[2024-01-25 18:06:50,336] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:50,337] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:50,337] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f3dedf5-3df5-463a-8097-bdc3c3dd0805/dqc_reference
[2024-01-25 18:06:51,454] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:51,455] [INFO] Task started: Prodigal
[2024-01-25 18:06:51,455] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a200e93-2181-401f-ad5d-8fb13b1a661b/GCF_025567565.1_ASM2556756v1_genomic.fna.gz | prodigal -d GCF_025567565.1_ASM2556756v1_genomic.fna/cds.fna -a GCF_025567565.1_ASM2556756v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:59,223] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:59,224] [INFO] Task started: HMMsearch
[2024-01-25 18:06:59,224] [INFO] Running command: hmmsearch --tblout GCF_025567565.1_ASM2556756v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f3dedf5-3df5-463a-8097-bdc3c3dd0805/dqc_reference/reference_markers.hmm GCF_025567565.1_ASM2556756v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:59,451] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:59,452] [INFO] Found 6/6 markers.
[2024-01-25 18:06:59,484] [INFO] Query marker FASTA was written to GCF_025567565.1_ASM2556756v1_genomic.fna/markers.fasta
[2024-01-25 18:06:59,485] [INFO] Task started: Blastn
[2024-01-25 18:06:59,485] [INFO] Running command: blastn -query GCF_025567565.1_ASM2556756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f3dedf5-3df5-463a-8097-bdc3c3dd0805/dqc_reference/reference_markers.fasta -out GCF_025567565.1_ASM2556756v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:00,136] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:00,141] [INFO] Selected 14 target genomes.
[2024-01-25 18:07:00,141] [INFO] Target genome list was writen to GCF_025567565.1_ASM2556756v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:00,157] [INFO] Task started: fastANI
[2024-01-25 18:07:00,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a200e93-2181-401f-ad5d-8fb13b1a661b/GCF_025567565.1_ASM2556756v1_genomic.fna.gz --refList GCF_025567565.1_ASM2556756v1_genomic.fna/target_genomes.txt --output GCF_025567565.1_ASM2556756v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:07,204] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:07,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f3dedf5-3df5-463a-8097-bdc3c3dd0805/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:07,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f3dedf5-3df5-463a-8097-bdc3c3dd0805/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:07,213] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:07:07,213] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:07:07,213] [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	80.406	327	1010	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	80.1778	76	1010	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.1669	199	1010	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	80.0254	225	1010	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	79.5247	238	1010	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	79.4248	228	1010	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	79.3553	123	1010	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	78.6778	110	1010	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	78.5286	145	1010	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	78.4898	141	1010	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.017	118	1010	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.2886	119	1010	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	77.2886	119	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:07,215] [INFO] DFAST Taxonomy check result was written to GCF_025567565.1_ASM2556756v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:07,215] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:07,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:07,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f3dedf5-3df5-463a-8097-bdc3c3dd0805/dqc_reference/checkm_data
[2024-01-25 18:07:07,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:07,258] [INFO] Task started: CheckM
[2024-01-25 18:07:07,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567565.1_ASM2556756v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567565.1_ASM2556756v1_genomic.fna/checkm_input GCF_025567565.1_ASM2556756v1_genomic.fna/checkm_result
[2024-01-25 18:07:33,735] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:33,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:33,772] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:33,772] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:33,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567565.1_ASM2556756v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:33,773] [INFO] Task started: Blastn
[2024-01-25 18:07:33,773] [INFO] Running command: blastn -query GCF_025567565.1_ASM2556756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f3dedf5-3df5-463a-8097-bdc3c3dd0805/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567565.1_ASM2556756v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:34,902] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:34,905] [INFO] Selected 19 target genomes.
[2024-01-25 18:07:34,906] [INFO] Target genome list was writen to GCF_025567565.1_ASM2556756v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:34,933] [INFO] Task started: fastANI
[2024-01-25 18:07:34,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a200e93-2181-401f-ad5d-8fb13b1a661b/GCF_025567565.1_ASM2556756v1_genomic.fna.gz --refList GCF_025567565.1_ASM2556756v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567565.1_ASM2556756v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:46,340] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:46,351] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:46,351] [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_902362775.1	s__Lawsonibacter sp900066645	98.5104	759	1010	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.83	98.51	0.84	0.79	7	conclusive
GCA_003573975.1	s__Lawsonibacter sp900066825	82.6277	443	1010	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.28	97.95	0.82	0.77	5	-
GCF_003478995.1	s__Lawsonibacter sp003478995	80.9662	414	1010	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902363045.1	s__Lawsonibacter sp902363045	80.9032	379	1010	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.07	97.96	0.86	0.80	4	-
GCA_003112755.1	s__Lawsonibacter asaccharolyticus	80.602	348	1010	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.88	98.69	0.87	0.78	6	-
GCA_900754605.1	s__Lawsonibacter sp900754605	80.3015	286	1010	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.97	98.72	0.79	0.78	3	-
GCA_900764755.1	s__Lawsonibacter sp900764755	80.2683	327	1010	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	99.46	99.46	0.86	0.86	2	-
GCA_900550705.1	s__Lawsonibacter sp900550705	80.1464	248	1010	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	79.9798	336	1010	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_002159175.1	s__An92 sp002159175	79.941	236	1010	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCA_910589085.1	s__Lawsonibacter sp910589085	79.8379	288	1010	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	79.7774	342	1010	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_904420465.1	s__Lawsonibacter sp904420465	79.71	322	1010	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	79.6993	313	1010	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	79.6843	320	1010	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	79.6306	320	1010	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	79.6239	345	1010	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	79.4686	309	1010	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_900553135.1	s__Lawsonibacter sp900553135	79.3294	249	1010	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:46,353] [INFO] GTDB search result was written to GCF_025567565.1_ASM2556756v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:46,353] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:46,356] [INFO] DFAST_QC result json was written to GCF_025567565.1_ASM2556756v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:46,356] [INFO] DFAST_QC completed!
[2024-01-25 18:07:46,356] [INFO] Total running time: 0h0m56s