[2023-06-12 23:06:02,599] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:06:02,601] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:06:02,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg0610ef42-edc4-42cf-9fcf-81781daba294/dqc_reference
[2023-06-12 23:06:03,941] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:06:03,942] [INFO] Task started: Prodigal
[2023-06-12 23:06:03,942] [INFO] Running command: gunzip -c /var/lib/cwl/stgc49868f6-7494-4f95-8bc1-c8f610c6515a/GCA_022744105.1_ASM2274410v1_genomic.fna.gz | prodigal -d GCA_022744105.1_ASM2274410v1_genomic.fna/cds.fna -a GCA_022744105.1_ASM2274410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:06:08,556] [INFO] Task succeeded: Prodigal
[2023-06-12 23:06:08,556] [INFO] Task started: HMMsearch
[2023-06-12 23:06:08,556] [INFO] Running command: hmmsearch --tblout GCA_022744105.1_ASM2274410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0610ef42-edc4-42cf-9fcf-81781daba294/dqc_reference/reference_markers.hmm GCA_022744105.1_ASM2274410v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:06:08,800] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:06:08,801] [INFO] Found 6/6 markers.
[2023-06-12 23:06:08,822] [INFO] Query marker FASTA was written to GCA_022744105.1_ASM2274410v1_genomic.fna/markers.fasta
[2023-06-12 23:06:08,823] [INFO] Task started: Blastn
[2023-06-12 23:06:08,823] [INFO] Running command: blastn -query GCA_022744105.1_ASM2274410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0610ef42-edc4-42cf-9fcf-81781daba294/dqc_reference/reference_markers.fasta -out GCA_022744105.1_ASM2274410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:06:09,427] [INFO] Task succeeded: Blastn
[2023-06-12 23:06:09,432] [INFO] Selected 19 target genomes.
[2023-06-12 23:06:09,433] [INFO] Target genome list was writen to GCA_022744105.1_ASM2274410v1_genomic.fna/target_genomes.txt
[2023-06-12 23:06:09,440] [INFO] Task started: fastANI
[2023-06-12 23:06:09,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgc49868f6-7494-4f95-8bc1-c8f610c6515a/GCA_022744105.1_ASM2274410v1_genomic.fna.gz --refList GCA_022744105.1_ASM2274410v1_genomic.fna/target_genomes.txt --output GCA_022744105.1_ASM2274410v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:06:17,838] [INFO] Task succeeded: fastANI
[2023-06-12 23:06:17,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0610ef42-edc4-42cf-9fcf-81781daba294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:06:17,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0610ef42-edc4-42cf-9fcf-81781daba294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:06:17,847] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:06:17,847] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 23:06:17,847] [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	78.9783	144	485	95	below_threshold
Dialister invisus	strain=DSM 15470	GCA_000160055.1	218538	218538	type	True	78.067	58	485	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:06:17,849] [INFO] DFAST Taxonomy check result was written to GCA_022744105.1_ASM2274410v1_genomic.fna/tc_result.tsv
[2023-06-12 23:06:17,850] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:06:17,850] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:06:17,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0610ef42-edc4-42cf-9fcf-81781daba294/dqc_reference/checkm_data
[2023-06-12 23:06:17,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:06:17,881] [INFO] Task started: CheckM
[2023-06-12 23:06:17,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022744105.1_ASM2274410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022744105.1_ASM2274410v1_genomic.fna/checkm_input GCA_022744105.1_ASM2274410v1_genomic.fna/checkm_result
[2023-06-12 23:06:38,881] [INFO] Task succeeded: CheckM
[2023-06-12 23:06:38,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:06:38,904] [INFO] ===== Completeness check finished =====
[2023-06-12 23:06:38,905] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:06:38,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022744105.1_ASM2274410v1_genomic.fna/markers.fasta)
[2023-06-12 23:06:38,905] [INFO] Task started: Blastn
[2023-06-12 23:06:38,906] [INFO] Running command: blastn -query GCA_022744105.1_ASM2274410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0610ef42-edc4-42cf-9fcf-81781daba294/dqc_reference/reference_markers_gtdb.fasta -out GCA_022744105.1_ASM2274410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:06:39,779] [INFO] Task succeeded: Blastn
[2023-06-12 23:06:39,784] [INFO] Selected 11 target genomes.
[2023-06-12 23:06:39,785] [INFO] Target genome list was writen to GCA_022744105.1_ASM2274410v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:06:39,820] [INFO] Task started: fastANI
[2023-06-12 23:06:39,821] [INFO] Running command: fastANI --query /var/lib/cwl/stgc49868f6-7494-4f95-8bc1-c8f610c6515a/GCA_022744105.1_ASM2274410v1_genomic.fna.gz --refList GCA_022744105.1_ASM2274410v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022744105.1_ASM2274410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:06:47,348] [INFO] Task succeeded: fastANI
[2023-06-12 23:06:47,360] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:06:47,361] [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_000434475.1	s__Dialister sp000434475	95.4473	395	485	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	96.42	95.78	0.79	0.72	9	conclusive
GCA_900543455.1	s__Dialister sp900543455	93.3079	397	485	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_900543165.1	s__Dialister sp900543165	92.9884	419	485	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	98.68	98.63	0.86	0.84	3	-
GCA_002297935.1	s__Dialister sp002297935	79.2282	171	485	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_900538805.1	s__Dialister sp900538805	79.0493	140	485	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	96.71	96.58	0.85	0.82	3	-
GCF_007164725.1	s__Dialister hominis	78.9551	148	485	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	99.17	99.05	0.95	0.90	7	-
GCA_002471975.1	s__Dialister sp002471975	78.9373	112	485	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_900541605.1	s__Dialister sp900541605	78.6428	144	485	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_900765565.1	s__Dialister sp900765565	78.0489	134	485	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	99.94	99.94	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-12 23:06:47,363] [INFO] GTDB search result was written to GCA_022744105.1_ASM2274410v1_genomic.fna/result_gtdb.tsv
[2023-06-12 23:06:47,363] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:06:47,366] [INFO] DFAST_QC result json was written to GCA_022744105.1_ASM2274410v1_genomic.fna/dqc_result.json
[2023-06-12 23:06:47,367] [INFO] DFAST_QC completed!
[2023-06-12 23:06:47,367] [INFO] Total running time: 0h0m45s