[2023-06-29 19:13:34,564] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:13:34,566] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:13:34,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg7094786f-a812-451f-b309-949109642dda/dqc_reference
[2023-06-29 19:13:35,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:13:35,762] [INFO] Task started: Prodigal
[2023-06-29 19:13:35,763] [INFO] Running command: gunzip -c /var/lib/cwl/stga80029db-76d5-49a2-9856-1b14c9d7db3d/GCA_023145655.1_ASM2314565v1_genomic.fna.gz | prodigal -d GCA_023145655.1_ASM2314565v1_genomic.fna/cds.fna -a GCA_023145655.1_ASM2314565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:13:38,852] [INFO] Task succeeded: Prodigal
[2023-06-29 19:13:38,852] [INFO] Task started: HMMsearch
[2023-06-29 19:13:38,852] [INFO] Running command: hmmsearch --tblout GCA_023145655.1_ASM2314565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7094786f-a812-451f-b309-949109642dda/dqc_reference/reference_markers.hmm GCA_023145655.1_ASM2314565v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:13:39,057] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:13:39,063] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga80029db-76d5-49a2-9856-1b14c9d7db3d/GCA_023145655.1_ASM2314565v1_genomic.fna.gz]
[2023-06-29 19:13:39,081] [INFO] Query marker FASTA was written to GCA_023145655.1_ASM2314565v1_genomic.fna/markers.fasta
[2023-06-29 19:13:39,082] [INFO] Task started: Blastn
[2023-06-29 19:13:39,082] [INFO] Running command: blastn -query GCA_023145655.1_ASM2314565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7094786f-a812-451f-b309-949109642dda/dqc_reference/reference_markers.fasta -out GCA_023145655.1_ASM2314565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:13:39,609] [INFO] Task succeeded: Blastn
[2023-06-29 19:13:39,613] [INFO] Selected 14 target genomes.
[2023-06-29 19:13:39,614] [INFO] Target genome list was writen to GCA_023145655.1_ASM2314565v1_genomic.fna/target_genomes.txt
[2023-06-29 19:13:39,617] [INFO] Task started: fastANI
[2023-06-29 19:13:39,617] [INFO] Running command: fastANI --query /var/lib/cwl/stga80029db-76d5-49a2-9856-1b14c9d7db3d/GCA_023145655.1_ASM2314565v1_genomic.fna.gz --refList GCA_023145655.1_ASM2314565v1_genomic.fna/target_genomes.txt --output GCA_023145655.1_ASM2314565v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:13:46,040] [INFO] Task succeeded: fastANI
[2023-06-29 19:13:46,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7094786f-a812-451f-b309-949109642dda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:13:46,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7094786f-a812-451f-b309-949109642dda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:13:46,044] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:13:46,044] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:13:46,045] [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
Desulfuromusa kysingii	strain=DSM 7343	GCA_900107645.1	37625	37625	type	True	76.7331	83	357	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:13:46,046] [INFO] DFAST Taxonomy check result was written to GCA_023145655.1_ASM2314565v1_genomic.fna/tc_result.tsv
[2023-06-29 19:13:46,047] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:13:46,047] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:13:46,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7094786f-a812-451f-b309-949109642dda/dqc_reference/checkm_data
[2023-06-29 19:13:46,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:13:46,064] [INFO] Task started: CheckM
[2023-06-29 19:13:46,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023145655.1_ASM2314565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023145655.1_ASM2314565v1_genomic.fna/checkm_input GCA_023145655.1_ASM2314565v1_genomic.fna/checkm_result
[2023-06-29 19:14:02,640] [INFO] Task succeeded: CheckM
[2023-06-29 19:14:02,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:14:02,662] [INFO] ===== Completeness check finished =====
[2023-06-29 19:14:02,663] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:14:02,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023145655.1_ASM2314565v1_genomic.fna/markers.fasta)
[2023-06-29 19:14:02,663] [INFO] Task started: Blastn
[2023-06-29 19:14:02,663] [INFO] Running command: blastn -query GCA_023145655.1_ASM2314565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7094786f-a812-451f-b309-949109642dda/dqc_reference/reference_markers_gtdb.fasta -out GCA_023145655.1_ASM2314565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:14:03,098] [INFO] Task succeeded: Blastn
[2023-06-29 19:14:03,102] [INFO] Selected 15 target genomes.
[2023-06-29 19:14:03,102] [INFO] Target genome list was writen to GCA_023145655.1_ASM2314565v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:14:03,108] [INFO] Task started: fastANI
[2023-06-29 19:14:03,109] [INFO] Running command: fastANI --query /var/lib/cwl/stga80029db-76d5-49a2-9856-1b14c9d7db3d/GCA_023145655.1_ASM2314565v1_genomic.fna.gz --refList GCA_023145655.1_ASM2314565v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023145655.1_ASM2314565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:14:09,542] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:09,549] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:14:09,549] [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_002049545.1	s__Desulfuromusa sp002049545	78.0502	133	357	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Desulfuromusa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744595.1	s__Desulfuromusa sp016744595	77.8543	115	357	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Desulfuromusa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744675.1	s__Desulfuromusa sp016744675	77.0758	85	357	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Desulfuromusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107645.1	s__Desulfuromusa kysingii	76.7331	83	357	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Desulfuromusa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:14:09,551] [INFO] GTDB search result was written to GCA_023145655.1_ASM2314565v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:14:09,552] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:14:09,555] [INFO] DFAST_QC result json was written to GCA_023145655.1_ASM2314565v1_genomic.fna/dqc_result.json
[2023-06-29 19:14:09,555] [INFO] DFAST_QC completed!
[2023-06-29 19:14:09,555] [INFO] Total running time: 0h0m35s