[2023-06-19 08:50:37,269] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:50:37,274] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:50:37,274] [INFO] DQC Reference Directory: /var/lib/cwl/stg69c68f5d-6f55-4ae9-a67d-130907ae6433/dqc_reference
[2023-06-19 08:50:38,655] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:50:38,656] [INFO] Task started: Prodigal
[2023-06-19 08:50:38,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ff4f761-1a78-4e31-bdaa-b4ec5419fe07/GCA_018005685.1_ASM1800568v1_genomic.fna.gz | prodigal -d GCA_018005685.1_ASM1800568v1_genomic.fna/cds.fna -a GCA_018005685.1_ASM1800568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:50:42,677] [INFO] Task succeeded: Prodigal
[2023-06-19 08:50:42,677] [INFO] Task started: HMMsearch
[2023-06-19 08:50:42,677] [INFO] Running command: hmmsearch --tblout GCA_018005685.1_ASM1800568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69c68f5d-6f55-4ae9-a67d-130907ae6433/dqc_reference/reference_markers.hmm GCA_018005685.1_ASM1800568v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:50:42,887] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:50:42,889] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7ff4f761-1a78-4e31-bdaa-b4ec5419fe07/GCA_018005685.1_ASM1800568v1_genomic.fna.gz]
[2023-06-19 08:50:42,918] [INFO] Query marker FASTA was written to GCA_018005685.1_ASM1800568v1_genomic.fna/markers.fasta
[2023-06-19 08:50:42,918] [INFO] Task started: Blastn
[2023-06-19 08:50:42,918] [INFO] Running command: blastn -query GCA_018005685.1_ASM1800568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c68f5d-6f55-4ae9-a67d-130907ae6433/dqc_reference/reference_markers.fasta -out GCA_018005685.1_ASM1800568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:50:43,562] [INFO] Task succeeded: Blastn
[2023-06-19 08:50:43,566] [INFO] Selected 8 target genomes.
[2023-06-19 08:50:43,566] [INFO] Target genome list was writen to GCA_018005685.1_ASM1800568v1_genomic.fna/target_genomes.txt
[2023-06-19 08:50:43,570] [INFO] Task started: fastANI
[2023-06-19 08:50:43,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff4f761-1a78-4e31-bdaa-b4ec5419fe07/GCA_018005685.1_ASM1800568v1_genomic.fna.gz --refList GCA_018005685.1_ASM1800568v1_genomic.fna/target_genomes.txt --output GCA_018005685.1_ASM1800568v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:50:50,294] [INFO] Task succeeded: fastANI
[2023-06-19 08:50:50,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69c68f5d-6f55-4ae9-a67d-130907ae6433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:50:50,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69c68f5d-6f55-4ae9-a67d-130907ae6433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:50:50,307] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 08:50:50,307] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 08:50:50,307] [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 oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	98.6597	501	504	95	conclusive
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	91.448	480	504	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	91.0253	485	504	95	below_threshold
Shewanella putrefaciens	strain=ATCC 8071	GCA_016406325.1	24	24	type	True	85.475	413	504	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	85.0279	432	504	95	below_threshold
Shewanella glacialipiscicola	strain=T147	GCA_019655235.1	614069	614069	type	True	84.8903	393	504	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	84.5403	413	504	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	84.4939	423	504	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:50:50,310] [INFO] DFAST Taxonomy check result was written to GCA_018005685.1_ASM1800568v1_genomic.fna/tc_result.tsv
[2023-06-19 08:50:50,310] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:50:50,310] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:50:50,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69c68f5d-6f55-4ae9-a67d-130907ae6433/dqc_reference/checkm_data
[2023-06-19 08:50:50,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:50:50,359] [INFO] Task started: CheckM
[2023-06-19 08:50:50,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018005685.1_ASM1800568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018005685.1_ASM1800568v1_genomic.fna/checkm_input GCA_018005685.1_ASM1800568v1_genomic.fna/checkm_result
[2023-06-19 08:51:09,680] [INFO] Task succeeded: CheckM
[2023-06-19 08:51:09,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:51:09,734] [INFO] ===== Completeness check finished =====
[2023-06-19 08:51:09,734] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:51:09,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018005685.1_ASM1800568v1_genomic.fna/markers.fasta)
[2023-06-19 08:51:09,735] [INFO] Task started: Blastn
[2023-06-19 08:51:09,735] [INFO] Running command: blastn -query GCA_018005685.1_ASM1800568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c68f5d-6f55-4ae9-a67d-130907ae6433/dqc_reference/reference_markers_gtdb.fasta -out GCA_018005685.1_ASM1800568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:51:10,344] [INFO] Task succeeded: Blastn
[2023-06-19 08:51:10,349] [INFO] Selected 7 target genomes.
[2023-06-19 08:51:10,349] [INFO] Target genome list was writen to GCA_018005685.1_ASM1800568v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:51:10,353] [INFO] Task started: fastANI
[2023-06-19 08:51:10,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff4f761-1a78-4e31-bdaa-b4ec5419fe07/GCA_018005685.1_ASM1800568v1_genomic.fna.gz --refList GCA_018005685.1_ASM1800568v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018005685.1_ASM1800568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:51:16,298] [INFO] Task succeeded: fastANI
[2023-06-19 08:51:16,307] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:51:16,307] [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_002966515.1	s__Shewanella sp002966515	98.5842	495	504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	conclusive
GCF_002838165.1	s__Shewanella sp002838165	91.3452	486	504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	-
GCF_900456975.1	s__Shewanella baltica	91.0253	485	504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_016406325.1	s__Shewanella putrefaciens	85.475	413	504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	-
GCF_900156405.1	s__Shewanella morhuae	84.4939	423	504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCA_002783505.1	s__Shewanella sp002783505	84.4515	415	504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217915.1	s__Shewanella sp000217915	83.7725	403	504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:51:16,309] [INFO] GTDB search result was written to GCA_018005685.1_ASM1800568v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:51:16,311] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:51:16,314] [INFO] DFAST_QC result json was written to GCA_018005685.1_ASM1800568v1_genomic.fna/dqc_result.json
[2023-06-19 08:51:16,314] [INFO] DFAST_QC completed!
[2023-06-19 08:51:16,314] [INFO] Total running time: 0h0m39s