[2023-06-19 03:53:35,887] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:53:35,918] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:53:35,918] [INFO] DQC Reference Directory: /var/lib/cwl/stg2aa33898-da71-4a3b-b4e0-9515ea06fb68/dqc_reference
[2023-06-19 03:53:37,266] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:53:37,267] [INFO] Task started: Prodigal
[2023-06-19 03:53:37,268] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ed15562-e4b3-4599-8f26-42914fe05208/GCA_018268785.1_ASM1826878v1_genomic.fna.gz | prodigal -d GCA_018268785.1_ASM1826878v1_genomic.fna/cds.fna -a GCA_018268785.1_ASM1826878v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:53:48,952] [INFO] Task succeeded: Prodigal
[2023-06-19 03:53:48,953] [INFO] Task started: HMMsearch
[2023-06-19 03:53:48,953] [INFO] Running command: hmmsearch --tblout GCA_018268785.1_ASM1826878v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2aa33898-da71-4a3b-b4e0-9515ea06fb68/dqc_reference/reference_markers.hmm GCA_018268785.1_ASM1826878v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:53:49,241] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:53:49,243] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2ed15562-e4b3-4599-8f26-42914fe05208/GCA_018268785.1_ASM1826878v1_genomic.fna.gz]
[2023-06-19 03:53:49,282] [INFO] Query marker FASTA was written to GCA_018268785.1_ASM1826878v1_genomic.fna/markers.fasta
[2023-06-19 03:53:49,282] [INFO] Task started: Blastn
[2023-06-19 03:53:49,282] [INFO] Running command: blastn -query GCA_018268785.1_ASM1826878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2aa33898-da71-4a3b-b4e0-9515ea06fb68/dqc_reference/reference_markers.fasta -out GCA_018268785.1_ASM1826878v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:53:49,869] [INFO] Task succeeded: Blastn
[2023-06-19 03:53:49,873] [INFO] Selected 22 target genomes.
[2023-06-19 03:53:49,874] [INFO] Target genome list was writen to GCA_018268785.1_ASM1826878v1_genomic.fna/target_genomes.txt
[2023-06-19 03:53:49,879] [INFO] Task started: fastANI
[2023-06-19 03:53:49,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ed15562-e4b3-4599-8f26-42914fe05208/GCA_018268785.1_ASM1826878v1_genomic.fna.gz --refList GCA_018268785.1_ASM1826878v1_genomic.fna/target_genomes.txt --output GCA_018268785.1_ASM1826878v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:54:04,256] [INFO] Task succeeded: fastANI
[2023-06-19 03:54:04,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2aa33898-da71-4a3b-b4e0-9515ea06fb68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:54:04,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2aa33898-da71-4a3b-b4e0-9515ea06fb68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:54:04,259] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:54:04,259] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 03:54:04,259] [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
--------------------------------------------------------------------------------
[2023-06-19 03:54:04,261] [INFO] DFAST Taxonomy check result was written to GCA_018268785.1_ASM1826878v1_genomic.fna/tc_result.tsv
[2023-06-19 03:54:04,262] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:54:04,262] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:54:04,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2aa33898-da71-4a3b-b4e0-9515ea06fb68/dqc_reference/checkm_data
[2023-06-19 03:54:04,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:54:04,310] [INFO] Task started: CheckM
[2023-06-19 03:54:04,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018268785.1_ASM1826878v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018268785.1_ASM1826878v1_genomic.fna/checkm_input GCA_018268785.1_ASM1826878v1_genomic.fna/checkm_result
[2023-06-19 03:54:41,332] [INFO] Task succeeded: CheckM
[2023-06-19 03:54:41,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 03:54:41,352] [INFO] ===== Completeness check finished =====
[2023-06-19 03:54:41,353] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:54:41,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018268785.1_ASM1826878v1_genomic.fna/markers.fasta)
[2023-06-19 03:54:41,353] [INFO] Task started: Blastn
[2023-06-19 03:54:41,354] [INFO] Running command: blastn -query GCA_018268785.1_ASM1826878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2aa33898-da71-4a3b-b4e0-9515ea06fb68/dqc_reference/reference_markers_gtdb.fasta -out GCA_018268785.1_ASM1826878v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:54:42,162] [INFO] Task succeeded: Blastn
[2023-06-19 03:54:42,167] [INFO] Selected 17 target genomes.
[2023-06-19 03:54:42,167] [INFO] Target genome list was writen to GCA_018268785.1_ASM1826878v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:54:42,175] [INFO] Task started: fastANI
[2023-06-19 03:54:42,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ed15562-e4b3-4599-8f26-42914fe05208/GCA_018268785.1_ASM1826878v1_genomic.fna.gz --refList GCA_018268785.1_ASM1826878v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018268785.1_ASM1826878v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:54:55,772] [INFO] Task succeeded: fastANI
[2023-06-19 03:54:55,787] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:54:55,788] [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_018268785.1	s__Acidoferrum sp018268785	100.0	1231	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	99.88	99.88	0.92	0.92	2	conclusive
GCA_013289835.1	s__Acidoferrum sp013289835	77.4155	210	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003224055.1	s__Acidoferrum sp003224055	77.2664	206	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970165.1	s__Acidoferrum sp903970165	77.218	168	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289585.1	s__Acidoferrum sp013289585	77.196	199	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478115.1	s__Acidoferrum typicum	77.182	154	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003154775.1	s__Acidoferrum sp003154775	77.178	157	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	99.95	99.89	0.97	0.96	6	-
GCA_003224525.1	s__Acidoferrum sp003224525	77.1728	184	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289955.1	s__Acidoferrum sp013289955	77.0002	195	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289825.1	s__Acidoferrum sp013289825	76.9922	154	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917435.1	s__Acidoferrum sp001917435	76.8881	159	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	99.54	99.43	0.87	0.83	4	-
GCA_003224085.1	s__Acidoferrum sp003224085	76.8328	186	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289855.1	s__Acidoferrum sp013289855	76.8096	183	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239815.1	s__Acidoferrum sp019239815	76.7165	141	1247	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 03:54:55,790] [INFO] GTDB search result was written to GCA_018268785.1_ASM1826878v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:54:55,791] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:54:55,794] [INFO] DFAST_QC result json was written to GCA_018268785.1_ASM1826878v1_genomic.fna/dqc_result.json
[2023-06-19 03:54:55,794] [INFO] DFAST_QC completed!
[2023-06-19 03:54:55,794] [INFO] Total running time: 0h1m20s