[2024-01-24 14:14:21,276] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:21,278] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:21,279] [INFO] DQC Reference Directory: /var/lib/cwl/stg1152b57d-6ae2-4080-aea8-fa3dc98eeaae/dqc_reference
[2024-01-24 14:14:24,203] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:24,204] [INFO] Task started: Prodigal
[2024-01-24 14:14:24,205] [INFO] Running command: gunzip -c /var/lib/cwl/stgc60633de-74bd-4e78-bfa0-c3941abfedce/GCF_030503435.1_ASM3050343v1_genomic.fna.gz | prodigal -d GCF_030503435.1_ASM3050343v1_genomic.fna/cds.fna -a GCF_030503435.1_ASM3050343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:00,462] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:00,462] [INFO] Task started: HMMsearch
[2024-01-24 14:15:00,462] [INFO] Running command: hmmsearch --tblout GCF_030503435.1_ASM3050343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1152b57d-6ae2-4080-aea8-fa3dc98eeaae/dqc_reference/reference_markers.hmm GCF_030503435.1_ASM3050343v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:00,872] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:00,874] [INFO] Found 6/6 markers.
[2024-01-24 14:15:00,945] [INFO] Query marker FASTA was written to GCF_030503435.1_ASM3050343v1_genomic.fna/markers.fasta
[2024-01-24 14:15:00,945] [INFO] Task started: Blastn
[2024-01-24 14:15:00,946] [INFO] Running command: blastn -query GCF_030503435.1_ASM3050343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1152b57d-6ae2-4080-aea8-fa3dc98eeaae/dqc_reference/reference_markers.fasta -out GCF_030503435.1_ASM3050343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:01,589] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:01,592] [INFO] Selected 28 target genomes.
[2024-01-24 14:15:01,592] [INFO] Target genome list was writen to GCF_030503435.1_ASM3050343v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:01,601] [INFO] Task started: fastANI
[2024-01-24 14:15:01,602] [INFO] Running command: fastANI --query /var/lib/cwl/stgc60633de-74bd-4e78-bfa0-c3941abfedce/GCF_030503435.1_ASM3050343v1_genomic.fna.gz --refList GCF_030503435.1_ASM3050343v1_genomic.fna/target_genomes.txt --output GCF_030503435.1_ASM3050343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:27,705] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:27,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1152b57d-6ae2-4080-aea8-fa3dc98eeaae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:27,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1152b57d-6ae2-4080-aea8-fa3dc98eeaae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:27,712] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:27,713] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:27,713] [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
Rhodocytophaga rosea	strain=172606-1	GCA_010119975.1	2704465	2704465	type	True	77.794	501	2930	95	below_threshold
Adhaeribacter radiodurans	strain=KUDC8001	GCA_014075995.1	2745197	2745197	type	True	75.6342	72	2930	95	below_threshold
Adhaeribacter rhizoryzae	strain=DK36	GCA_008629685.1	2607907	2607907	type	True	75.5165	88	2930	95	below_threshold
Adhaeribacter pallidiroseus	strain=HMF7616	GCA_003340495.1	2072847	2072847	type	True	75.4203	65	2930	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:27,715] [INFO] DFAST Taxonomy check result was written to GCF_030503435.1_ASM3050343v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:27,716] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:27,716] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:27,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1152b57d-6ae2-4080-aea8-fa3dc98eeaae/dqc_reference/checkm_data
[2024-01-24 14:15:27,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:27,812] [INFO] Task started: CheckM
[2024-01-24 14:15:27,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030503435.1_ASM3050343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030503435.1_ASM3050343v1_genomic.fna/checkm_input GCF_030503435.1_ASM3050343v1_genomic.fna/checkm_result
[2024-01-24 14:17:06,713] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:06,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:06,732] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:06,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:06,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030503435.1_ASM3050343v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:06,733] [INFO] Task started: Blastn
[2024-01-24 14:17:06,733] [INFO] Running command: blastn -query GCF_030503435.1_ASM3050343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1152b57d-6ae2-4080-aea8-fa3dc98eeaae/dqc_reference/reference_markers_gtdb.fasta -out GCF_030503435.1_ASM3050343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:09,267] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:09,271] [INFO] Selected 33 target genomes.
[2024-01-24 14:17:09,272] [INFO] Target genome list was writen to GCF_030503435.1_ASM3050343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:09,312] [INFO] Task started: fastANI
[2024-01-24 14:17:09,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgc60633de-74bd-4e78-bfa0-c3941abfedce/GCF_030503435.1_ASM3050343v1_genomic.fna.gz --refList GCF_030503435.1_ASM3050343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030503435.1_ASM3050343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:41,117] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:41,123] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:17:41,123] [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_010119975.1	s__Rhodocytophaga rosea	77.8288	497	2930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__172606-1;g__Rhodocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014075995.1	s__Adhaeribacter radiodurans	75.6462	71	2930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340495.1	s__Adhaeribacter pallidiroseus	75.4203	65	2930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:41,125] [INFO] GTDB search result was written to GCF_030503435.1_ASM3050343v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:41,125] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:41,128] [INFO] DFAST_QC result json was written to GCF_030503435.1_ASM3050343v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:41,128] [INFO] DFAST_QC completed!
[2024-01-24 14:17:41,128] [INFO] Total running time: 0h3m20s