[2024-01-25 18:44:05,764] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:05,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:05,765] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ad6e9b3-2969-4921-a99d-5887c6005b24/dqc_reference
[2024-01-25 18:44:06,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:06,910] [INFO] Task started: Prodigal
[2024-01-25 18:44:06,910] [INFO] Running command: gunzip -c /var/lib/cwl/stgc19d02f3-a313-43bb-9213-a7c6d282bfee/GCF_021560015.1_ASM2156001v1_genomic.fna.gz | prodigal -d GCF_021560015.1_ASM2156001v1_genomic.fna/cds.fna -a GCF_021560015.1_ASM2156001v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:16,112] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:16,112] [INFO] Task started: HMMsearch
[2024-01-25 18:44:16,112] [INFO] Running command: hmmsearch --tblout GCF_021560015.1_ASM2156001v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ad6e9b3-2969-4921-a99d-5887c6005b24/dqc_reference/reference_markers.hmm GCF_021560015.1_ASM2156001v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:16,427] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:16,428] [INFO] Found 6/6 markers.
[2024-01-25 18:44:16,469] [INFO] Query marker FASTA was written to GCF_021560015.1_ASM2156001v1_genomic.fna/markers.fasta
[2024-01-25 18:44:16,469] [INFO] Task started: Blastn
[2024-01-25 18:44:16,469] [INFO] Running command: blastn -query GCF_021560015.1_ASM2156001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ad6e9b3-2969-4921-a99d-5887c6005b24/dqc_reference/reference_markers.fasta -out GCF_021560015.1_ASM2156001v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:17,150] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:17,152] [INFO] Selected 8 target genomes.
[2024-01-25 18:44:17,153] [INFO] Target genome list was writen to GCF_021560015.1_ASM2156001v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:17,155] [INFO] Task started: fastANI
[2024-01-25 18:44:17,155] [INFO] Running command: fastANI --query /var/lib/cwl/stgc19d02f3-a313-43bb-9213-a7c6d282bfee/GCF_021560015.1_ASM2156001v1_genomic.fna.gz --refList GCF_021560015.1_ASM2156001v1_genomic.fna/target_genomes.txt --output GCF_021560015.1_ASM2156001v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:26,444] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:26,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ad6e9b3-2969-4921-a99d-5887c6005b24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:26,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ad6e9b3-2969-4921-a99d-5887c6005b24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:26,451] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:44:26,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:26,452] [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
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	100.0	1594	1594	95	conclusive
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	99.9657	1546	1594	95	conclusive
Shewanella livingstonensis	strain=LMG 19866	GCA_003855395.1	150120	150120	type	True	85.7251	1253	1594	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	84.5895	1186	1594	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	84.5156	1141	1594	95	below_threshold
Shewanella polaris	strain=SM1901	GCA_006385555.1	2588449	2588449	type	True	83.6458	1118	1594	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	81.2444	839	1594	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	81.0813	825	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:26,453] [INFO] DFAST Taxonomy check result was written to GCF_021560015.1_ASM2156001v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:26,453] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:26,453] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:26,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ad6e9b3-2969-4921-a99d-5887c6005b24/dqc_reference/checkm_data
[2024-01-25 18:44:26,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:26,499] [INFO] Task started: CheckM
[2024-01-25 18:44:26,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021560015.1_ASM2156001v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021560015.1_ASM2156001v1_genomic.fna/checkm_input GCF_021560015.1_ASM2156001v1_genomic.fna/checkm_result
[2024-01-25 18:44:56,825] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:56,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:56,848] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:56,848] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:56,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021560015.1_ASM2156001v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:56,849] [INFO] Task started: Blastn
[2024-01-25 18:44:56,849] [INFO] Running command: blastn -query GCF_021560015.1_ASM2156001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ad6e9b3-2969-4921-a99d-5887c6005b24/dqc_reference/reference_markers_gtdb.fasta -out GCF_021560015.1_ASM2156001v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:57,956] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:57,959] [INFO] Selected 7 target genomes.
[2024-01-25 18:44:57,959] [INFO] Target genome list was writen to GCF_021560015.1_ASM2156001v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:57,966] [INFO] Task started: fastANI
[2024-01-25 18:44:57,966] [INFO] Running command: fastANI --query /var/lib/cwl/stgc19d02f3-a313-43bb-9213-a7c6d282bfee/GCF_021560015.1_ASM2156001v1_genomic.fna.gz --refList GCF_021560015.1_ASM2156001v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021560015.1_ASM2156001v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:07,092] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:07,098] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:07,099] [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_003797885.1	s__Shewanella vesiculosa	99.9663	1545	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	conclusive
GCF_010092445.1	s__Shewanella sp002836315	85.947	1262	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.47	98.34	0.91	0.90	4	-
GCF_003855395.1	s__Shewanella livingstonensis	85.7158	1254	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797125.1	s__Shewanella frigidimarina	85.643	1247	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_014164505.1	s__Shewanella sp014164505	85.5843	977	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855155.1	s__Shewanella sp002836275	84.6046	1186	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.14	98.29	0.96	0.92	3	-
GCF_006385555.1	s__Shewanella polaris	83.6528	1117	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:07,100] [INFO] GTDB search result was written to GCF_021560015.1_ASM2156001v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:07,100] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:07,103] [INFO] DFAST_QC result json was written to GCF_021560015.1_ASM2156001v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:07,103] [INFO] DFAST_QC completed!
[2024-01-25 18:45:07,103] [INFO] Total running time: 0h1m1s