[2024-01-24 12:44:33,457] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:33,459] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:33,460] [INFO] DQC Reference Directory: /var/lib/cwl/stgd415d8ad-e1a1-404b-b2b7-dcc59252de7a/dqc_reference
[2024-01-24 12:44:34,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:34,599] [INFO] Task started: Prodigal
[2024-01-24 12:44:34,599] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7f8d477-9a23-4309-a72b-20627795523e/GCF_023283985.1_ASM2328398v1_genomic.fna.gz | prodigal -d GCF_023283985.1_ASM2328398v1_genomic.fna/cds.fna -a GCF_023283985.1_ASM2328398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:45,286] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:45,286] [INFO] Task started: HMMsearch
[2024-01-24 12:44:45,286] [INFO] Running command: hmmsearch --tblout GCF_023283985.1_ASM2328398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd415d8ad-e1a1-404b-b2b7-dcc59252de7a/dqc_reference/reference_markers.hmm GCF_023283985.1_ASM2328398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:45,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:45,532] [INFO] Found 6/6 markers.
[2024-01-24 12:44:45,573] [INFO] Query marker FASTA was written to GCF_023283985.1_ASM2328398v1_genomic.fna/markers.fasta
[2024-01-24 12:44:45,573] [INFO] Task started: Blastn
[2024-01-24 12:44:45,574] [INFO] Running command: blastn -query GCF_023283985.1_ASM2328398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd415d8ad-e1a1-404b-b2b7-dcc59252de7a/dqc_reference/reference_markers.fasta -out GCF_023283985.1_ASM2328398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:46,324] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:46,327] [INFO] Selected 11 target genomes.
[2024-01-24 12:44:46,327] [INFO] Target genome list was writen to GCF_023283985.1_ASM2328398v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:46,345] [INFO] Task started: fastANI
[2024-01-24 12:44:46,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7f8d477-9a23-4309-a72b-20627795523e/GCF_023283985.1_ASM2328398v1_genomic.fna.gz --refList GCF_023283985.1_ASM2328398v1_genomic.fna/target_genomes.txt --output GCF_023283985.1_ASM2328398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:56,199] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:56,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd415d8ad-e1a1-404b-b2b7-dcc59252de7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:56,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd415d8ad-e1a1-404b-b2b7-dcc59252de7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:56,210] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:56,210] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:56,210] [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 electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	100.0	1715	1718	95	conclusive
Shewanella olleyana	strain=LMG 21437	GCA_023283825.1	135626	135626	type	True	84.427	1082	1718	95	below_threshold
Shewanella japonica	strain=KCTC 22435	GCA_002075795.1	93973	93973	type	True	82.0155	1000	1718	95	below_threshold
Shewanella donghaensis	strain=LT17	GCA_007567505.1	238836	238836	type	True	81.2811	908	1718	95	below_threshold
Shewanella intestini	strain=MCCC 1A01895	GCA_018221465.1	2017544	2017544	type	True	78.6363	376	1718	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	78.5591	372	1718	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	78.4351	400	1718	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	78.3722	408	1718	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	78.2612	417	1718	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	78.2541	427	1718	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	78.1404	289	1718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:56,211] [INFO] DFAST Taxonomy check result was written to GCF_023283985.1_ASM2328398v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:56,212] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:56,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:56,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd415d8ad-e1a1-404b-b2b7-dcc59252de7a/dqc_reference/checkm_data
[2024-01-24 12:44:56,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:56,262] [INFO] Task started: CheckM
[2024-01-24 12:44:56,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023283985.1_ASM2328398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023283985.1_ASM2328398v1_genomic.fna/checkm_input GCF_023283985.1_ASM2328398v1_genomic.fna/checkm_result
[2024-01-24 12:45:31,696] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:31,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:31,715] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:31,715] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:31,715] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023283985.1_ASM2328398v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:31,716] [INFO] Task started: Blastn
[2024-01-24 12:45:31,716] [INFO] Running command: blastn -query GCF_023283985.1_ASM2328398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd415d8ad-e1a1-404b-b2b7-dcc59252de7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_023283985.1_ASM2328398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:32,798] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:32,801] [INFO] Selected 6 target genomes.
[2024-01-24 12:45:32,801] [INFO] Target genome list was writen to GCF_023283985.1_ASM2328398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:32,815] [INFO] Task started: fastANI
[2024-01-24 12:45:32,815] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7f8d477-9a23-4309-a72b-20627795523e/GCF_023283985.1_ASM2328398v1_genomic.fna.gz --refList GCF_023283985.1_ASM2328398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023283985.1_ASM2328398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:39,842] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:39,849] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:39,849] [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_002873615.1	s__Shewanella sp002873615	98.1163	1451	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009663145.1	s__Shewanella sp009663145	86.2293	1193	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002075795.1	s__Shewanella japonica	82.0318	996	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.37	97.91	0.95	0.93	6	-
GCF_002873135.1	s__Shewanella sp002873135	81.8072	834	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.89	98.82	0.90	0.89	4	-
GCF_007567505.1	s__Shewanella donghaensis	81.2922	907	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001957135.1	s__Shewanella sp001957135	81.071	779	1718	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 12:45:39,851] [INFO] GTDB search result was written to GCF_023283985.1_ASM2328398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:39,851] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:39,856] [INFO] DFAST_QC result json was written to GCF_023283985.1_ASM2328398v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:39,856] [INFO] DFAST_QC completed!
[2024-01-24 12:45:39,857] [INFO] Total running time: 0h1m6s