[2024-01-24 12:47:22,039] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:22,042] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:22,042] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2af59ff-cb3e-4a4c-a4b3-14a9f966e3cb/dqc_reference
[2024-01-24 12:47:23,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:23,279] [INFO] Task started: Prodigal
[2024-01-24 12:47:23,280] [INFO] Running command: gunzip -c /var/lib/cwl/stgc50b47a2-e38d-4fa0-b3af-86701e6ad546/GCF_900343095.1_PRJEB25867_genomic.fna.gz | prodigal -d GCF_900343095.1_PRJEB25867_genomic.fna/cds.fna -a GCF_900343095.1_PRJEB25867_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:29,318] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:29,318] [INFO] Task started: HMMsearch
[2024-01-24 12:47:29,318] [INFO] Running command: hmmsearch --tblout GCF_900343095.1_PRJEB25867_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2af59ff-cb3e-4a4c-a4b3-14a9f966e3cb/dqc_reference/reference_markers.hmm GCF_900343095.1_PRJEB25867_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:29,565] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:29,567] [INFO] Found 6/6 markers.
[2024-01-24 12:47:29,600] [INFO] Query marker FASTA was written to GCF_900343095.1_PRJEB25867_genomic.fna/markers.fasta
[2024-01-24 12:47:29,601] [INFO] Task started: Blastn
[2024-01-24 12:47:29,601] [INFO] Running command: blastn -query GCF_900343095.1_PRJEB25867_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2af59ff-cb3e-4a4c-a4b3-14a9f966e3cb/dqc_reference/reference_markers.fasta -out GCF_900343095.1_PRJEB25867_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:30,215] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:30,219] [INFO] Selected 21 target genomes.
[2024-01-24 12:47:30,219] [INFO] Target genome list was writen to GCF_900343095.1_PRJEB25867_genomic.fna/target_genomes.txt
[2024-01-24 12:47:30,230] [INFO] Task started: fastANI
[2024-01-24 12:47:30,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgc50b47a2-e38d-4fa0-b3af-86701e6ad546/GCF_900343095.1_PRJEB25867_genomic.fna.gz --refList GCF_900343095.1_PRJEB25867_genomic.fna/target_genomes.txt --output GCF_900343095.1_PRJEB25867_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:44,372] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:44,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2af59ff-cb3e-4a4c-a4b3-14a9f966e3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:44,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2af59ff-cb3e-4a4c-a4b3-14a9f966e3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:44,381] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:44,381] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:44,381] [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 invisus	strain=DSM 15470	GCA_000160055.1	218538	218538	type	True	80.1865	69	773	95	below_threshold
Dialister succinatiphilus	strain=YIT 11850	GCA_000242435.1	487173	487173	type	True	79.2539	207	773	95	below_threshold
Allisonella histaminiformans	strain=DSM 15230	GCA_900103425.1	209880	209880	type	True	79.1589	56	773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:44,384] [INFO] DFAST Taxonomy check result was written to GCF_900343095.1_PRJEB25867_genomic.fna/tc_result.tsv
[2024-01-24 12:47:44,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:44,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:44,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2af59ff-cb3e-4a4c-a4b3-14a9f966e3cb/dqc_reference/checkm_data
[2024-01-24 12:47:44,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:44,421] [INFO] Task started: CheckM
[2024-01-24 12:47:44,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900343095.1_PRJEB25867_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900343095.1_PRJEB25867_genomic.fna/checkm_input GCF_900343095.1_PRJEB25867_genomic.fna/checkm_result
[2024-01-24 12:48:10,117] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:10,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:10,137] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:10,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:10,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900343095.1_PRJEB25867_genomic.fna/markers.fasta)
[2024-01-24 12:48:10,138] [INFO] Task started: Blastn
[2024-01-24 12:48:10,139] [INFO] Running command: blastn -query GCF_900343095.1_PRJEB25867_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2af59ff-cb3e-4a4c-a4b3-14a9f966e3cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900343095.1_PRJEB25867_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:11,025] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:11,030] [INFO] Selected 19 target genomes.
[2024-01-24 12:48:11,031] [INFO] Target genome list was writen to GCF_900343095.1_PRJEB25867_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:11,061] [INFO] Task started: fastANI
[2024-01-24 12:48:11,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgc50b47a2-e38d-4fa0-b3af-86701e6ad546/GCF_900343095.1_PRJEB25867_genomic.fna.gz --refList GCF_900343095.1_PRJEB25867_genomic.fna/target_genomes_gtdb.txt --output GCF_900343095.1_PRJEB25867_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:20,305] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:20,320] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:20,321] [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	99.1889	695	773	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_900538805.1	s__Dialister sp900538805	79.3993	204	773	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	78.9225	176	773	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	78.9045	129	773	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_900543165.1	s__Dialister sp900543165	78.8942	184	773	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_002471975.1	s__Dialister sp002471975	78.8125	157	773	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_900765565.1	s__Dialister sp900765565	78.6828	171	773	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_900314595.1	s__Dialister sp900314595	78.6273	174	773	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_002297935.1	s__Dialister sp002297935	78.4583	149	773	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_900541605.1	s__Dialister sp900541605	78.4332	169	773	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	98.13	96.92	0.86	0.81	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:20,325] [INFO] GTDB search result was written to GCF_900343095.1_PRJEB25867_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:20,326] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:20,330] [INFO] DFAST_QC result json was written to GCF_900343095.1_PRJEB25867_genomic.fna/dqc_result.json
[2024-01-24 12:48:20,330] [INFO] DFAST_QC completed!
[2024-01-24 12:48:20,331] [INFO] Total running time: 0h0m58s