[2023-06-29 22:29:46,479] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:29:46,482] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:29:46,482] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4394242-d9ac-4cff-b332-2d8b1ac86dcc/dqc_reference
[2023-06-29 22:29:47,868] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:29:47,869] [INFO] Task started: Prodigal
[2023-06-29 22:29:47,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg512eb9c3-048a-4ccc-bc6b-fbe04960d432/GCA_019233845.1_ASM1923384v1_genomic.fna.gz | prodigal -d GCA_019233845.1_ASM1923384v1_genomic.fna/cds.fna -a GCA_019233845.1_ASM1923384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:29:59,225] [INFO] Task succeeded: Prodigal
[2023-06-29 22:29:59,225] [INFO] Task started: HMMsearch
[2023-06-29 22:29:59,225] [INFO] Running command: hmmsearch --tblout GCA_019233845.1_ASM1923384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4394242-d9ac-4cff-b332-2d8b1ac86dcc/dqc_reference/reference_markers.hmm GCA_019233845.1_ASM1923384v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:29:59,582] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:29:59,583] [INFO] Found 6/6 markers.
[2023-06-29 22:29:59,625] [INFO] Query marker FASTA was written to GCA_019233845.1_ASM1923384v1_genomic.fna/markers.fasta
[2023-06-29 22:29:59,625] [INFO] Task started: Blastn
[2023-06-29 22:29:59,625] [INFO] Running command: blastn -query GCA_019233845.1_ASM1923384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4394242-d9ac-4cff-b332-2d8b1ac86dcc/dqc_reference/reference_markers.fasta -out GCA_019233845.1_ASM1923384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:30:00,373] [INFO] Task succeeded: Blastn
[2023-06-29 22:30:00,381] [INFO] Selected 34 target genomes.
[2023-06-29 22:30:00,381] [INFO] Target genome list was writen to GCA_019233845.1_ASM1923384v1_genomic.fna/target_genomes.txt
[2023-06-29 22:30:00,385] [INFO] Task started: fastANI
[2023-06-29 22:30:00,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg512eb9c3-048a-4ccc-bc6b-fbe04960d432/GCA_019233845.1_ASM1923384v1_genomic.fna.gz --refList GCA_019233845.1_ASM1923384v1_genomic.fna/target_genomes.txt --output GCA_019233845.1_ASM1923384v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:30:23,269] [INFO] Task succeeded: fastANI
[2023-06-29 22:30:23,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4394242-d9ac-4cff-b332-2d8b1ac86dcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:30:23,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4394242-d9ac-4cff-b332-2d8b1ac86dcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:30:23,282] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:30:23,282] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:30:23,283] [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
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	75.0697	57	1224	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	75.0297	70	1224	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	74.9304	78	1224	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	74.9034	56	1224	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	74.8676	73	1224	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	74.8483	56	1224	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	74.8081	53	1224	95	below_threshold
Paraburkholderia acidipaludis	strain=NBRC 101816	GCA_000684975.1	660537	660537	type	True	74.7845	62	1224	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	74.7082	90	1224	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	74.6859	53	1224	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:30:23,285] [INFO] DFAST Taxonomy check result was written to GCA_019233845.1_ASM1923384v1_genomic.fna/tc_result.tsv
[2023-06-29 22:30:23,285] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:30:23,285] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:30:23,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4394242-d9ac-4cff-b332-2d8b1ac86dcc/dqc_reference/checkm_data
[2023-06-29 22:30:23,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:30:23,332] [INFO] Task started: CheckM
[2023-06-29 22:30:23,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019233845.1_ASM1923384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019233845.1_ASM1923384v1_genomic.fna/checkm_input GCA_019233845.1_ASM1923384v1_genomic.fna/checkm_result
[2023-06-29 22:30:59,396] [INFO] Task succeeded: CheckM
[2023-06-29 22:30:59,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:30:59,420] [INFO] ===== Completeness check finished =====
[2023-06-29 22:30:59,421] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:30:59,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019233845.1_ASM1923384v1_genomic.fna/markers.fasta)
[2023-06-29 22:30:59,422] [INFO] Task started: Blastn
[2023-06-29 22:30:59,422] [INFO] Running command: blastn -query GCA_019233845.1_ASM1923384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4394242-d9ac-4cff-b332-2d8b1ac86dcc/dqc_reference/reference_markers_gtdb.fasta -out GCA_019233845.1_ASM1923384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:31:00,713] [INFO] Task succeeded: Blastn
[2023-06-29 22:31:00,718] [INFO] Selected 10 target genomes.
[2023-06-29 22:31:00,718] [INFO] Target genome list was writen to GCA_019233845.1_ASM1923384v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:31:00,726] [INFO] Task started: fastANI
[2023-06-29 22:31:00,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg512eb9c3-048a-4ccc-bc6b-fbe04960d432/GCA_019233845.1_ASM1923384v1_genomic.fna.gz --refList GCA_019233845.1_ASM1923384v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019233845.1_ASM1923384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:31:11,462] [INFO] Task succeeded: fastANI
[2023-06-29 22:31:11,473] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:31:11,473] [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_019247495.1	s__JADGNZ01 sp019247495	99.6494	1143	1224	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JADGNZ01	95.0	99.75	99.65	0.94	0.93	3	conclusive
GCA_017883235.1	s__JADGNZ01 sp017883235	81.4326	819	1224	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JADGNZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883205.1	s__JADGNZ01 sp017883205	80.6064	795	1224	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JADGNZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019244185.1	s__QHVT01 sp019244185	78.9082	524	1224	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_003223645.1	s__QHVT01 sp003223645	78.3281	499	1224	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242175.1	s__QHVT01 sp019242175	78.1379	374	1224	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650215.1	s__QHVT01 sp016650215	77.6058	238	1224	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223635.1	s__QHVS01 sp003223635	77.4219	296	1224	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220315.1	s__20CM-2-70-11 sp003220315	75.1798	59	1224	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__20CM-2-70-11	95.0	99.38	99.31	0.92	0.87	7	-
--------------------------------------------------------------------------------
[2023-06-29 22:31:11,476] [INFO] GTDB search result was written to GCA_019233845.1_ASM1923384v1_genomic.fna/result_gtdb.tsv
[2023-06-29 22:31:11,476] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:31:11,480] [INFO] DFAST_QC result json was written to GCA_019233845.1_ASM1923384v1_genomic.fna/dqc_result.json
[2023-06-29 22:31:11,480] [INFO] DFAST_QC completed!
[2023-06-29 22:31:11,480] [INFO] Total running time: 0h1m25s