[2024-01-24 15:26:33,096] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:33,098] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:33,098] [INFO] DQC Reference Directory: /var/lib/cwl/stg194bf13a-52c9-4226-87f0-d0e50145af93/dqc_reference
[2024-01-24 15:26:35,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:35,760] [INFO] Task started: Prodigal
[2024-01-24 15:26:35,760] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc7f97e6-ba9c-442a-bbcf-b7dac9b69024/GCF_004291315.1_ASM429131v1_genomic.fna.gz | prodigal -d GCF_004291315.1_ASM429131v1_genomic.fna/cds.fna -a GCF_004291315.1_ASM429131v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:18,177] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:18,177] [INFO] Task started: HMMsearch
[2024-01-24 15:27:18,178] [INFO] Running command: hmmsearch --tblout GCF_004291315.1_ASM429131v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg194bf13a-52c9-4226-87f0-d0e50145af93/dqc_reference/reference_markers.hmm GCF_004291315.1_ASM429131v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:18,527] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:18,529] [INFO] Found 6/6 markers.
[2024-01-24 15:27:18,592] [INFO] Query marker FASTA was written to GCF_004291315.1_ASM429131v1_genomic.fna/markers.fasta
[2024-01-24 15:27:18,592] [INFO] Task started: Blastn
[2024-01-24 15:27:18,593] [INFO] Running command: blastn -query GCF_004291315.1_ASM429131v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg194bf13a-52c9-4226-87f0-d0e50145af93/dqc_reference/reference_markers.fasta -out GCF_004291315.1_ASM429131v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:19,211] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:19,217] [INFO] Selected 12 target genomes.
[2024-01-24 15:27:19,217] [INFO] Target genome list was writen to GCF_004291315.1_ASM429131v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:19,224] [INFO] Task started: fastANI
[2024-01-24 15:27:19,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7f97e6-ba9c-442a-bbcf-b7dac9b69024/GCF_004291315.1_ASM429131v1_genomic.fna.gz --refList GCF_004291315.1_ASM429131v1_genomic.fna/target_genomes.txt --output GCF_004291315.1_ASM429131v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:38,191] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:38,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg194bf13a-52c9-4226-87f0-d0e50145af93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:38,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg194bf13a-52c9-4226-87f0-d0e50145af93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:38,202] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:38,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:38,203] [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
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	100.0	2586	2587	95	conclusive
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	99.9966	2587	2587	95	conclusive
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	77.1112	353	2587	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	77.0294	314	2587	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	76.7581	205	2587	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.7344	246	2587	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	76.6631	254	2587	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	76.6625	244	2587	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	76.6568	235	2587	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	76.5428	239	2587	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:38,204] [INFO] DFAST Taxonomy check result was written to GCF_004291315.1_ASM429131v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:38,205] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:38,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:38,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg194bf13a-52c9-4226-87f0-d0e50145af93/dqc_reference/checkm_data
[2024-01-24 15:27:38,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:38,281] [INFO] Task started: CheckM
[2024-01-24 15:27:38,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004291315.1_ASM429131v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004291315.1_ASM429131v1_genomic.fna/checkm_input GCF_004291315.1_ASM429131v1_genomic.fna/checkm_result
[2024-01-24 15:29:33,422] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:33,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:33,447] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:33,447] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:33,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004291315.1_ASM429131v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:33,449] [INFO] Task started: Blastn
[2024-01-24 15:29:33,449] [INFO] Running command: blastn -query GCF_004291315.1_ASM429131v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg194bf13a-52c9-4226-87f0-d0e50145af93/dqc_reference/reference_markers_gtdb.fasta -out GCF_004291315.1_ASM429131v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:34,214] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:34,219] [INFO] Selected 11 target genomes.
[2024-01-24 15:29:34,219] [INFO] Target genome list was writen to GCF_004291315.1_ASM429131v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:34,227] [INFO] Task started: fastANI
[2024-01-24 15:29:34,228] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7f97e6-ba9c-442a-bbcf-b7dac9b69024/GCF_004291315.1_ASM429131v1_genomic.fna.gz --refList GCF_004291315.1_ASM429131v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004291315.1_ASM429131v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:50,605] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:50,624] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:50,624] [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
GCF_007970185.1	s__Pseudobacter ginsenosidimutans	99.9966	2587	2587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003991355.1	s__Pseudobacter rhizosphaerae	89.1924	1873	2587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744805.1	s__Pseudobacter sp017744805	82.6854	1105	2587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927185.1	s__Pseudobacter sp012927185	80.0863	974	2587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849455.1	s__Pseudobacter sp017849455	77.8013	524	2587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003555545.1	s__Paraflavitalea soli	77.1179	352	2587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759375.1	s__Paraflavitalea devenefica	77.0121	316	2587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356035.1	s__Niastella sp017356035	76.8716	256	2587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001302245.1	s__PMP191F sp001302245	76.8136	229	2587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCF_900110245.1	s__Niastella yeongjuensis	76.5428	239	2587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001898405.1	s__46-32 sp001898405	76.5286	146	2587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	98.21	96.99	0.89	0.84	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:50,626] [INFO] GTDB search result was written to GCF_004291315.1_ASM429131v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:50,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:50,630] [INFO] DFAST_QC result json was written to GCF_004291315.1_ASM429131v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:50,630] [INFO] DFAST_QC completed!
[2024-01-24 15:29:50,630] [INFO] Total running time: 0h3m18s