[2024-01-25 17:50:50,541] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:50,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:50,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg69ecfd98-9b80-4ad9-ab76-6fe66ff1d39c/dqc_reference
[2024-01-25 17:50:51,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:51,672] [INFO] Task started: Prodigal
[2024-01-25 17:50:51,672] [INFO] Running command: gunzip -c /var/lib/cwl/stg788b77f8-5de0-431f-b34e-6033dd2b14dd/GCF_000423205.1_ASM42320v1_genomic.fna.gz | prodigal -d GCF_000423205.1_ASM42320v1_genomic.fna/cds.fna -a GCF_000423205.1_ASM42320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:00,703] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:00,704] [INFO] Task started: HMMsearch
[2024-01-25 17:51:00,704] [INFO] Running command: hmmsearch --tblout GCF_000423205.1_ASM42320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69ecfd98-9b80-4ad9-ab76-6fe66ff1d39c/dqc_reference/reference_markers.hmm GCF_000423205.1_ASM42320v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:00,905] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:00,906] [INFO] Found 6/6 markers.
[2024-01-25 17:51:00,931] [INFO] Query marker FASTA was written to GCF_000423205.1_ASM42320v1_genomic.fna/markers.fasta
[2024-01-25 17:51:00,931] [INFO] Task started: Blastn
[2024-01-25 17:51:00,931] [INFO] Running command: blastn -query GCF_000423205.1_ASM42320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69ecfd98-9b80-4ad9-ab76-6fe66ff1d39c/dqc_reference/reference_markers.fasta -out GCF_000423205.1_ASM42320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:01,609] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:01,612] [INFO] Selected 21 target genomes.
[2024-01-25 17:51:01,612] [INFO] Target genome list was writen to GCF_000423205.1_ASM42320v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:01,641] [INFO] Task started: fastANI
[2024-01-25 17:51:01,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg788b77f8-5de0-431f-b34e-6033dd2b14dd/GCF_000423205.1_ASM42320v1_genomic.fna.gz --refList GCF_000423205.1_ASM42320v1_genomic.fna/target_genomes.txt --output GCF_000423205.1_ASM42320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:17,295] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:17,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69ecfd98-9b80-4ad9-ab76-6fe66ff1d39c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:17,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69ecfd98-9b80-4ad9-ab76-6fe66ff1d39c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:17,301] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:51:17,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:17,301] [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
Jonesia quinghaiensis	strain=DSM 15701	GCA_000423205.1	262806	262806	type	True	100.0	1008	1008	95	conclusive
Jonesia denitrificans	strain=FDAARGOS 1440	GCA_019048465.1	43674	43674	type	True	78.839	295	1008	95	below_threshold
Jonesia denitrificans	strain=DSM 20603	GCA_000024065.1	43674	43674	type	True	78.8199	301	1008	95	below_threshold
Jonesia denitrificans	strain=NCTC10816	GCA_900475835.1	43674	43674	type	True	78.7913	302	1008	95	below_threshold
Sanguibacter gelidistatuariae	strain=ISLP-3	GCA_900096585.1	1814289	1814289	type	True	77.0538	66	1008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:17,302] [INFO] DFAST Taxonomy check result was written to GCF_000423205.1_ASM42320v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:17,303] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:17,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:17,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69ecfd98-9b80-4ad9-ab76-6fe66ff1d39c/dqc_reference/checkm_data
[2024-01-25 17:51:17,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:17,335] [INFO] Task started: CheckM
[2024-01-25 17:51:17,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423205.1_ASM42320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423205.1_ASM42320v1_genomic.fna/checkm_input GCF_000423205.1_ASM42320v1_genomic.fna/checkm_result
[2024-01-25 17:51:46,825] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:46,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:46,845] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:46,846] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:46,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423205.1_ASM42320v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:46,846] [INFO] Task started: Blastn
[2024-01-25 17:51:46,846] [INFO] Running command: blastn -query GCF_000423205.1_ASM42320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69ecfd98-9b80-4ad9-ab76-6fe66ff1d39c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423205.1_ASM42320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:47,887] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:47,890] [INFO] Selected 25 target genomes.
[2024-01-25 17:51:47,891] [INFO] Target genome list was writen to GCF_000423205.1_ASM42320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:47,922] [INFO] Task started: fastANI
[2024-01-25 17:51:47,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg788b77f8-5de0-431f-b34e-6033dd2b14dd/GCF_000423205.1_ASM42320v1_genomic.fna.gz --refList GCF_000423205.1_ASM42320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423205.1_ASM42320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:07,733] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:07,739] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:07,739] [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_000423205.1	s__Jonesia quinghaiensis	100.0	1008	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Jonesia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000024065.1	s__Jonesia denitrificans	78.8199	301	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Jonesia	95.0	100.00	100.00	1.00	1.00	4	-
GCF_000312125.1	s__Timonella senegalensis	78.0633	111	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Timonella	95.0	98.10	97.43	0.93	0.89	5	-
GCF_900096585.1	s__Sanguibacter gelidistatuariae	77.0538	66	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552735.1	s__Sanguibacter suarezii	76.707	78	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946865.1	s__Antribacter gilvus	76.3263	52	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Antribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:07,741] [INFO] GTDB search result was written to GCF_000423205.1_ASM42320v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:07,741] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:07,745] [INFO] DFAST_QC result json was written to GCF_000423205.1_ASM42320v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:07,746] [INFO] DFAST_QC completed!
[2024-01-25 17:52:07,746] [INFO] Total running time: 0h1m17s