[2023-06-18 21:39:28,777] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:39:28,778] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:39:28,779] [INFO] DQC Reference Directory: /var/lib/cwl/stge8ee35e1-83fa-449a-ae25-f8db29274b1f/dqc_reference
[2023-06-18 21:39:30,018] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:39:30,019] [INFO] Task started: Prodigal
[2023-06-18 21:39:30,019] [INFO] Running command: gunzip -c /var/lib/cwl/stgafb29ca1-f32f-420d-bdbe-c2cb46945989/GCA_018376255.1_ASM1837625v1_genomic.fna.gz | prodigal -d GCA_018376255.1_ASM1837625v1_genomic.fna/cds.fna -a GCA_018376255.1_ASM1837625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:39:34,123] [INFO] Task succeeded: Prodigal
[2023-06-18 21:39:34,124] [INFO] Task started: HMMsearch
[2023-06-18 21:39:34,124] [INFO] Running command: hmmsearch --tblout GCA_018376255.1_ASM1837625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8ee35e1-83fa-449a-ae25-f8db29274b1f/dqc_reference/reference_markers.hmm GCA_018376255.1_ASM1837625v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:39:34,369] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:39:34,371] [INFO] Found 6/6 markers.
[2023-06-18 21:39:34,393] [INFO] Query marker FASTA was written to GCA_018376255.1_ASM1837625v1_genomic.fna/markers.fasta
[2023-06-18 21:39:34,394] [INFO] Task started: Blastn
[2023-06-18 21:39:34,394] [INFO] Running command: blastn -query GCA_018376255.1_ASM1837625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8ee35e1-83fa-449a-ae25-f8db29274b1f/dqc_reference/reference_markers.fasta -out GCA_018376255.1_ASM1837625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:39:35,022] [INFO] Task succeeded: Blastn
[2023-06-18 21:39:35,027] [INFO] Selected 21 target genomes.
[2023-06-18 21:39:35,028] [INFO] Target genome list was writen to GCA_018376255.1_ASM1837625v1_genomic.fna/target_genomes.txt
[2023-06-18 21:39:35,036] [INFO] Task started: fastANI
[2023-06-18 21:39:35,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgafb29ca1-f32f-420d-bdbe-c2cb46945989/GCA_018376255.1_ASM1837625v1_genomic.fna.gz --refList GCA_018376255.1_ASM1837625v1_genomic.fna/target_genomes.txt --output GCA_018376255.1_ASM1837625v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:39:48,516] [INFO] Task succeeded: fastANI
[2023-06-18 21:39:48,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8ee35e1-83fa-449a-ae25-f8db29274b1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:39:48,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8ee35e1-83fa-449a-ae25-f8db29274b1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:39:48,524] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:39:48,524] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 21:39:48,525] [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
Dialister succinatiphilus	strain=YIT 11850	GCA_000242435.1	487173	487173	type	True	79.3764	173	531	95	below_threshold
Dialister invisus	strain=DSM 15470	GCA_000160055.1	218538	218538	type	True	78.5582	52	531	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 21:39:48,527] [INFO] DFAST Taxonomy check result was written to GCA_018376255.1_ASM1837625v1_genomic.fna/tc_result.tsv
[2023-06-18 21:39:48,528] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:39:48,528] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:39:48,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8ee35e1-83fa-449a-ae25-f8db29274b1f/dqc_reference/checkm_data
[2023-06-18 21:39:48,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:39:48,559] [INFO] Task started: CheckM
[2023-06-18 21:39:48,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018376255.1_ASM1837625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018376255.1_ASM1837625v1_genomic.fna/checkm_input GCA_018376255.1_ASM1837625v1_genomic.fna/checkm_result
[2023-06-18 21:40:08,244] [INFO] Task succeeded: CheckM
[2023-06-18 21:40:08,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:40:08,275] [INFO] ===== Completeness check finished =====
[2023-06-18 21:40:08,276] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:40:08,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018376255.1_ASM1837625v1_genomic.fna/markers.fasta)
[2023-06-18 21:40:08,276] [INFO] Task started: Blastn
[2023-06-18 21:40:08,277] [INFO] Running command: blastn -query GCA_018376255.1_ASM1837625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8ee35e1-83fa-449a-ae25-f8db29274b1f/dqc_reference/reference_markers_gtdb.fasta -out GCA_018376255.1_ASM1837625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:40:09,116] [INFO] Task succeeded: Blastn
[2023-06-18 21:40:09,120] [INFO] Selected 19 target genomes.
[2023-06-18 21:40:09,120] [INFO] Target genome list was writen to GCA_018376255.1_ASM1837625v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:40:09,133] [INFO] Task started: fastANI
[2023-06-18 21:40:09,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgafb29ca1-f32f-420d-bdbe-c2cb46945989/GCA_018376255.1_ASM1837625v1_genomic.fna.gz --refList GCA_018376255.1_ASM1837625v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018376255.1_ASM1837625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:40:17,395] [INFO] Task succeeded: fastANI
[2023-06-18 21:40:17,410] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:40:17,410] [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
GCF_007164725.1	s__Dialister hominis	99.3606	515	531	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	99.17	99.05	0.95	0.90	7	conclusive
GCA_002471975.1	s__Dialister sp002471975	79.6064	127	531	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	99.86	99.84	0.93	0.92	3	-
GCA_900538805.1	s__Dialister sp900538805	79.1847	178	531	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	96.71	96.58	0.85	0.82	3	-
GCA_002320515.1	s__Dialister sp002320515	79.032	160	531	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	97.66	97.44	0.86	0.82	5	-
GCA_900759415.1	s__Dialister sp900759415	79.011	114	531	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	97.64	97.64	0.87	0.87	2	-
GCA_900314595.1	s__Dialister sp900314595	78.8754	146	531	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	99.02	98.53	0.83	0.77	4	-
GCA_900541605.1	s__Dialister sp900541605	78.7769	143	531	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	98.13	96.92	0.86	0.81	3	-
GCA_002297935.1	s__Dialister sp002297935	78.7751	115	531	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765565.1	s__Dialister sp900765565	78.6364	140	531	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	99.94	99.94	0.92	0.92	2	-
GCA_900543165.1	s__Dialister sp900543165	78.6339	156	531	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	98.68	98.63	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-18 21:40:17,415] [INFO] GTDB search result was written to GCA_018376255.1_ASM1837625v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:40:17,416] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:40:17,420] [INFO] DFAST_QC result json was written to GCA_018376255.1_ASM1837625v1_genomic.fna/dqc_result.json
[2023-06-18 21:40:17,421] [INFO] DFAST_QC completed!
[2023-06-18 21:40:17,421] [INFO] Total running time: 0h0m49s