[2024-01-24 12:23:03,918] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,922] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f4af0a0-b9bd-4333-9b71-d2fba1132fbe/dqc_reference
[2024-01-24 12:23:05,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,177] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,177] [INFO] Running command: gunzip -c /var/lib/cwl/stg39d930f1-be23-4c24-866b-6efe960d70b7/GCF_009910845.1_ASM991084v1_genomic.fna.gz | prodigal -d GCF_009910845.1_ASM991084v1_genomic.fna/cds.fna -a GCF_009910845.1_ASM991084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:13,449] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:13,450] [INFO] Task started: HMMsearch
[2024-01-24 12:23:13,450] [INFO] Running command: hmmsearch --tblout GCF_009910845.1_ASM991084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f4af0a0-b9bd-4333-9b71-d2fba1132fbe/dqc_reference/reference_markers.hmm GCF_009910845.1_ASM991084v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:13,764] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:13,766] [INFO] Found 6/6 markers.
[2024-01-24 12:23:13,806] [INFO] Query marker FASTA was written to GCF_009910845.1_ASM991084v1_genomic.fna/markers.fasta
[2024-01-24 12:23:13,806] [INFO] Task started: Blastn
[2024-01-24 12:23:13,806] [INFO] Running command: blastn -query GCF_009910845.1_ASM991084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f4af0a0-b9bd-4333-9b71-d2fba1132fbe/dqc_reference/reference_markers.fasta -out GCF_009910845.1_ASM991084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:14,405] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:14,409] [INFO] Selected 23 target genomes.
[2024-01-24 12:23:14,409] [INFO] Target genome list was writen to GCF_009910845.1_ASM991084v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:14,437] [INFO] Task started: fastANI
[2024-01-24 12:23:14,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg39d930f1-be23-4c24-866b-6efe960d70b7/GCF_009910845.1_ASM991084v1_genomic.fna.gz --refList GCF_009910845.1_ASM991084v1_genomic.fna/target_genomes.txt --output GCF_009910845.1_ASM991084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:29,075] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:29,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f4af0a0-b9bd-4333-9b71-d2fba1132fbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:29,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f4af0a0-b9bd-4333-9b71-d2fba1132fbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:29,084] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:29,085] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:29,085] [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
Chengkuizengella marina	strain=YPA3-1-1	GCA_009910845.1	2507566	2507566	type	True	100.0	1412	1415	95	conclusive
Chengkuizengella sediminis	strain=J15A17	GCA_010078385.1	1885917	1885917	type	True	88.4052	1159	1415	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:29,087] [INFO] DFAST Taxonomy check result was written to GCF_009910845.1_ASM991084v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:29,087] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:29,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:29,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f4af0a0-b9bd-4333-9b71-d2fba1132fbe/dqc_reference/checkm_data
[2024-01-24 12:23:29,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:29,138] [INFO] Task started: CheckM
[2024-01-24 12:23:29,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009910845.1_ASM991084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009910845.1_ASM991084v1_genomic.fna/checkm_input GCF_009910845.1_ASM991084v1_genomic.fna/checkm_result
[2024-01-24 12:23:58,478] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:58,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:58,507] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:58,507] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:58,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009910845.1_ASM991084v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:58,508] [INFO] Task started: Blastn
[2024-01-24 12:23:58,509] [INFO] Running command: blastn -query GCF_009910845.1_ASM991084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f4af0a0-b9bd-4333-9b71-d2fba1132fbe/dqc_reference/reference_markers_gtdb.fasta -out GCF_009910845.1_ASM991084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:59,240] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:59,244] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:59,244] [INFO] Target genome list was writen to GCF_009910845.1_ASM991084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:59,871] [INFO] Task started: fastANI
[2024-01-24 12:23:59,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg39d930f1-be23-4c24-866b-6efe960d70b7/GCF_009910845.1_ASM991084v1_genomic.fna.gz --refList GCF_009910845.1_ASM991084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009910845.1_ASM991084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:15,440] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:15,446] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:15,446] [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_009910845.1	s__Chengkuizengella marina	100.0	1412	1415	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__SCSIO-06110;g__Chengkuizengella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010078385.1	s__Chengkuizengella sediminis	88.3931	1160	1415	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__SCSIO-06110;g__Chengkuizengella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:15,448] [INFO] GTDB search result was written to GCF_009910845.1_ASM991084v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:15,448] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:15,451] [INFO] DFAST_QC result json was written to GCF_009910845.1_ASM991084v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:15,451] [INFO] DFAST_QC completed!
[2024-01-24 12:24:15,451] [INFO] Total running time: 0h1m12s