[2024-01-25 18:42:05,667] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:05,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:05,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg231924e9-3f1f-4f08-a9d8-481c6375befd/dqc_reference
[2024-01-25 18:42:06,803] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:06,804] [INFO] Task started: Prodigal
[2024-01-25 18:42:06,804] [INFO] Running command: gunzip -c /var/lib/cwl/stg6997b37a-226e-4d8c-9be0-2a61fcd94432/GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna.gz | prodigal -d GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/cds.fna -a GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:23,903] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:23,904] [INFO] Task started: HMMsearch
[2024-01-25 18:42:23,904] [INFO] Running command: hmmsearch --tblout GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg231924e9-3f1f-4f08-a9d8-481c6375befd/dqc_reference/reference_markers.hmm GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:24,158] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:24,159] [INFO] Found 6/6 markers.
[2024-01-25 18:42:24,198] [INFO] Query marker FASTA was written to GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/markers.fasta
[2024-01-25 18:42:24,198] [INFO] Task started: Blastn
[2024-01-25 18:42:24,198] [INFO] Running command: blastn -query GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/markers.fasta -db /var/lib/cwl/stg231924e9-3f1f-4f08-a9d8-481c6375befd/dqc_reference/reference_markers.fasta -out GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:24,763] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:24,765] [INFO] Selected 15 target genomes.
[2024-01-25 18:42:24,766] [INFO] Target genome list was writen to GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/target_genomes.txt
[2024-01-25 18:42:24,767] [INFO] Task started: fastANI
[2024-01-25 18:42:24,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg6997b37a-226e-4d8c-9be0-2a61fcd94432/GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna.gz --refList GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/target_genomes.txt --output GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:32,106] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:32,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg231924e9-3f1f-4f08-a9d8-481c6375befd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:32,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg231924e9-3f1f-4f08-a9d8-481c6375befd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:32,116] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:42:32,116] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:42:32,117] [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
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	79.567	362	1439	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.6682	272	1439	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.6115	262	1439	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.4662	111	1439	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.4358	217	1439	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	78.1023	156	1439	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	78.0821	151	1439	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.7533	181	1439	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.7482	148	1439	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.5814	138	1439	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.4943	119	1439	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.1192	110	1439	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	77.0932	94	1439	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	76.9472	97	1439	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.828	61	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:32,118] [INFO] DFAST Taxonomy check result was written to GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/tc_result.tsv
[2024-01-25 18:42:32,120] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:32,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:32,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg231924e9-3f1f-4f08-a9d8-481c6375befd/dqc_reference/checkm_data
[2024-01-25 18:42:32,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:32,165] [INFO] Task started: CheckM
[2024-01-25 18:42:32,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/checkm_input GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/checkm_result
[2024-01-25 18:43:05,975] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:05,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:06,003] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:06,003] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:06,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/markers.fasta)
[2024-01-25 18:43:06,004] [INFO] Task started: Blastn
[2024-01-25 18:43:06,004] [INFO] Running command: blastn -query GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/markers.fasta -db /var/lib/cwl/stg231924e9-3f1f-4f08-a9d8-481c6375befd/dqc_reference/reference_markers_gtdb.fasta -out GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:06,965] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:06,968] [INFO] Selected 13 target genomes.
[2024-01-25 18:43:06,968] [INFO] Target genome list was writen to GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:06,990] [INFO] Task started: fastANI
[2024-01-25 18:43:06,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg6997b37a-226e-4d8c-9be0-2a61fcd94432/GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna.gz --refList GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/target_genomes_gtdb.txt --output GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:17,422] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:17,431] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:43:17,431] [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_910584605.1	s__Lawsonibacter sp910584605	85.7717	604	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575265.1	s__Lawsonibacter sp910575265	84.8939	719	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000492175.1	s__Lawsonibacter sp000492175	84.5547	687	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585815.1	s__Lawsonibacter sp910585815	84.5149	664	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917615.1	s__Lawsonibacter sp009917615	84.4564	718	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578735.1	s__Lawsonibacter sp910578735	84.4518	567	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911645.1	s__Lawsonibacter sp009911645	83.8901	697	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911595.1	s__Lawsonibacter sp009911595	83.8485	667	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588635.1	s__Lawsonibacter sp910588635	83.8079	556	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589085.1	s__Lawsonibacter sp910589085	83.5443	504	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612335.1	s__Lawsonibacter sp003612335	82.8103	614	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287875.1	s__Lawsonibacter sp014287875	80.1445	398	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.47	96.91	0.89	0.83	4	-
GCA_900549405.1	s__Lawsonibacter sp900549405	80.0989	309	1439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.96	97.96	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:17,432] [INFO] GTDB search result was written to GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:17,433] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:17,436] [INFO] DFAST_QC result json was written to GCF_943192995.1_Flintibacter_sp_nov_DSM110149_genomic.fna/dqc_result.json
[2024-01-25 18:43:17,436] [INFO] DFAST_QC completed!
[2024-01-25 18:43:17,437] [INFO] Total running time: 0h1m12s