[2023-06-27 00:13:11,559] [INFO] DFAST_QC pipeline started.
[2023-06-27 00:13:11,580] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 00:13:11,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg5024b3d5-8d05-4de2-920e-4fbcfa8a8d6d/dqc_reference
[2023-06-27 00:13:13,214] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 00:13:13,216] [INFO] Task started: Prodigal
[2023-06-27 00:13:13,216] [INFO] Running command: gunzip -c /var/lib/cwl/stg50870110-7d08-40e3-8527-3d2a1ef88b61/GCA_002373355.1_ASM237335v1_genomic.fna.gz | prodigal -d GCA_002373355.1_ASM237335v1_genomic.fna/cds.fna -a GCA_002373355.1_ASM237335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 00:13:16,451] [INFO] Task succeeded: Prodigal
[2023-06-27 00:13:16,452] [INFO] Task started: HMMsearch
[2023-06-27 00:13:16,452] [INFO] Running command: hmmsearch --tblout GCA_002373355.1_ASM237335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5024b3d5-8d05-4de2-920e-4fbcfa8a8d6d/dqc_reference/reference_markers.hmm GCA_002373355.1_ASM237335v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 00:13:16,694] [INFO] Task succeeded: HMMsearch
[2023-06-27 00:13:16,697] [INFO] Found 6/6 markers.
[2023-06-27 00:13:16,727] [INFO] Query marker FASTA was written to GCA_002373355.1_ASM237335v1_genomic.fna/markers.fasta
[2023-06-27 00:13:16,727] [INFO] Task started: Blastn
[2023-06-27 00:13:16,728] [INFO] Running command: blastn -query GCA_002373355.1_ASM237335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5024b3d5-8d05-4de2-920e-4fbcfa8a8d6d/dqc_reference/reference_markers.fasta -out GCA_002373355.1_ASM237335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:13:17,328] [INFO] Task succeeded: Blastn
[2023-06-27 00:13:17,333] [INFO] Selected 10 target genomes.
[2023-06-27 00:13:17,333] [INFO] Target genome list was writen to GCA_002373355.1_ASM237335v1_genomic.fna/target_genomes.txt
[2023-06-27 00:13:17,338] [INFO] Task started: fastANI
[2023-06-27 00:13:17,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg50870110-7d08-40e3-8527-3d2a1ef88b61/GCA_002373355.1_ASM237335v1_genomic.fna.gz --refList GCA_002373355.1_ASM237335v1_genomic.fna/target_genomes.txt --output GCA_002373355.1_ASM237335v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 00:13:22,628] [INFO] Task succeeded: fastANI
[2023-06-27 00:13:22,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5024b3d5-8d05-4de2-920e-4fbcfa8a8d6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 00:13:22,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5024b3d5-8d05-4de2-920e-4fbcfa8a8d6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 00:13:22,641] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 00:13:22,642] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 00:13:22,642] [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	76.2626	65	460	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 00:13:22,646] [INFO] DFAST Taxonomy check result was written to GCA_002373355.1_ASM237335v1_genomic.fna/tc_result.tsv
[2023-06-27 00:13:22,649] [INFO] ===== Taxonomy check completed =====
[2023-06-27 00:13:22,650] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 00:13:22,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5024b3d5-8d05-4de2-920e-4fbcfa8a8d6d/dqc_reference/checkm_data
[2023-06-27 00:13:22,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 00:13:22,684] [INFO] Task started: CheckM
[2023-06-27 00:13:22,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002373355.1_ASM237335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002373355.1_ASM237335v1_genomic.fna/checkm_input GCA_002373355.1_ASM237335v1_genomic.fna/checkm_result
[2023-06-27 00:13:41,412] [INFO] Task succeeded: CheckM
[2023-06-27 00:13:41,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 00:13:41,448] [INFO] ===== Completeness check finished =====
[2023-06-27 00:13:41,448] [INFO] ===== Start GTDB Search =====
[2023-06-27 00:13:41,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002373355.1_ASM237335v1_genomic.fna/markers.fasta)
[2023-06-27 00:13:41,449] [INFO] Task started: Blastn
[2023-06-27 00:13:41,449] [INFO] Running command: blastn -query GCA_002373355.1_ASM237335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5024b3d5-8d05-4de2-920e-4fbcfa8a8d6d/dqc_reference/reference_markers_gtdb.fasta -out GCA_002373355.1_ASM237335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:13:42,263] [INFO] Task succeeded: Blastn
[2023-06-27 00:13:42,268] [INFO] Selected 14 target genomes.
[2023-06-27 00:13:42,269] [INFO] Target genome list was writen to GCA_002373355.1_ASM237335v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 00:13:42,282] [INFO] Task started: fastANI
[2023-06-27 00:13:42,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg50870110-7d08-40e3-8527-3d2a1ef88b61/GCA_002373355.1_ASM237335v1_genomic.fna.gz --refList GCA_002373355.1_ASM237335v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002373355.1_ASM237335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 00:13:46,970] [INFO] Task succeeded: fastANI
[2023-06-27 00:13:46,991] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 00:13:46,992] [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_002494125.1	s__Eubacterium_R sp002494125	98.2395	322	460	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.97	97.69	0.80	0.75	3	conclusive
GCA_902791235.1	s__Eubacterium_R sp902791235	78.8648	209	460	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.69	97.69	0.83	0.83	2	-
GCA_905234495.1	s__Eubacterium_R sp905234495	78.7497	212	460	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_900767025.1	s__Eubacterium_R sp900767025	77.6429	122	460	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_910577195.1	s__Eubacterium_R sp910577195	77.5048	114	460	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	96.35	96.35	0.82	0.82	2	-
GCA_015065445.1	s__Eubacterium_R sp015065445	77.3407	85	460	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_000436835.1	s__Eubacterium_R sp000436835	77.2251	104	460	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.32	97.52	0.92	0.86	14	-
GCA_009774735.1	s__Eubacterium_R sp009774735	77.0493	93	460	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.57	98.57	0.83	0.83	2	-
GCA_900544515.1	s__Eubacterium_R sp900544515	76.9573	97	460	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_002493325.1	s__Eubacterium_R sp002493325	76.8821	106	460	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.54	97.36	0.89	0.85	3	-
GCA_900761545.1	s__Eubacterium_R sp900761545	76.7507	62	460	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_002493595.1	s__Eubacterium_R sp002493595	76.7437	83	460	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_014465955.1	s__Eubacterium_R sp014465955	76.5887	76	460	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	-
GCF_900167205.1	s__Eubacterium_R coprostanoligenes	76.2626	65	460	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.02	97.98	0.90	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-27 00:13:46,995] [INFO] GTDB search result was written to GCA_002373355.1_ASM237335v1_genomic.fna/result_gtdb.tsv
[2023-06-27 00:13:46,996] [INFO] ===== GTDB Search completed =====
[2023-06-27 00:13:47,003] [INFO] DFAST_QC result json was written to GCA_002373355.1_ASM237335v1_genomic.fna/dqc_result.json
[2023-06-27 00:13:47,003] [INFO] DFAST_QC completed!
[2023-06-27 00:13:47,003] [INFO] Total running time: 0h0m35s