[2024-01-24 11:59:12,931] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:12,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:12,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg8305d7e5-ab2a-444b-bd73-6d7d749d3c9e/dqc_reference
[2024-01-24 11:59:14,382] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,383] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,383] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb07f083-fd04-4df5-b2be-a30bc222479c/GCF_900456975.1_50884_G01_genomic.fna.gz | prodigal -d GCF_900456975.1_50884_G01_genomic.fna/cds.fna -a GCF_900456975.1_50884_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:29,080] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:29,080] [INFO] Task started: HMMsearch
[2024-01-24 11:59:29,080] [INFO] Running command: hmmsearch --tblout GCF_900456975.1_50884_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8305d7e5-ab2a-444b-bd73-6d7d749d3c9e/dqc_reference/reference_markers.hmm GCF_900456975.1_50884_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:29,414] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:29,415] [INFO] Found 6/6 markers.
[2024-01-24 11:59:29,464] [INFO] Query marker FASTA was written to GCF_900456975.1_50884_G01_genomic.fna/markers.fasta
[2024-01-24 11:59:29,465] [INFO] Task started: Blastn
[2024-01-24 11:59:29,465] [INFO] Running command: blastn -query GCF_900456975.1_50884_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8305d7e5-ab2a-444b-bd73-6d7d749d3c9e/dqc_reference/reference_markers.fasta -out GCF_900456975.1_50884_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:30,270] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:30,274] [INFO] Selected 11 target genomes.
[2024-01-24 11:59:30,274] [INFO] Target genome list was writen to GCF_900456975.1_50884_G01_genomic.fna/target_genomes.txt
[2024-01-24 11:59:30,278] [INFO] Task started: fastANI
[2024-01-24 11:59:30,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb07f083-fd04-4df5-b2be-a30bc222479c/GCF_900456975.1_50884_G01_genomic.fna.gz --refList GCF_900456975.1_50884_G01_genomic.fna/target_genomes.txt --output GCF_900456975.1_50884_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:43,767] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:43,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8305d7e5-ab2a-444b-bd73-6d7d749d3c9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:43,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8305d7e5-ab2a-444b-bd73-6d7d749d3c9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:43,778] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:43,779] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:43,779] [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 baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	100.0	1762	1766	95	conclusive
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	94.3204	1373	1766	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	91.0984	1412	1766	95	below_threshold
Shewanella glacialipiscicola	strain=T147	GCA_019655235.1	614069	614069	type	True	85.5994	1027	1766	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	85.4729	1145	1766	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	85.2574	1167	1766	95	below_threshold
Shewanella putrefaciens	strain=ATCC 8071	GCA_016406325.1	24	24	type	True	84.9889	1111	1766	95	below_threshold
Shewanella putrefaciens	strain=NBRC 3908	GCA_001591325.1	24	24	type	True	84.8282	1068	1766	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	84.6455	1117	1766	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	81.5596	1018	1766	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	81.387	1047	1766	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:43,783] [INFO] DFAST Taxonomy check result was written to GCF_900456975.1_50884_G01_genomic.fna/tc_result.tsv
[2024-01-24 11:59:43,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:43,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:43,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8305d7e5-ab2a-444b-bd73-6d7d749d3c9e/dqc_reference/checkm_data
[2024-01-24 11:59:43,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:43,842] [INFO] Task started: CheckM
[2024-01-24 11:59:43,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900456975.1_50884_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900456975.1_50884_G01_genomic.fna/checkm_input GCF_900456975.1_50884_G01_genomic.fna/checkm_result
[2024-01-24 12:00:29,871] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:29,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:29,898] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:29,898] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:29,899] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900456975.1_50884_G01_genomic.fna/markers.fasta)
[2024-01-24 12:00:29,899] [INFO] Task started: Blastn
[2024-01-24 12:00:29,899] [INFO] Running command: blastn -query GCF_900456975.1_50884_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8305d7e5-ab2a-444b-bd73-6d7d749d3c9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900456975.1_50884_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:31,043] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:31,047] [INFO] Selected 8 target genomes.
[2024-01-24 12:00:31,047] [INFO] Target genome list was writen to GCF_900456975.1_50884_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:31,053] [INFO] Task started: fastANI
[2024-01-24 12:00:31,054] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb07f083-fd04-4df5-b2be-a30bc222479c/GCF_900456975.1_50884_G01_genomic.fna.gz --refList GCF_900456975.1_50884_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900456975.1_50884_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:42,096] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:42,111] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:42,111] [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_900456975.1	s__Shewanella baltica	100.0	1764	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	conclusive
GCF_002838165.1	s__Shewanella sp002838165	94.2082	1471	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	-
GCF_002966515.1	s__Shewanella sp002966515	91.1512	1424	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCA_002783505.1	s__Shewanella sp002783505	86.0755	1148	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156405.1	s__Shewanella morhuae	85.2604	1166	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_016406325.1	s__Shewanella putrefaciens	85.0041	1109	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	-
GCF_016406305.1	s__Shewanella putrefaciens_C	84.954	1167	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014665.1	s__Shewanella sp000014665	82.1502	1032	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:42,112] [INFO] GTDB search result was written to GCF_900456975.1_50884_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:42,113] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:42,116] [INFO] DFAST_QC result json was written to GCF_900456975.1_50884_G01_genomic.fna/dqc_result.json
[2024-01-24 12:00:42,116] [INFO] DFAST_QC completed!
[2024-01-24 12:00:42,116] [INFO] Total running time: 0h1m29s