[2023-06-18 17:27:59,057] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:27:59,062] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:27:59,062] [INFO] DQC Reference Directory: /var/lib/cwl/stg754e18e1-6327-4948-b73e-938a71f12e4e/dqc_reference
[2023-06-18 17:28:01,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:28:01,655] [INFO] Task started: Prodigal
[2023-06-18 17:28:01,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg2da039c3-2150-4c0c-89bb-3a242fedae54/GCA_014465855.1_ASM1446585v1_genomic.fna.gz | prodigal -d GCA_014465855.1_ASM1446585v1_genomic.fna/cds.fna -a GCA_014465855.1_ASM1446585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:28:06,218] [INFO] Task succeeded: Prodigal
[2023-06-18 17:28:06,218] [INFO] Task started: HMMsearch
[2023-06-18 17:28:06,218] [INFO] Running command: hmmsearch --tblout GCA_014465855.1_ASM1446585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg754e18e1-6327-4948-b73e-938a71f12e4e/dqc_reference/reference_markers.hmm GCA_014465855.1_ASM1446585v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:28:06,461] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:28:06,463] [INFO] Found 6/6 markers.
[2023-06-18 17:28:06,489] [INFO] Query marker FASTA was written to GCA_014465855.1_ASM1446585v1_genomic.fna/markers.fasta
[2023-06-18 17:28:06,490] [INFO] Task started: Blastn
[2023-06-18 17:28:06,490] [INFO] Running command: blastn -query GCA_014465855.1_ASM1446585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg754e18e1-6327-4948-b73e-938a71f12e4e/dqc_reference/reference_markers.fasta -out GCA_014465855.1_ASM1446585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:28:07,699] [INFO] Task succeeded: Blastn
[2023-06-18 17:28:07,705] [INFO] Selected 20 target genomes.
[2023-06-18 17:28:07,706] [INFO] Target genome list was writen to GCA_014465855.1_ASM1446585v1_genomic.fna/target_genomes.txt
[2023-06-18 17:28:07,805] [INFO] Task started: fastANI
[2023-06-18 17:28:07,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg2da039c3-2150-4c0c-89bb-3a242fedae54/GCA_014465855.1_ASM1446585v1_genomic.fna.gz --refList GCA_014465855.1_ASM1446585v1_genomic.fna/target_genomes.txt --output GCA_014465855.1_ASM1446585v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:28:16,485] [INFO] Task succeeded: fastANI
[2023-06-18 17:28:16,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg754e18e1-6327-4948-b73e-938a71f12e4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:28:16,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg754e18e1-6327-4948-b73e-938a71f12e4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:28:16,493] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:28:16,494] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:28:16,494] [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
Eubacterium coprostanoligenes	strain=ATCC 51222	GCA_900167205.1	290054	290054	type	True	77.1395	100	580	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:28:16,497] [INFO] DFAST Taxonomy check result was written to GCA_014465855.1_ASM1446585v1_genomic.fna/tc_result.tsv
[2023-06-18 17:28:16,498] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:28:16,498] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:28:16,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg754e18e1-6327-4948-b73e-938a71f12e4e/dqc_reference/checkm_data
[2023-06-18 17:28:16,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:28:16,529] [INFO] Task started: CheckM
[2023-06-18 17:28:16,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014465855.1_ASM1446585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014465855.1_ASM1446585v1_genomic.fna/checkm_input GCA_014465855.1_ASM1446585v1_genomic.fna/checkm_result
[2023-06-18 17:28:37,194] [INFO] Task succeeded: CheckM
[2023-06-18 17:28:37,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:28:37,230] [INFO] ===== Completeness check finished =====
[2023-06-18 17:28:37,232] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:28:37,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014465855.1_ASM1446585v1_genomic.fna/markers.fasta)
[2023-06-18 17:28:37,234] [INFO] Task started: Blastn
[2023-06-18 17:28:37,234] [INFO] Running command: blastn -query GCA_014465855.1_ASM1446585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg754e18e1-6327-4948-b73e-938a71f12e4e/dqc_reference/reference_markers_gtdb.fasta -out GCA_014465855.1_ASM1446585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:28:38,278] [INFO] Task succeeded: Blastn
[2023-06-18 17:28:38,282] [INFO] Selected 16 target genomes.
[2023-06-18 17:28:38,282] [INFO] Target genome list was writen to GCA_014465855.1_ASM1446585v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:28:38,318] [INFO] Task started: fastANI
[2023-06-18 17:28:38,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg2da039c3-2150-4c0c-89bb-3a242fedae54/GCA_014465855.1_ASM1446585v1_genomic.fna.gz --refList GCA_014465855.1_ASM1446585v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014465855.1_ASM1446585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:28:43,999] [INFO] Task succeeded: fastANI
[2023-06-18 17:28:44,022] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:28:44,022] [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_900539775.1	s__Eubacterium_R sp900539775	99.7783	566	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.81	98.50	0.97	0.95	6	conclusive
GCA_000433975.1	s__Eubacterium_R sp000433975	88.9084	518	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.06	97.98	0.95	0.88	9	-
GCA_900543795.1	s__Eubacterium_R sp900543795	78.5852	245	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.98	99.95	0.93	0.89	3	-
GCA_900540305.1	s__Eubacterium_R sp900540305	78.5843	222	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.62	98.42	0.88	0.85	3	-
GCA_900555015.1	s__Eubacterium_R sp900555015	78.5128	132	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539425.1	s__Eubacterium_R sp900539425	78.0442	193	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.89	97.76	0.89	0.86	5	-
GCA_905234995.1	s__Eubacterium_R sp905234995	77.7605	158	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539845.1	s__Eubacterium_R faecavium	77.7412	175	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.18	98.52	0.94	0.90	5	-
GCA_910577215.1	s__Eubacterium_R sp910577215	77.724	171	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584985.1	s__Eubacterium_R sp910584985	77.652	162	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539165.1	s__Eubacterium_R sp900539165	77.1827	89	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.98	99.98	0.94	0.94	2	-
GCA_900540235.1	s__Eubacterium_R sp900540235	77.1719	129	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.09	96.24	0.90	0.86	3	-
GCA_017543725.1	s__Eubacterium_R sp017543725	76.3587	55	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 17:28:44,025] [INFO] GTDB search result was written to GCA_014465855.1_ASM1446585v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:28:44,026] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:28:44,034] [INFO] DFAST_QC result json was written to GCA_014465855.1_ASM1446585v1_genomic.fna/dqc_result.json
[2023-06-18 17:28:44,034] [INFO] DFAST_QC completed!
[2023-06-18 17:28:44,034] [INFO] Total running time: 0h0m45s