[2024-01-24 13:18:31,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:31,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:31,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d6652ed-c492-4344-8e85-21141bca2bdd/dqc_reference
[2024-01-24 13:18:33,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:33,288] [INFO] Task started: Prodigal
[2024-01-24 13:18:33,289] [INFO] Running command: gunzip -c /var/lib/cwl/stgee5b7c82-c642-4d8e-9248-ae4605f31be5/GCF_000347635.1_ASM34763v1_genomic.fna.gz | prodigal -d GCF_000347635.1_ASM34763v1_genomic.fna/cds.fna -a GCF_000347635.1_ASM34763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:45,764] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:45,764] [INFO] Task started: HMMsearch
[2024-01-24 13:18:45,765] [INFO] Running command: hmmsearch --tblout GCF_000347635.1_ASM34763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d6652ed-c492-4344-8e85-21141bca2bdd/dqc_reference/reference_markers.hmm GCF_000347635.1_ASM34763v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:46,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:46,173] [INFO] Found 6/6 markers.
[2024-01-24 13:18:46,233] [INFO] Query marker FASTA was written to GCF_000347635.1_ASM34763v1_genomic.fna/markers.fasta
[2024-01-24 13:18:46,233] [INFO] Task started: Blastn
[2024-01-24 13:18:46,233] [INFO] Running command: blastn -query GCF_000347635.1_ASM34763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d6652ed-c492-4344-8e85-21141bca2bdd/dqc_reference/reference_markers.fasta -out GCF_000347635.1_ASM34763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:46,885] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:46,888] [INFO] Selected 17 target genomes.
[2024-01-24 13:18:46,888] [INFO] Target genome list was writen to GCF_000347635.1_ASM34763v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:46,895] [INFO] Task started: fastANI
[2024-01-24 13:18:46,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgee5b7c82-c642-4d8e-9248-ae4605f31be5/GCF_000347635.1_ASM34763v1_genomic.fna.gz --refList GCF_000347635.1_ASM34763v1_genomic.fna/target_genomes.txt --output GCF_000347635.1_ASM34763v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:01,792] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:01,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d6652ed-c492-4344-8e85-21141bca2bdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:01,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d6652ed-c492-4344-8e85-21141bca2bdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:01,802] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:01,802] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:01,802] [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
Paraglaciecola psychrophila	strain=170	GCA_000347635.1	326544	326544	type	True	100.0	1803	1804	95	conclusive
Paraglaciecola psychrophila	strain=170	GCA_000315075.1	326544	326544	type	True	99.9327	1720	1804	95	conclusive
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	81.4892	942	1804	95	below_threshold
Shewanella glacialimarina	strain=TZS-4	GCA_020511155.1	2590884	2590884	type	True	78.5372	52	1804	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	78.2388	63	1804	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	78.0707	269	1804	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	78.0262	269	1804	95	below_threshold
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	77.9859	164	1804	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	77.7203	219	1804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:01,807] [INFO] DFAST Taxonomy check result was written to GCF_000347635.1_ASM34763v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:01,808] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:01,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:01,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d6652ed-c492-4344-8e85-21141bca2bdd/dqc_reference/checkm_data
[2024-01-24 13:19:01,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:01,867] [INFO] Task started: CheckM
[2024-01-24 13:19:01,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000347635.1_ASM34763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000347635.1_ASM34763v1_genomic.fna/checkm_input GCF_000347635.1_ASM34763v1_genomic.fna/checkm_result
[2024-01-24 13:19:42,890] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:42,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:42,913] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:42,913] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:42,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000347635.1_ASM34763v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:42,914] [INFO] Task started: Blastn
[2024-01-24 13:19:42,914] [INFO] Running command: blastn -query GCF_000347635.1_ASM34763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d6652ed-c492-4344-8e85-21141bca2bdd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000347635.1_ASM34763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:43,757] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:43,761] [INFO] Selected 7 target genomes.
[2024-01-24 13:19:43,761] [INFO] Target genome list was writen to GCF_000347635.1_ASM34763v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:43,771] [INFO] Task started: fastANI
[2024-01-24 13:19:43,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgee5b7c82-c642-4d8e-9248-ae4605f31be5/GCF_000347635.1_ASM34763v1_genomic.fna.gz --refList GCF_000347635.1_ASM34763v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000347635.1_ASM34763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:52,036] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:52,043] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:52,044] [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_000347635.1	s__Paraglaciecola psychrophila	100.0	1803	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_002835935.1	s__Paraglaciecola sp002835935	85.7213	1230	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232445.1	s__Paraglaciecola arctica_A	83.0363	502	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479025.1	s__Paraglaciecola sp905479025	82.8586	523	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314995.1	s__Paraglaciecola arctica	81.4749	945	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861065.1	s__Paraglaciecola arctica_B	79.1241	586	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796765.1	s__Paraglaciecola sp009796765	78.5599	291	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:52,045] [INFO] GTDB search result was written to GCF_000347635.1_ASM34763v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:52,046] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:52,049] [INFO] DFAST_QC result json was written to GCF_000347635.1_ASM34763v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:52,049] [INFO] DFAST_QC completed!
[2024-01-24 13:19:52,049] [INFO] Total running time: 0h1m20s