445.1_ASM1871444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018714445.1_ASM1871444v1_genomic.fna/checkm_input GCA_018714445.1_ASM1871444v1_genomic.fna/checkm_result
[2023-06-18 23:33:20,400] [INFO] Task succeeded: CheckM
[2023-06-18 23:33:20,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:33:20,423] [INFO] ===== Completeness check finished =====
[2023-06-18 23:33:20,423] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:33:20,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018714445.1_ASM1871444v1_genomic.fna/markers.fasta)
[2023-06-18 23:33:20,424] [INFO] Task started: Blastn
[2023-06-18 23:33:20,424] [INFO] Running command: blastn -query GCA_018714445.1_ASM1871444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeecfd3fd-bec0-42db-9c0a-ffffb54cda59/dqc_reference/reference_markers_gtdb.fasta -out GCA_018714445.1_ASM1871444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:33:21,262] [INFO] Task succeeded: Blastn
[2023-06-18 23:33:21,267] [INFO] Selected 16 target genomes.
[2023-06-18 23:33:21,267] [INFO] Target genome list was writen to GCA_018714445.1_ASM1871444v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:33:21,300] [INFO] Task started: fastANI
[2023-06-18 23:33:21,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg825f517c-9842-4bc2-b8bc-a57c251b8319/GCA_018714445.1_ASM1871444v1_genomic.fna.gz --refList GCA_018714445.1_ASM1871444v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018714445.1_ASM1871444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:33:28,710] [INFO] Task succeeded: fastANI
[2023-06-18 23:33:28,734] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:33:28,735] [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_018714445.1	s__Fimadaptatus faecigallinarum	100.0	835	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Fimadaptatus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900553645.1	s__Fimadaptatus sp900553645	78.9694	214	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Fimadaptatus	95.0	97.34	97.34	0.85	0.85	2	-
GCA_900553265.1	s__Faecivicinus sp900553265	77.0014	85	838	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	76.8979	83	838	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_018716805.1	s__Faecivicinus avistercoris	76.74	98	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Faecivicinus	95.0	96.88	96.88	0.84	0.84	2	-
GCA_902801165.1	s__UBA2862 sp902801165	76.6864	72	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793325.1	s__UBA2862 sp902793325	76.6625	91	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713325.1	s__Onthenecus intestinigallinarum	76.6308	106	838	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_004555155.1	s__Faecivicinus sp004555155	76.6247	72	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Faecivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765735.1	s__UBA2862 sp002350605	76.5829	73	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	99.72	99.72	0.89	0.89	2	-
GCA_902773515.1	s__UBA2862 sp902773515	76.5754	72	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056395.1	s__Faecivicinus sp015056395	76.5238	76	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Faecivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432405.1	s__UBA2862 sp017432405	76.3299	73	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765395.1	s__UBA2862 sp902765395	76.3294	72	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017552535.1	s__RUG14130 sp017552535	76.3063	50	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG14130	95.0	97.52	97.52	0.84	0.84	2	-
GCA_017434085.1	s__UBA2862 sp017434085	75.7225	54	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 23:33:28,738] [INFO] GTDB search result was written to GCA_018714445.1_ASM1871444v1_genomic.fna/result_gtdb.tsv
[2023-06-18 23:33:28,738] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:33:28,742] [INFO] DFAST_QC result json was written to GCA_018714445.1_ASM1871444v1_genomic.fna/dqc_result.json
[2023-06-18 23:33:28,743] [INFO] DFAST_QC completed!
[2023-06-18 23:33:28,743] [INFO] Total running time: 0h1m2s