[2023-06-29 12:50:37,941] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:50:37,945] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:50:37,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg852d07b4-fc79-45a8-a3ef-05aff6f08c03/dqc_reference
[2023-06-29 12:50:39,164] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:50:39,165] [INFO] Task started: Prodigal
[2023-06-29 12:50:39,165] [INFO] Running command: gunzip -c /var/lib/cwl/stgf53d0d98-b3b0-4450-a5e2-0a373f23d8ab/GCA_023708885.1_ASM2370888v1_genomic.fna.gz | prodigal -d GCA_023708885.1_ASM2370888v1_genomic.fna/cds.fna -a GCA_023708885.1_ASM2370888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:50:45,260] [INFO] Task succeeded: Prodigal
[2023-06-29 12:50:45,260] [INFO] Task started: HMMsearch
[2023-06-29 12:50:45,260] [INFO] Running command: hmmsearch --tblout GCA_023708885.1_ASM2370888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg852d07b4-fc79-45a8-a3ef-05aff6f08c03/dqc_reference/reference_markers.hmm GCA_023708885.1_ASM2370888v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:50:45,497] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:50:45,498] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf53d0d98-b3b0-4450-a5e2-0a373f23d8ab/GCA_023708885.1_ASM2370888v1_genomic.fna.gz]
[2023-06-29 12:50:45,522] [INFO] Query marker FASTA was written to GCA_023708885.1_ASM2370888v1_genomic.fna/markers.fasta
[2023-06-29 12:50:45,522] [INFO] Task started: Blastn
[2023-06-29 12:50:45,522] [INFO] Running command: blastn -query GCA_023708885.1_ASM2370888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg852d07b4-fc79-45a8-a3ef-05aff6f08c03/dqc_reference/reference_markers.fasta -out GCA_023708885.1_ASM2370888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:50:46,101] [INFO] Task succeeded: Blastn
[2023-06-29 12:50:46,106] [INFO] Selected 17 target genomes.
[2023-06-29 12:50:46,107] [INFO] Target genome list was writen to GCA_023708885.1_ASM2370888v1_genomic.fna/target_genomes.txt
[2023-06-29 12:50:46,110] [INFO] Task started: fastANI
[2023-06-29 12:50:46,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgf53d0d98-b3b0-4450-a5e2-0a373f23d8ab/GCA_023708885.1_ASM2370888v1_genomic.fna.gz --refList GCA_023708885.1_ASM2370888v1_genomic.fna/target_genomes.txt --output GCA_023708885.1_ASM2370888v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:50:53,646] [INFO] Task succeeded: fastANI
[2023-06-29 12:50:53,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg852d07b4-fc79-45a8-a3ef-05aff6f08c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:50:53,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg852d07b4-fc79-45a8-a3ef-05aff6f08c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:50:53,656] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:50:53,656] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:50:53,657] [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	81.0528	410	731	95	below_threshold
Allisonella histaminiformans	strain=DSM 15230	GCA_900103425.1	209880	209880	type	True	77.4687	63	731	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:50:53,659] [INFO] DFAST Taxonomy check result was written to GCA_023708885.1_ASM2370888v1_genomic.fna/tc_result.tsv
[2023-06-29 12:50:53,659] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:50:53,660] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:50:53,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg852d07b4-fc79-45a8-a3ef-05aff6f08c03/dqc_reference/checkm_data
[2023-06-29 12:50:53,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:50:53,693] [INFO] Task started: CheckM
[2023-06-29 12:50:53,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708885.1_ASM2370888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708885.1_ASM2370888v1_genomic.fna/checkm_input GCA_023708885.1_ASM2370888v1_genomic.fna/checkm_result
[2023-06-29 12:51:17,587] [INFO] Task succeeded: CheckM
[2023-06-29 12:51:17,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:51:17,611] [INFO] ===== Completeness check finished =====
[2023-06-29 12:51:17,611] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:51:17,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708885.1_ASM2370888v1_genomic.fna/markers.fasta)
[2023-06-29 12:51:17,612] [INFO] Task started: Blastn
[2023-06-29 12:51:17,612] [INFO] Running command: blastn -query GCA_023708885.1_ASM2370888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg852d07b4-fc79-45a8-a3ef-05aff6f08c03/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708885.1_ASM2370888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:51:18,371] [INFO] Task succeeded: Blastn
[2023-06-29 12:51:18,374] [INFO] Selected 7 target genomes.
[2023-06-29 12:51:18,374] [INFO] Target genome list was writen to GCA_023708885.1_ASM2370888v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:51:18,376] [INFO] Task started: fastANI
[2023-06-29 12:51:18,376] [INFO] Running command: fastANI --query /var/lib/cwl/stgf53d0d98-b3b0-4450-a5e2-0a373f23d8ab/GCA_023708885.1_ASM2370888v1_genomic.fna.gz --refList GCA_023708885.1_ASM2370888v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708885.1_ASM2370888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:51:24,063] [INFO] Task succeeded: fastANI
[2023-06-29 12:51:24,078] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:51:24,078] [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_900541605.1	s__Dialister sp900541605	99.5872	546	731	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	98.13	96.92	0.86	0.81	3	conclusive
GCA_900765565.1	s__Dialister sp900765565	87.7154	503	731	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_900538805.1	s__Dialister sp900538805	81.5117	403	731	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	81.0891	376	731	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	97.66	97.44	0.86	0.82	5	-
GCF_000242435.1	s__Dialister succinatiphilus	81.0498	409	731	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	97.14	96.38	0.90	0.85	7	-
GCA_000434475.1	s__Dialister sp000434475	78.2198	179	731	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	96.42	95.78	0.79	0.72	9	-
GCA_900543165.1	s__Dialister sp900543165	77.9343	192	731	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	98.68	98.63	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-29 12:51:24,080] [INFO] GTDB search result was written to GCA_023708885.1_ASM2370888v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:51:24,081] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:51:24,084] [INFO] DFAST_QC result json was written to GCA_023708885.1_ASM2370888v1_genomic.fna/dqc_result.json
[2023-06-29 12:51:24,084] [INFO] DFAST_QC completed!
[2023-06-29 12:51:24,084] [INFO] Total running time: 0h0m46s