[2023-06-13 22:54:24,116] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:54:24,118] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:54:24,119] [INFO] DQC Reference Directory: /var/lib/cwl/stgea8a8d85-a5df-4b23-9527-71c065e89513/dqc_reference
[2023-06-13 22:54:25,336] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:54:25,337] [INFO] Task started: Prodigal
[2023-06-13 22:54:25,337] [INFO] Running command: gunzip -c /var/lib/cwl/stgf59045cb-dbc2-465d-a9df-24a31271a9ed/GCA_022778095.1_ASM2277809v1_genomic.fna.gz | prodigal -d GCA_022778095.1_ASM2277809v1_genomic.fna/cds.fna -a GCA_022778095.1_ASM2277809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:54:32,593] [INFO] Task succeeded: Prodigal
[2023-06-13 22:54:32,594] [INFO] Task started: HMMsearch
[2023-06-13 22:54:32,594] [INFO] Running command: hmmsearch --tblout GCA_022778095.1_ASM2277809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea8a8d85-a5df-4b23-9527-71c065e89513/dqc_reference/reference_markers.hmm GCA_022778095.1_ASM2277809v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:54:32,854] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:54:32,856] [INFO] Found 6/6 markers.
[2023-06-13 22:54:32,892] [INFO] Query marker FASTA was written to GCA_022778095.1_ASM2277809v1_genomic.fna/markers.fasta
[2023-06-13 22:54:32,892] [INFO] Task started: Blastn
[2023-06-13 22:54:32,892] [INFO] Running command: blastn -query GCA_022778095.1_ASM2277809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea8a8d85-a5df-4b23-9527-71c065e89513/dqc_reference/reference_markers.fasta -out GCA_022778095.1_ASM2277809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:54:33,583] [INFO] Task succeeded: Blastn
[2023-06-13 22:54:33,588] [INFO] Selected 22 target genomes.
[2023-06-13 22:54:33,589] [INFO] Target genome list was writen to GCA_022778095.1_ASM2277809v1_genomic.fna/target_genomes.txt
[2023-06-13 22:54:33,592] [INFO] Task started: fastANI
[2023-06-13 22:54:33,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgf59045cb-dbc2-465d-a9df-24a31271a9ed/GCA_022778095.1_ASM2277809v1_genomic.fna.gz --refList GCA_022778095.1_ASM2277809v1_genomic.fna/target_genomes.txt --output GCA_022778095.1_ASM2277809v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:54:45,457] [INFO] Task succeeded: fastANI
[2023-06-13 22:54:45,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea8a8d85-a5df-4b23-9527-71c065e89513/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:54:45,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea8a8d85-a5df-4b23-9527-71c065e89513/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:54:45,471] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:54:45,471] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 22:54:45,472] [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
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	80.6014	85	801	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	79.4812	97	801	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.8795	89	801	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.7079	71	801	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.6299	91	801	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.5015	82	801	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.1278	83	801	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	77.0042	57	801	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.0042	57	801	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 22:54:45,474] [INFO] DFAST Taxonomy check result was written to GCA_022778095.1_ASM2277809v1_genomic.fna/tc_result.tsv
[2023-06-13 22:54:45,474] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:54:45,474] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:54:45,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea8a8d85-a5df-4b23-9527-71c065e89513/dqc_reference/checkm_data
[2023-06-13 22:54:45,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:54:45,511] [INFO] Task started: CheckM
[2023-06-13 22:54:45,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022778095.1_ASM2277809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022778095.1_ASM2277809v1_genomic.fna/checkm_input GCA_022778095.1_ASM2277809v1_genomic.fna/checkm_result
[2023-06-13 22:55:13,470] [INFO] Task succeeded: CheckM
[2023-06-13 22:55:13,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 10.61%
Strain heterogeneity: 12.50%
--------------------------------------------------------------------------------
[2023-06-13 22:55:13,499] [INFO] ===== Completeness check finished =====
[2023-06-13 22:55:13,500] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:55:13,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022778095.1_ASM2277809v1_genomic.fna/markers.fasta)
[2023-06-13 22:55:13,500] [INFO] Task started: Blastn
[2023-06-13 22:55:13,501] [INFO] Running command: blastn -query GCA_022778095.1_ASM2277809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea8a8d85-a5df-4b23-9527-71c065e89513/dqc_reference/reference_markers_gtdb.fasta -out GCA_022778095.1_ASM2277809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:55:14,746] [INFO] Task succeeded: Blastn
[2023-06-13 22:55:14,751] [INFO] Selected 15 target genomes.
[2023-06-13 22:55:14,752] [INFO] Target genome list was writen to GCA_022778095.1_ASM2277809v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:55:14,779] [INFO] Task started: fastANI
[2023-06-13 22:55:14,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgf59045cb-dbc2-465d-a9df-24a31271a9ed/GCA_022778095.1_ASM2277809v1_genomic.fna.gz --refList GCA_022778095.1_ASM2277809v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022778095.1_ASM2277809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:55:21,200] [INFO] Task succeeded: fastANI
[2023-06-13 22:55:21,221] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 22:55:21,222] [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_002437585.1	s__Faecousia sp002437585	82.0101	349	801	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	81.962	345	801	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	81.2919	247	801	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_002436765.1	s__Faecousia sp002436765	81.1363	254	801	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.53	99.53	0.91	0.91	2	-
GCA_000434635.1	s__Faecousia sp000434635	80.9547	281	801	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	80.8037	263	801	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_018712645.1	s__Faecousia faecavium	80.4869	239	801	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	80.3701	237	801	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_900762245.1	s__Faecousia sp900762245	79.7757	213	801	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_017465745.1	s__Faecousia sp017465745	79.736	214	801	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_002493965.1	s__Faecousia sp002493965	79.6539	233	801	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.87	99.72	0.89	0.74	6	-
GCA_015067615.1	s__Faecousia sp015067615	79.1643	194	801	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_017939025.1	s__Faecousia sp017939025	79.0815	159	801	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_900549705.1	s__Faecousia sp900549705	79.0148	156	801	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.98	96.52	0.84	0.77	3	-
GCA_017473455.1	s__Faecousia sp017473455	77.6704	100	801	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 22:55:21,224] [INFO] GTDB search result was written to GCA_022778095.1_ASM2277809v1_genomic.fna/result_gtdb.tsv
[2023-06-13 22:55:21,225] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:55:21,228] [INFO] DFAST_QC result json was written to GCA_022778095.1_ASM2277809v1_genomic.fna/dqc_result.json
[2023-06-13 22:55:21,228] [INFO] DFAST_QC completed!
[2023-06-13 22:55:21,229] [INFO] Total running time: 0h0m57s