[2023-06-13 14:58:47,700] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:58:47,709] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:58:47,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg59ad0797-f7b5-4375-a7c3-543b855c8752/dqc_reference
[2023-06-13 14:58:49,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:58:49,517] [INFO] Task started: Prodigal
[2023-06-13 14:58:49,518] [INFO] Running command: gunzip -c /var/lib/cwl/stg69a8bd64-14df-4d17-b930-ae145ac77e20/GCA_022795175.1_ASM2279517v1_genomic.fna.gz | prodigal -d GCA_022795175.1_ASM2279517v1_genomic.fna/cds.fna -a GCA_022795175.1_ASM2279517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:58:57,498] [INFO] Task succeeded: Prodigal
[2023-06-13 14:58:57,498] [INFO] Task started: HMMsearch
[2023-06-13 14:58:57,498] [INFO] Running command: hmmsearch --tblout GCA_022795175.1_ASM2279517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59ad0797-f7b5-4375-a7c3-543b855c8752/dqc_reference/reference_markers.hmm GCA_022795175.1_ASM2279517v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:58:57,795] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:58:57,796] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg69a8bd64-14df-4d17-b930-ae145ac77e20/GCA_022795175.1_ASM2279517v1_genomic.fna.gz]
[2023-06-13 14:58:57,825] [INFO] Query marker FASTA was written to GCA_022795175.1_ASM2279517v1_genomic.fna/markers.fasta
[2023-06-13 14:58:57,825] [INFO] Task started: Blastn
[2023-06-13 14:58:57,825] [INFO] Running command: blastn -query GCA_022795175.1_ASM2279517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59ad0797-f7b5-4375-a7c3-543b855c8752/dqc_reference/reference_markers.fasta -out GCA_022795175.1_ASM2279517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:58:58,337] [INFO] Task succeeded: Blastn
[2023-06-13 14:58:58,341] [INFO] Selected 20 target genomes.
[2023-06-13 14:58:58,341] [INFO] Target genome list was writen to GCA_022795175.1_ASM2279517v1_genomic.fna/target_genomes.txt
[2023-06-13 14:58:58,342] [INFO] Task started: fastANI
[2023-06-13 14:58:58,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg69a8bd64-14df-4d17-b930-ae145ac77e20/GCA_022795175.1_ASM2279517v1_genomic.fna.gz --refList GCA_022795175.1_ASM2279517v1_genomic.fna/target_genomes.txt --output GCA_022795175.1_ASM2279517v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:59:13,326] [INFO] Task succeeded: fastANI
[2023-06-13 14:59:13,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59ad0797-f7b5-4375-a7c3-543b855c8752/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:59:13,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59ad0797-f7b5-4375-a7c3-543b855c8752/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:59:13,333] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:59:13,333] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:59:13,333] [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
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.2033	50	1159	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.2001	73	1159	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.178	74	1159	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.1509	114	1159	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.1451	109	1159	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.0866	102	1159	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	75.9689	88	1159	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:59:13,335] [INFO] DFAST Taxonomy check result was written to GCA_022795175.1_ASM2279517v1_genomic.fna/tc_result.tsv
[2023-06-13 14:59:13,336] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:59:13,336] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:59:13,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59ad0797-f7b5-4375-a7c3-543b855c8752/dqc_reference/checkm_data
[2023-06-13 14:59:13,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:59:13,386] [INFO] Task started: CheckM
[2023-06-13 14:59:13,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022795175.1_ASM2279517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022795175.1_ASM2279517v1_genomic.fna/checkm_input GCA_022795175.1_ASM2279517v1_genomic.fna/checkm_result
[2023-06-13 14:59:40,198] [INFO] Task succeeded: CheckM
[2023-06-13 14:59:40,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:59:40,215] [INFO] ===== Completeness check finished =====
[2023-06-13 14:59:40,215] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:59:40,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022795175.1_ASM2279517v1_genomic.fna/markers.fasta)
[2023-06-13 14:59:40,216] [INFO] Task started: Blastn
[2023-06-13 14:59:40,216] [INFO] Running command: blastn -query GCA_022795175.1_ASM2279517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59ad0797-f7b5-4375-a7c3-543b855c8752/dqc_reference/reference_markers_gtdb.fasta -out GCA_022795175.1_ASM2279517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:59:40,877] [INFO] Task succeeded: Blastn
[2023-06-13 14:59:40,880] [INFO] Selected 17 target genomes.
[2023-06-13 14:59:40,880] [INFO] Target genome list was writen to GCA_022795175.1_ASM2279517v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:59:40,884] [INFO] Task started: fastANI
[2023-06-13 14:59:40,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg69a8bd64-14df-4d17-b930-ae145ac77e20/GCA_022795175.1_ASM2279517v1_genomic.fna.gz --refList GCA_022795175.1_ASM2279517v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022795175.1_ASM2279517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:59:54,191] [INFO] Task succeeded: fastANI
[2023-06-13 14:59:54,200] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:59:54,200] [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_910575255.1	s__Ventrimonas sp910575255	99.3487	1083	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.31	99.12	0.89	0.88	4	conclusive
GCA_910588875.1	s__Ventrimonas sp910588875	82.923	554	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586255.1	s__Ventrimonas sp910586255	80.5211	538	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669055.1	s__Ventrimonas sp003669055	80.3624	522	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003611875.1	s__Ventrimonas sp003611875	79.1076	458	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.50	99.24	0.91	0.86	4	-
GCA_910586205.1	s__Ventrimonas sp910586205	78.7752	424	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577655.1	s__Ventrimonas sp910577655	77.1507	242	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715565.1	s__Ventrimonas merdavium	77.1218	172	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCA_004554205.1	s__Ventrimonas sp004554205	76.9612	130	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540335.1	s__Ventrimonas sp900540335	76.849	172	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.37	99.36	0.86	0.81	3	-
GCA_018715905.1	s__Caccovicinus merdipullorum	76.801	93	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	98.94	98.69	0.87	0.79	3	-
GCA_910584785.1	s__Caccovicinus sp910584785	76.4314	110	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770345.1	s__Enterocloster sp900770345	76.3975	121	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158075.1	s__Enterocloster asparagiformis	76.1221	109	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.72	98.33	0.90	0.88	5	-
--------------------------------------------------------------------------------
[2023-06-13 14:59:54,202] [INFO] GTDB search result was written to GCA_022795175.1_ASM2279517v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:59:54,203] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:59:54,206] [INFO] DFAST_QC result json was written to GCA_022795175.1_ASM2279517v1_genomic.fna/dqc_result.json
[2023-06-13 14:59:54,206] [INFO] DFAST_QC completed!
[2023-06-13 14:59:54,206] [INFO] Total running time: 0h1m7s