[2024-01-24 13:28:44,499] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:44,501] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:44,501] [INFO] DQC Reference Directory: /var/lib/cwl/stga55ff1c7-4b67-461f-82df-a0c9ae4de681/dqc_reference
[2024-01-24 13:28:45,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:45,809] [INFO] Task started: Prodigal
[2024-01-24 13:28:45,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg640b1a1b-99c9-412b-a979-67486d7984f9/GCF_030068545.1_ASM3006854v1_genomic.fna.gz | prodigal -d GCF_030068545.1_ASM3006854v1_genomic.fna/cds.fna -a GCF_030068545.1_ASM3006854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:29:22,545] [INFO] Task succeeded: Prodigal
[2024-01-24 13:29:22,546] [INFO] Task started: HMMsearch
[2024-01-24 13:29:22,546] [INFO] Running command: hmmsearch --tblout GCF_030068545.1_ASM3006854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga55ff1c7-4b67-461f-82df-a0c9ae4de681/dqc_reference/reference_markers.hmm GCF_030068545.1_ASM3006854v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:29:23,024] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:29:23,026] [INFO] Found 6/6 markers.
[2024-01-24 13:29:23,106] [INFO] Query marker FASTA was written to GCF_030068545.1_ASM3006854v1_genomic.fna/markers.fasta
[2024-01-24 13:29:23,107] [INFO] Task started: Blastn
[2024-01-24 13:29:23,107] [INFO] Running command: blastn -query GCF_030068545.1_ASM3006854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga55ff1c7-4b67-461f-82df-a0c9ae4de681/dqc_reference/reference_markers.fasta -out GCF_030068545.1_ASM3006854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:23,749] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:23,759] [INFO] Selected 28 target genomes.
[2024-01-24 13:29:23,759] [INFO] Target genome list was writen to GCF_030068545.1_ASM3006854v1_genomic.fna/target_genomes.txt
[2024-01-24 13:29:23,790] [INFO] Task started: fastANI
[2024-01-24 13:29:23,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg640b1a1b-99c9-412b-a979-67486d7984f9/GCF_030068545.1_ASM3006854v1_genomic.fna.gz --refList GCF_030068545.1_ASM3006854v1_genomic.fna/target_genomes.txt --output GCF_030068545.1_ASM3006854v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:46,028] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:46,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga55ff1c7-4b67-461f-82df-a0c9ae4de681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:46,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga55ff1c7-4b67-461f-82df-a0c9ae4de681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:46,035] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:29:46,035] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:29:46,035] [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
Sporocytophaga myxococcoides	strain=DSM 11118	GCA_000426725.1	153721	153721	type	True	74.9556	59	3133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:46,040] [INFO] DFAST Taxonomy check result was written to GCF_030068545.1_ASM3006854v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:46,041] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:46,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:46,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga55ff1c7-4b67-461f-82df-a0c9ae4de681/dqc_reference/checkm_data
[2024-01-24 13:29:46,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:46,138] [INFO] Task started: CheckM
[2024-01-24 13:29:46,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030068545.1_ASM3006854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030068545.1_ASM3006854v1_genomic.fna/checkm_input GCF_030068545.1_ASM3006854v1_genomic.fna/checkm_result
[2024-01-24 13:31:28,884] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:28,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:28,918] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:28,918] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:28,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030068545.1_ASM3006854v1_genomic.fna/markers.fasta)
[2024-01-24 13:31:28,919] [INFO] Task started: Blastn
[2024-01-24 13:31:28,920] [INFO] Running command: blastn -query GCF_030068545.1_ASM3006854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga55ff1c7-4b67-461f-82df-a0c9ae4de681/dqc_reference/reference_markers_gtdb.fasta -out GCF_030068545.1_ASM3006854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:29,672] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:29,676] [INFO] Selected 32 target genomes.
[2024-01-24 13:31:29,677] [INFO] Target genome list was writen to GCF_030068545.1_ASM3006854v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:29,737] [INFO] Task started: fastANI
[2024-01-24 13:31:29,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg640b1a1b-99c9-412b-a979-67486d7984f9/GCF_030068545.1_ASM3006854v1_genomic.fna.gz --refList GCF_030068545.1_ASM3006854v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030068545.1_ASM3006854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:53,721] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:53,725] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:31:53,725] [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_000426725.1	s__Sporocytophaga myxococcoides	74.9599	58	3133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cytophagaceae;g__Sporocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115665.1	s__Pseudarcicella hirudinis	74.8771	57	3133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Pseudarcicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:53,728] [INFO] GTDB search result was written to GCF_030068545.1_ASM3006854v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:53,729] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:53,732] [INFO] DFAST_QC result json was written to GCF_030068545.1_ASM3006854v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:53,732] [INFO] DFAST_QC completed!
[2024-01-24 13:31:53,732] [INFO] Total running time: 0h3m9s