[2023-06-26 23:51:39,990] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:51:39,993] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:51:39,993] [INFO] DQC Reference Directory: /var/lib/cwl/stg415f9251-9649-4b44-b5a4-6be47255d868/dqc_reference
[2023-06-26 23:51:41,295] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:51:41,296] [INFO] Task started: Prodigal
[2023-06-26 23:51:41,296] [INFO] Running command: gunzip -c /var/lib/cwl/stg315cd387-51c6-4ab4-ab07-005544366a8a/GCA_002431385.1_ASM243138v1_genomic.fna.gz | prodigal -d GCA_002431385.1_ASM243138v1_genomic.fna/cds.fna -a GCA_002431385.1_ASM243138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:51:47,181] [INFO] Task succeeded: Prodigal
[2023-06-26 23:51:47,182] [INFO] Task started: HMMsearch
[2023-06-26 23:51:47,182] [INFO] Running command: hmmsearch --tblout GCA_002431385.1_ASM243138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg415f9251-9649-4b44-b5a4-6be47255d868/dqc_reference/reference_markers.hmm GCA_002431385.1_ASM243138v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:51:47,414] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:51:47,416] [INFO] Found 6/6 markers.
[2023-06-26 23:51:47,440] [INFO] Query marker FASTA was written to GCA_002431385.1_ASM243138v1_genomic.fna/markers.fasta
[2023-06-26 23:51:47,441] [INFO] Task started: Blastn
[2023-06-26 23:51:47,441] [INFO] Running command: blastn -query GCA_002431385.1_ASM243138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg415f9251-9649-4b44-b5a4-6be47255d868/dqc_reference/reference_markers.fasta -out GCA_002431385.1_ASM243138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:51:48,118] [INFO] Task succeeded: Blastn
[2023-06-26 23:51:48,155] [INFO] Selected 30 target genomes.
[2023-06-26 23:51:48,156] [INFO] Target genome list was writen to GCA_002431385.1_ASM243138v1_genomic.fna/target_genomes.txt
[2023-06-26 23:51:48,181] [INFO] Task started: fastANI
[2023-06-26 23:51:48,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg315cd387-51c6-4ab4-ab07-005544366a8a/GCA_002431385.1_ASM243138v1_genomic.fna.gz --refList GCA_002431385.1_ASM243138v1_genomic.fna/target_genomes.txt --output GCA_002431385.1_ASM243138v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:52:06,339] [INFO] Task succeeded: fastANI
[2023-06-26 23:52:06,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg415f9251-9649-4b44-b5a4-6be47255d868/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:52:06,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg415f9251-9649-4b44-b5a4-6be47255d868/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:52:06,354] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:52:06,355] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 23:52:06,355] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.3614	92	695	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.3063	96	695	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.1262	91	695	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.014	77	695	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.9228	84	695	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	76.8963	59	695	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.8591	61	695	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.8556	60	695	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.7334	100	695	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.7002	106	695	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.6095	84	695	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.5879	50	695	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	76.5879	50	695	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.5276	72	695	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	75.6239	72	695	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:52:06,357] [INFO] DFAST Taxonomy check result was written to GCA_002431385.1_ASM243138v1_genomic.fna/tc_result.tsv
[2023-06-26 23:52:06,358] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:52:06,358] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:52:06,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg415f9251-9649-4b44-b5a4-6be47255d868/dqc_reference/checkm_data
[2023-06-26 23:52:06,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:52:06,399] [INFO] Task started: CheckM
[2023-06-26 23:52:06,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002431385.1_ASM243138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002431385.1_ASM243138v1_genomic.fna/checkm_input GCA_002431385.1_ASM243138v1_genomic.fna/checkm_result
[2023-06-26 23:52:30,645] [INFO] Task succeeded: CheckM
[2023-06-26 23:52:30,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.41%
Contamintation: 7.15%
Strain heterogeneity: 87.50%
--------------------------------------------------------------------------------
[2023-06-26 23:52:30,691] [INFO] ===== Completeness check finished =====
[2023-06-26 23:52:30,691] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:52:30,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002431385.1_ASM243138v1_genomic.fna/markers.fasta)
[2023-06-26 23:52:30,692] [INFO] Task started: Blastn
[2023-06-26 23:52:30,692] [INFO] Running command: blastn -query GCA_002431385.1_ASM243138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg415f9251-9649-4b44-b5a4-6be47255d868/dqc_reference/reference_markers_gtdb.fasta -out GCA_002431385.1_ASM243138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:52:31,746] [INFO] Task succeeded: Blastn
[2023-06-26 23:52:31,750] [INFO] Selected 12 target genomes.
[2023-06-26 23:52:31,750] [INFO] Target genome list was writen to GCA_002431385.1_ASM243138v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:52:31,760] [INFO] Task started: fastANI
[2023-06-26 23:52:31,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg315cd387-51c6-4ab4-ab07-005544366a8a/GCA_002431385.1_ASM243138v1_genomic.fna.gz --refList GCA_002431385.1_ASM243138v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002431385.1_ASM243138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:52:37,689] [INFO] Task succeeded: fastANI
[2023-06-26 23:52:37,704] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 23:52:37,705] [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_002436765.1	s__Faecousia sp002436765	99.4536	545	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.53	99.53	0.91	0.91	2	conclusive
GCA_000434635.1	s__Faecousia sp000434635	91.8471	493	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.30	97.16	0.81	0.81	4	-
GCA_900546075.1	s__Faecousia sp900546075	91.6195	452	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.06	96.74	0.84	0.78	6	-
GCA_002437585.1	s__Faecousia sp002437585	82.9391	366	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.35	99.16	0.96	0.95	3	-
GCA_900544945.1	s__Faecousia sp900544945	81.5039	295	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.60	96.52	0.82	0.81	4	-
GCA_004562395.1	s__Faecousia sp004562395	81.3195	277	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461445.1	s__Faecousia sp017461445	80.3144	312	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555705.1	s__Faecousia sp004555705	80.2845	266	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715835.1	s__Faecousia intestinavium	80.0423	226	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900763965.1	s__Faecousia sp900763965	79.8518	210	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018710805.1	s__Faecousia faecipullorum	79.504	195	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770015.1	s__Faecousia sp900770015	79.2306	206	695	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:52:37,707] [INFO] GTDB search result was written to GCA_002431385.1_ASM243138v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:52:37,708] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:52:37,711] [INFO] DFAST_QC result json was written to GCA_002431385.1_ASM243138v1_genomic.fna/dqc_result.json
[2023-06-26 23:52:37,712] [INFO] DFAST_QC completed!
[2023-06-26 23:52:37,712] [INFO] Total running time: 0h0m58s