[2023-06-18 17:20:11,823] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:20:11,880] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:20:11,880] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b97b7b5-b573-4757-86af-12d10bb99052/dqc_reference
[2023-06-18 17:20:13,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:20:13,295] [INFO] Task started: Prodigal
[2023-06-18 17:20:13,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg701d8140-a2fe-4091-9aa9-6827c71fb1cd/GCA_013694845.1_ASM1369484v1_genomic.fna.gz | prodigal -d GCA_013694845.1_ASM1369484v1_genomic.fna/cds.fna -a GCA_013694845.1_ASM1369484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:20:25,154] [INFO] Task succeeded: Prodigal
[2023-06-18 17:20:25,154] [INFO] Task started: HMMsearch
[2023-06-18 17:20:25,154] [INFO] Running command: hmmsearch --tblout GCA_013694845.1_ASM1369484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b97b7b5-b573-4757-86af-12d10bb99052/dqc_reference/reference_markers.hmm GCA_013694845.1_ASM1369484v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:20:25,394] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:20:25,395] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg701d8140-a2fe-4091-9aa9-6827c71fb1cd/GCA_013694845.1_ASM1369484v1_genomic.fna.gz]
[2023-06-18 17:20:25,439] [INFO] Query marker FASTA was written to GCA_013694845.1_ASM1369484v1_genomic.fna/markers.fasta
[2023-06-18 17:20:25,439] [INFO] Task started: Blastn
[2023-06-18 17:20:25,440] [INFO] Running command: blastn -query GCA_013694845.1_ASM1369484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b97b7b5-b573-4757-86af-12d10bb99052/dqc_reference/reference_markers.fasta -out GCA_013694845.1_ASM1369484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:20:26,147] [INFO] Task succeeded: Blastn
[2023-06-18 17:20:26,150] [INFO] Selected 26 target genomes.
[2023-06-18 17:20:26,151] [INFO] Target genome list was writen to GCA_013694845.1_ASM1369484v1_genomic.fna/target_genomes.txt
[2023-06-18 17:20:26,155] [INFO] Task started: fastANI
[2023-06-18 17:20:26,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg701d8140-a2fe-4091-9aa9-6827c71fb1cd/GCA_013694845.1_ASM1369484v1_genomic.fna.gz --refList GCA_013694845.1_ASM1369484v1_genomic.fna/target_genomes.txt --output GCA_013694845.1_ASM1369484v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:20:47,486] [INFO] Task succeeded: fastANI
[2023-06-18 17:20:47,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b97b7b5-b573-4757-86af-12d10bb99052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:20:47,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b97b7b5-b573-4757-86af-12d10bb99052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:20:47,494] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:20:47,494] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:20:47,494] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	76.3651	158	1406	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	75.0262	54	1406	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	74.9279	54	1406	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	74.8483	81	1406	95	below_threshold
Herbidospora sakaeratensis	strain=NBRC 102641	GCA_001570525.1	564415	564415	type	True	74.799	80	1406	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	74.7421	88	1406	95	below_threshold
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	74.6997	79	1406	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	74.6847	88	1406	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	74.6652	72	1406	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:20:47,496] [INFO] DFAST Taxonomy check result was written to GCA_013694845.1_ASM1369484v1_genomic.fna/tc_result.tsv
[2023-06-18 17:20:47,496] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:20:47,496] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:20:47,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b97b7b5-b573-4757-86af-12d10bb99052/dqc_reference/checkm_data
[2023-06-18 17:20:47,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:20:47,551] [INFO] Task started: CheckM
[2023-06-18 17:20:47,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013694845.1_ASM1369484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013694845.1_ASM1369484v1_genomic.fna/checkm_input GCA_013694845.1_ASM1369484v1_genomic.fna/checkm_result
[2023-06-18 17:21:23,252] [INFO] Task succeeded: CheckM
[2023-06-18 17:21:23,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 4.92%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-18 17:21:23,282] [INFO] ===== Completeness check finished =====
[2023-06-18 17:21:23,282] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:21:23,283] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013694845.1_ASM1369484v1_genomic.fna/markers.fasta)
[2023-06-18 17:21:23,283] [INFO] Task started: Blastn
[2023-06-18 17:21:23,283] [INFO] Running command: blastn -query GCA_013694845.1_ASM1369484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b97b7b5-b573-4757-86af-12d10bb99052/dqc_reference/reference_markers_gtdb.fasta -out GCA_013694845.1_ASM1369484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:21:24,519] [INFO] Task succeeded: Blastn
[2023-06-18 17:21:24,523] [INFO] Selected 14 target genomes.
[2023-06-18 17:21:24,523] [INFO] Target genome list was writen to GCA_013694845.1_ASM1369484v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:21:24,525] [INFO] Task started: fastANI
[2023-06-18 17:21:24,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg701d8140-a2fe-4091-9aa9-6827c71fb1cd/GCA_013694845.1_ASM1369484v1_genomic.fna.gz --refList GCA_013694845.1_ASM1369484v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013694845.1_ASM1369484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:21:36,530] [INFO] Task succeeded: fastANI
[2023-06-18 17:21:36,538] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:21:36,538] [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_013694845.1	s__JACDCA01 sp013694845	99.9999	1385	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACDCA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013817065.1	s__JACDCA01 sp013817065	78.6171	369	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACDCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694635.1	s__JACDCA01 sp013694635	77.9411	262	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACDCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813355.1	s__JACCRT01 sp013813355	77.9363	89	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACCRT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697225.1	s__JACCXG01 sp013697225	77.5347	128	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACCXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767455.1	s__2-12-FULL-66-21 sp001767455	77.493	322	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__2-12-FULL-66-21	95.0	99.91	99.91	0.96	0.96	2	-
GCA_003223835.1	s__Gp6-AA38 sp003223835	77.0982	260	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__Gp6-AA38	95.0	98.48	98.48	0.89	0.89	2	-
GCA_003222675.1	s__QHWT01 sp003222675	77.0083	269	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362195.1	s__QHWT01 sp013362195	76.9313	214	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016184455.1	s__Gp6-AA40 sp016184455	76.6106	145	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213695.1	s__Gp6-AA40 sp016213695	76.413	116	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222535.1	s__Gp6-AA45 sp003222535	76.2499	172	1406	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.30	99.28	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-18 17:21:36,540] [INFO] GTDB search result was written to GCA_013694845.1_ASM1369484v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:21:36,541] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:21:36,544] [INFO] DFAST_QC result json was written to GCA_013694845.1_ASM1369484v1_genomic.fna/dqc_result.json
[2023-06-18 17:21:36,544] [INFO] DFAST_QC completed!
[2023-06-18 17:21:36,544] [INFO] Total running time: 0h1m25s