[2024-01-24 10:49:34,727] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:34,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:34,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgae9b4404-40a7-463c-aafd-baa8d53afb23/dqc_reference
[2024-01-24 10:49:35,941] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:35,942] [INFO] Task started: Prodigal
[2024-01-24 10:49:35,942] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6d39f82-4a9b-459e-ae5e-3105f45b1a85/GCF_023283475.1_ASM2328347v1_genomic.fna.gz | prodigal -d GCF_023283475.1_ASM2328347v1_genomic.fna/cds.fna -a GCF_023283475.1_ASM2328347v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:48,409] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:48,410] [INFO] Task started: HMMsearch
[2024-01-24 10:49:48,410] [INFO] Running command: hmmsearch --tblout GCF_023283475.1_ASM2328347v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae9b4404-40a7-463c-aafd-baa8d53afb23/dqc_reference/reference_markers.hmm GCF_023283475.1_ASM2328347v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:48,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:48,770] [INFO] Found 6/6 markers.
[2024-01-24 10:49:48,810] [INFO] Query marker FASTA was written to GCF_023283475.1_ASM2328347v1_genomic.fna/markers.fasta
[2024-01-24 10:49:48,811] [INFO] Task started: Blastn
[2024-01-24 10:49:48,811] [INFO] Running command: blastn -query GCF_023283475.1_ASM2328347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae9b4404-40a7-463c-aafd-baa8d53afb23/dqc_reference/reference_markers.fasta -out GCF_023283475.1_ASM2328347v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:49,653] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:49,657] [INFO] Selected 11 target genomes.
[2024-01-24 10:49:49,658] [INFO] Target genome list was writen to GCF_023283475.1_ASM2328347v1_genomic.fna/target_genomes.txt
[2024-01-24 10:49:50,451] [INFO] Task started: fastANI
[2024-01-24 10:49:50,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d39f82-4a9b-459e-ae5e-3105f45b1a85/GCF_023283475.1_ASM2328347v1_genomic.fna.gz --refList GCF_023283475.1_ASM2328347v1_genomic.fna/target_genomes.txt --output GCF_023283475.1_ASM2328347v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:50:01,650] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:01,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae9b4404-40a7-463c-aafd-baa8d53afb23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:50:01,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae9b4404-40a7-463c-aafd-baa8d53afb23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:50:01,664] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 10:50:01,664] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:50:01,664] [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 chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	100.0	1447	1452	95	inconclusive
Shewanella chilikensis	strain=JC5	GCA_003217175.1	558541	558541	type	True	99.9892	1422	1452	95	inconclusive
Shewanella chilikensis	strain=KCTC 22540	GCA_014651975.1	558541	558541	type	True	99.9781	1405	1452	95	inconclusive
Shewanella chilikensis	strain=JC5	GCA_002836945.1	558541	558541	type	True	99.9631	1388	1452	95	inconclusive
Shewanella indica	strain=KJW27	GCA_002836975.1	768528	768528	type	True	95.7278	1336	1452	95	inconclusive
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	94.5021	1261	1452	95	below_threshold
Shewanella carassii	strain=08MAS2251	GCA_002777975.1	1987584	1987584	type	True	93.509	1244	1452	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	78.5508	401	1452	95	below_threshold
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	78.4102	411	1452	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	78.1891	388	1452	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	77.9193	338	1452	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:50:01,666] [INFO] DFAST Taxonomy check result was written to GCF_023283475.1_ASM2328347v1_genomic.fna/tc_result.tsv
[2024-01-24 10:50:01,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:50:01,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:50:01,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae9b4404-40a7-463c-aafd-baa8d53afb23/dqc_reference/checkm_data
[2024-01-24 10:50:01,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:50:01,719] [INFO] Task started: CheckM
[2024-01-24 10:50:01,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023283475.1_ASM2328347v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023283475.1_ASM2328347v1_genomic.fna/checkm_input GCF_023283475.1_ASM2328347v1_genomic.fna/checkm_result
[2024-01-24 10:50:42,457] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:42,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:42,479] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:42,479] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:42,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023283475.1_ASM2328347v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:42,480] [INFO] Task started: Blastn
[2024-01-24 10:50:42,480] [INFO] Running command: blastn -query GCF_023283475.1_ASM2328347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae9b4404-40a7-463c-aafd-baa8d53afb23/dqc_reference/reference_markers_gtdb.fasta -out GCF_023283475.1_ASM2328347v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:43,767] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:43,772] [INFO] Selected 9 target genomes.
[2024-01-24 10:50:43,772] [INFO] Target genome list was writen to GCF_023283475.1_ASM2328347v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:43,779] [INFO] Task started: fastANI
[2024-01-24 10:50:43,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d39f82-4a9b-459e-ae5e-3105f45b1a85/GCF_023283475.1_ASM2328347v1_genomic.fna.gz --refList GCF_023283475.1_ASM2328347v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023283475.1_ASM2328347v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:53,302] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:53,314] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:53,315] [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_002836945.1	s__Shewanella chilikensis	99.9631	1388	1452	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	conclusive
GCF_002836975.1	s__Shewanella indica	95.7278	1336	1452	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	-
GCF_009183365.2	s__Shewanella algae	94.4602	1335	1452	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
GCF_002777975.1	s__Shewanella carassii	93.509	1244	1452	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017354985.1	s__Shewanella sp017354985	78.9259	450	1452	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_003957745.1	s__Shewanella khirikhana	78.509	473	1452	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353085.1	s__Shewanella corallii	78.4435	321	1452	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831655.1	s__Shewanella insulae	78.1921	393	1452	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018394335.1	s__Shewanella dokdonensis	78.1316	241	1452	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:53,317] [INFO] GTDB search result was written to GCF_023283475.1_ASM2328347v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:53,318] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:53,321] [INFO] DFAST_QC result json was written to GCF_023283475.1_ASM2328347v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:53,321] [INFO] DFAST_QC completed!
[2024-01-24 10:50:53,322] [INFO] Total running time: 0h1m19s