[2023-06-12 23:45:36,714] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:45:36,717] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:45:36,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg3117e1fa-4f2d-450b-b34b-d66fc8313b8c/dqc_reference
[2023-06-12 23:45:38,065] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:45:38,066] [INFO] Task started: Prodigal
[2023-06-12 23:45:38,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg11e8316e-8082-4bdf-98e4-bd3760194b1c/GCA_022793835.1_ASM2279383v1_genomic.fna.gz | prodigal -d GCA_022793835.1_ASM2279383v1_genomic.fna/cds.fna -a GCA_022793835.1_ASM2279383v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:45:43,703] [INFO] Task succeeded: Prodigal
[2023-06-12 23:45:43,703] [INFO] Task started: HMMsearch
[2023-06-12 23:45:43,704] [INFO] Running command: hmmsearch --tblout GCA_022793835.1_ASM2279383v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3117e1fa-4f2d-450b-b34b-d66fc8313b8c/dqc_reference/reference_markers.hmm GCA_022793835.1_ASM2279383v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:45:43,940] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:45:43,941] [INFO] Found 6/6 markers.
[2023-06-12 23:45:43,966] [INFO] Query marker FASTA was written to GCA_022793835.1_ASM2279383v1_genomic.fna/markers.fasta
[2023-06-12 23:45:43,966] [INFO] Task started: Blastn
[2023-06-12 23:45:43,967] [INFO] Running command: blastn -query GCA_022793835.1_ASM2279383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3117e1fa-4f2d-450b-b34b-d66fc8313b8c/dqc_reference/reference_markers.fasta -out GCA_022793835.1_ASM2279383v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:45:44,661] [INFO] Task succeeded: Blastn
[2023-06-12 23:45:44,671] [INFO] Selected 23 target genomes.
[2023-06-12 23:45:44,672] [INFO] Target genome list was writen to GCA_022793835.1_ASM2279383v1_genomic.fna/target_genomes.txt
[2023-06-12 23:45:44,677] [INFO] Task started: fastANI
[2023-06-12 23:45:44,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg11e8316e-8082-4bdf-98e4-bd3760194b1c/GCA_022793835.1_ASM2279383v1_genomic.fna.gz --refList GCA_022793835.1_ASM2279383v1_genomic.fna/target_genomes.txt --output GCA_022793835.1_ASM2279383v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:45:59,591] [INFO] Task succeeded: fastANI
[2023-06-12 23:45:59,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3117e1fa-4f2d-450b-b34b-d66fc8313b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:45:59,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3117e1fa-4f2d-450b-b34b-d66fc8313b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:45:59,595] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:45:59,596] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-12 23:45:59,596] [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
--------------------------------------------------------------------------------
[2023-06-12 23:45:59,598] [INFO] DFAST Taxonomy check result was written to GCA_022793835.1_ASM2279383v1_genomic.fna/tc_result.tsv
[2023-06-12 23:45:59,599] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:45:59,599] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:45:59,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3117e1fa-4f2d-450b-b34b-d66fc8313b8c/dqc_reference/checkm_data
[2023-06-12 23:45:59,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:45:59,636] [INFO] Task started: CheckM
[2023-06-12 23:45:59,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022793835.1_ASM2279383v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022793835.1_ASM2279383v1_genomic.fna/checkm_input GCA_022793835.1_ASM2279383v1_genomic.fna/checkm_result
[2023-06-12 23:46:23,881] [INFO] Task succeeded: CheckM
[2023-06-12 23:46:23,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:46:23,907] [INFO] ===== Completeness check finished =====
[2023-06-12 23:46:23,907] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:46:23,907] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022793835.1_ASM2279383v1_genomic.fna/markers.fasta)
[2023-06-12 23:46:23,908] [INFO] Task started: Blastn
[2023-06-12 23:46:23,908] [INFO] Running command: blastn -query GCA_022793835.1_ASM2279383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3117e1fa-4f2d-450b-b34b-d66fc8313b8c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022793835.1_ASM2279383v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:46:25,018] [INFO] Task succeeded: Blastn
[2023-06-12 23:46:25,023] [INFO] Selected 23 target genomes.
[2023-06-12 23:46:25,023] [INFO] Target genome list was writen to GCA_022793835.1_ASM2279383v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:46:25,035] [INFO] Task started: fastANI
[2023-06-12 23:46:25,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg11e8316e-8082-4bdf-98e4-bd3760194b1c/GCA_022793835.1_ASM2279383v1_genomic.fna.gz --refList GCA_022793835.1_ASM2279383v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022793835.1_ASM2279383v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:46:32,997] [INFO] Task succeeded: fastANI
[2023-06-12 23:46:33,015] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:46:33,015] [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_910589155.1	s__Faecousia sp910589155	98.6106	575	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900546915.1	s__Faecousia gallistercoris	78.3425	84	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.45	99.22	0.91	0.80	6	-
GCA_900544975.1	s__Faecousia sp900544975	78.2671	113	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.46	99.22	0.93	0.93	4	-
GCA_900544405.1	s__Faecousia sp900544405	78.081	81	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.57	97.43	0.89	0.88	3	-
GCA_018715805.1	s__Faecousia intestinigallinarum	77.9886	99	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545515.1	s__Faecousia sp000435995	77.9864	111	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.49	98.99	0.94	0.88	3	-
GCA_018713285.1	s__Faecousia excrementigallinarum	77.6655	84	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004562395.1	s__Faecousia sp004562395	77.6538	66	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067545.1	s__Faecousia sp015067545	77.5578	72	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918045.1	s__Faecousia sp018918045	77.4841	84	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712145.1	s__Faecousia faecigallinarum	77.3947	103	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905205195.1	s__Faecousia sp900762935	77.3359	97	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.08	99.08	0.92	0.92	2	-
GCA_002436765.1	s__Faecousia sp002436765	77.315	93	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.53	99.53	0.91	0.91	2	-
GCA_900544945.1	s__Faecousia sp900544945	77.3148	98	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.60	96.52	0.82	0.81	4	-
GCA_002437585.1	s__Faecousia sp002437585	77.2533	89	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.35	99.16	0.96	0.95	3	-
GCA_015068165.1	s__Faecousia sp015068165	77.1737	57	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549705.1	s__Faecousia sp900549705	77.1522	72	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.98	96.52	0.84	0.77	3	-
GCA_017506735.1	s__Faecousia sp017506735	77.1495	61	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556935.1	s__Faecousia sp900556935	77.1353	58	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017416325.1	s__Faecousia sp017416325	76.9161	58	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017631155.1	s__Faecousia sp017631155	76.1959	52	636	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 23:46:33,017] [INFO] GTDB search result was written to GCA_022793835.1_ASM2279383v1_genomic.fna/result_gtdb.tsv
[2023-06-12 23:46:33,018] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:46:33,024] [INFO] DFAST_QC result json was written to GCA_022793835.1_ASM2279383v1_genomic.fna/dqc_result.json
[2023-06-12 23:46:33,025] [INFO] DFAST_QC completed!
[2023-06-12 23:46:33,025] [INFO] Total running time: 0h0m56s