[2023-06-18 14:01:26,314] [INFO] DFAST_QC pipeline started.
[2023-06-18 14:01:26,318] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 14:01:26,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f18e56a-bc02-4fb9-aa1e-b5f2a64de517/dqc_reference
[2023-06-18 14:01:27,565] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 14:01:27,566] [INFO] Task started: Prodigal
[2023-06-18 14:01:27,566] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4675f60-14b1-4799-8259-ab6017579b17/GCA_018336025.1_ASM1833602v1_genomic.fna.gz | prodigal -d GCA_018336025.1_ASM1833602v1_genomic.fna/cds.fna -a GCA_018336025.1_ASM1833602v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 14:01:33,659] [INFO] Task succeeded: Prodigal
[2023-06-18 14:01:33,660] [INFO] Task started: HMMsearch
[2023-06-18 14:01:33,660] [INFO] Running command: hmmsearch --tblout GCA_018336025.1_ASM1833602v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f18e56a-bc02-4fb9-aa1e-b5f2a64de517/dqc_reference/reference_markers.hmm GCA_018336025.1_ASM1833602v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 14:01:33,895] [INFO] Task succeeded: HMMsearch
[2023-06-18 14:01:33,897] [INFO] Found 6/6 markers.
[2023-06-18 14:01:33,929] [INFO] Query marker FASTA was written to GCA_018336025.1_ASM1833602v1_genomic.fna/markers.fasta
[2023-06-18 14:01:33,929] [INFO] Task started: Blastn
[2023-06-18 14:01:33,929] [INFO] Running command: blastn -query GCA_018336025.1_ASM1833602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f18e56a-bc02-4fb9-aa1e-b5f2a64de517/dqc_reference/reference_markers.fasta -out GCA_018336025.1_ASM1833602v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:01:34,493] [INFO] Task succeeded: Blastn
[2023-06-18 14:01:34,497] [INFO] Selected 12 target genomes.
[2023-06-18 14:01:34,497] [INFO] Target genome list was writen to GCA_018336025.1_ASM1833602v1_genomic.fna/target_genomes.txt
[2023-06-18 14:01:34,500] [INFO] Task started: fastANI
[2023-06-18 14:01:34,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4675f60-14b1-4799-8259-ab6017579b17/GCA_018336025.1_ASM1833602v1_genomic.fna.gz --refList GCA_018336025.1_ASM1833602v1_genomic.fna/target_genomes.txt --output GCA_018336025.1_ASM1833602v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 14:01:41,585] [INFO] Task succeeded: fastANI
[2023-06-18 14:01:41,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f18e56a-bc02-4fb9-aa1e-b5f2a64de517/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 14:01:41,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f18e56a-bc02-4fb9-aa1e-b5f2a64de517/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 14:01:41,587] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 14:01:41,588] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 14:01:41,588] [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
--------------------------------------------------------------------------------
[2023-06-18 14:01:41,590] [INFO] DFAST Taxonomy check result was written to GCA_018336025.1_ASM1833602v1_genomic.fna/tc_result.tsv
[2023-06-18 14:01:41,591] [INFO] ===== Taxonomy check completed =====
[2023-06-18 14:01:41,591] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 14:01:41,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f18e56a-bc02-4fb9-aa1e-b5f2a64de517/dqc_reference/checkm_data
[2023-06-18 14:01:41,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 14:01:41,627] [INFO] Task started: CheckM
[2023-06-18 14:01:41,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018336025.1_ASM1833602v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018336025.1_ASM1833602v1_genomic.fna/checkm_input GCA_018336025.1_ASM1833602v1_genomic.fna/checkm_result
[2023-06-18 14:02:05,558] [INFO] Task succeeded: CheckM
[2023-06-18 14:02:05,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-18 14:02:05,588] [INFO] ===== Completeness check finished =====
[2023-06-18 14:02:05,588] [INFO] ===== Start GTDB Search =====
[2023-06-18 14:02:05,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018336025.1_ASM1833602v1_genomic.fna/markers.fasta)
[2023-06-18 14:02:05,589] [INFO] Task started: Blastn
[2023-06-18 14:02:05,589] [INFO] Running command: blastn -query GCA_018336025.1_ASM1833602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f18e56a-bc02-4fb9-aa1e-b5f2a64de517/dqc_reference/reference_markers_gtdb.fasta -out GCA_018336025.1_ASM1833602v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:02:06,354] [INFO] Task succeeded: Blastn
[2023-06-18 14:02:06,392] [INFO] Selected 13 target genomes.
[2023-06-18 14:02:06,392] [INFO] Target genome list was writen to GCA_018336025.1_ASM1833602v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 14:02:06,523] [INFO] Task started: fastANI
[2023-06-18 14:02:06,523] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4675f60-14b1-4799-8259-ab6017579b17/GCA_018336025.1_ASM1833602v1_genomic.fna.gz --refList GCA_018336025.1_ASM1833602v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018336025.1_ASM1833602v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 14:02:13,734] [INFO] Task succeeded: fastANI
[2023-06-18 14:02:13,740] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 14:02:13,741] [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_018333655.1	s__BS524 sp018333655	99.0146	636	770	d__Bacteria;p__Firmicutes_H;c__UBA994;o__UBA994;f__UBA994;g__BS524	95.0	99.58	99.16	0.93	0.89	3	conclusive
GCA_018334055.1	s__BS524 sp018334055	77.7975	119	770	d__Bacteria;p__Firmicutes_H;c__UBA994;o__UBA994;f__UBA994;g__BS524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018725275.1	s__BS524 sp018725275	77.5873	90	770	d__Bacteria;p__Firmicutes_H;c__UBA994;o__UBA994;f__UBA994;g__BS524	95.0	98.68	98.26	0.82	0.80	3	-
--------------------------------------------------------------------------------
[2023-06-18 14:02:13,743] [INFO] GTDB search result was written to GCA_018336025.1_ASM1833602v1_genomic.fna/result_gtdb.tsv
[2023-06-18 14:02:13,743] [INFO] ===== GTDB Search completed =====
[2023-06-18 14:02:13,745] [INFO] DFAST_QC result json was written to GCA_018336025.1_ASM1833602v1_genomic.fna/dqc_result.json
[2023-06-18 14:02:13,746] [INFO] DFAST_QC completed!
[2023-06-18 14:02:13,746] [INFO] Total running time: 0h0m47s