[2023-06-29 00:38:45,173] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:38:45,176] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:38:45,176] [INFO] DQC Reference Directory: /var/lib/cwl/stg6795016c-406b-43f0-be00-883d1e220e24/dqc_reference
[2023-06-29 00:38:46,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:38:46,411] [INFO] Task started: Prodigal
[2023-06-29 00:38:46,411] [INFO] Running command: gunzip -c /var/lib/cwl/stge5dd991e-d148-4da5-b8e4-671535193a52/GCA_020062805.1_ASM2006280v1_genomic.fna.gz | prodigal -d GCA_020062805.1_ASM2006280v1_genomic.fna/cds.fna -a GCA_020062805.1_ASM2006280v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:38:50,572] [INFO] Task succeeded: Prodigal
[2023-06-29 00:38:50,573] [INFO] Task started: HMMsearch
[2023-06-29 00:38:50,573] [INFO] Running command: hmmsearch --tblout GCA_020062805.1_ASM2006280v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6795016c-406b-43f0-be00-883d1e220e24/dqc_reference/reference_markers.hmm GCA_020062805.1_ASM2006280v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:38:50,785] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:38:50,787] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge5dd991e-d148-4da5-b8e4-671535193a52/GCA_020062805.1_ASM2006280v1_genomic.fna.gz]
[2023-06-29 00:38:50,806] [INFO] Query marker FASTA was written to GCA_020062805.1_ASM2006280v1_genomic.fna/markers.fasta
[2023-06-29 00:38:50,807] [INFO] Task started: Blastn
[2023-06-29 00:38:50,807] [INFO] Running command: blastn -query GCA_020062805.1_ASM2006280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6795016c-406b-43f0-be00-883d1e220e24/dqc_reference/reference_markers.fasta -out GCA_020062805.1_ASM2006280v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:51,420] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:51,425] [INFO] Selected 14 target genomes.
[2023-06-29 00:38:51,426] [INFO] Target genome list was writen to GCA_020062805.1_ASM2006280v1_genomic.fna/target_genomes.txt
[2023-06-29 00:38:51,430] [INFO] Task started: fastANI
[2023-06-29 00:38:51,431] [INFO] Running command: fastANI --query /var/lib/cwl/stge5dd991e-d148-4da5-b8e4-671535193a52/GCA_020062805.1_ASM2006280v1_genomic.fna.gz --refList GCA_020062805.1_ASM2006280v1_genomic.fna/target_genomes.txt --output GCA_020062805.1_ASM2006280v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:39:00,500] [INFO] Task succeeded: fastANI
[2023-06-29 00:39:00,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6795016c-406b-43f0-be00-883d1e220e24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:39:00,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6795016c-406b-43f0-be00-883d1e220e24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:39:00,502] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:39:00,502] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 00:39:00,502] [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
--------------------------------------------------------------------------------
[2023-06-29 00:39:00,504] [INFO] DFAST Taxonomy check result was written to GCA_020062805.1_ASM2006280v1_genomic.fna/tc_result.tsv
[2023-06-29 00:39:00,505] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:39:00,505] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:39:00,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6795016c-406b-43f0-be00-883d1e220e24/dqc_reference/checkm_data
[2023-06-29 00:39:00,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:39:00,531] [INFO] Task started: CheckM
[2023-06-29 00:39:00,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020062805.1_ASM2006280v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020062805.1_ASM2006280v1_genomic.fna/checkm_input GCA_020062805.1_ASM2006280v1_genomic.fna/checkm_result
[2023-06-29 00:39:19,640] [INFO] Task succeeded: CheckM
[2023-06-29 00:39:19,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:39:19,669] [INFO] ===== Completeness check finished =====
[2023-06-29 00:39:19,669] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:39:19,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020062805.1_ASM2006280v1_genomic.fna/markers.fasta)
[2023-06-29 00:39:19,670] [INFO] Task started: Blastn
[2023-06-29 00:39:19,670] [INFO] Running command: blastn -query GCA_020062805.1_ASM2006280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6795016c-406b-43f0-be00-883d1e220e24/dqc_reference/reference_markers_gtdb.fasta -out GCA_020062805.1_ASM2006280v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:39:20,531] [INFO] Task succeeded: Blastn
[2023-06-29 00:39:20,536] [INFO] Selected 11 target genomes.
[2023-06-29 00:39:20,536] [INFO] Target genome list was writen to GCA_020062805.1_ASM2006280v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:39:20,546] [INFO] Task started: fastANI
[2023-06-29 00:39:20,546] [INFO] Running command: fastANI --query /var/lib/cwl/stge5dd991e-d148-4da5-b8e4-671535193a52/GCA_020062805.1_ASM2006280v1_genomic.fna.gz --refList GCA_020062805.1_ASM2006280v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020062805.1_ASM2006280v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:39:26,750] [INFO] Task succeeded: fastANI
[2023-06-29 00:39:26,760] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 00:39:26,760] [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_002479455.1	s__Bipolaricaulis sp002479455	94.1171	305	384	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__Bipolaricaulales;f__Bipolaricaulaceae;g__Bipolaricaulis	95.0	95.08	95.08	0.81	0.81	2	-
GCA_014360985.1	s__Bipolaricaulis sp014360985	81.2595	188	384	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__Bipolaricaulales;f__Bipolaricaulaceae;g__Bipolaricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014361015.1	s__Bipolaricaulis sp014361015	81.2293	184	384	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__Bipolaricaulales;f__Bipolaricaulaceae;g__Bipolaricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004102645.1	s__Bipolaricaulis sibiricus	80.9542	214	384	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__Bipolaricaulales;f__Bipolaricaulaceae;g__Bipolaricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900465355.1	s__Bipolaricaulis anaerobius	80.9007	186	384	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__Bipolaricaulales;f__Bipolaricaulaceae;g__Bipolaricaulis	95.0	98.26	97.81	0.98	0.98	4	-
GCA_011057175.1	s__Bipolaricaulis sp011057175	80.5855	138	384	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__Bipolaricaulales;f__Bipolaricaulaceae;g__Bipolaricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:39:26,762] [INFO] GTDB search result was written to GCA_020062805.1_ASM2006280v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:39:26,762] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:39:26,765] [INFO] DFAST_QC result json was written to GCA_020062805.1_ASM2006280v1_genomic.fna/dqc_result.json
[2023-06-29 00:39:26,765] [INFO] DFAST_QC completed!
[2023-06-29 00:39:26,765] [INFO] Total running time: 0h0m42s