[2024-01-24 14:46:56,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:56,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:56,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e73dcab-2497-4d96-bb5f-1929d7922ca1/dqc_reference
[2024-01-24 14:46:57,994] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:57,995] [INFO] Task started: Prodigal
[2024-01-24 14:46:57,996] [INFO] Running command: gunzip -c /var/lib/cwl/stgd67c47c3-c660-4fd8-9f3c-b91b6b7ae833/GCF_018394335.1_ASM1839433v1_genomic.fna.gz | prodigal -d GCF_018394335.1_ASM1839433v1_genomic.fna/cds.fna -a GCF_018394335.1_ASM1839433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:09,865] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:09,865] [INFO] Task started: HMMsearch
[2024-01-24 14:47:09,865] [INFO] Running command: hmmsearch --tblout GCF_018394335.1_ASM1839433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e73dcab-2497-4d96-bb5f-1929d7922ca1/dqc_reference/reference_markers.hmm GCF_018394335.1_ASM1839433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:10,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:10,221] [INFO] Found 6/6 markers.
[2024-01-24 14:47:10,277] [INFO] Query marker FASTA was written to GCF_018394335.1_ASM1839433v1_genomic.fna/markers.fasta
[2024-01-24 14:47:10,278] [INFO] Task started: Blastn
[2024-01-24 14:47:10,278] [INFO] Running command: blastn -query GCF_018394335.1_ASM1839433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e73dcab-2497-4d96-bb5f-1929d7922ca1/dqc_reference/reference_markers.fasta -out GCF_018394335.1_ASM1839433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:11,130] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:11,133] [INFO] Selected 14 target genomes.
[2024-01-24 14:47:11,134] [INFO] Target genome list was writen to GCF_018394335.1_ASM1839433v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:11,140] [INFO] Task started: fastANI
[2024-01-24 14:47:11,140] [INFO] Running command: fastANI --query /var/lib/cwl/stgd67c47c3-c660-4fd8-9f3c-b91b6b7ae833/GCF_018394335.1_ASM1839433v1_genomic.fna.gz --refList GCF_018394335.1_ASM1839433v1_genomic.fna/target_genomes.txt --output GCF_018394335.1_ASM1839433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:24,277] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:24,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e73dcab-2497-4d96-bb5f-1929d7922ca1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:24,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e73dcab-2497-4d96-bb5f-1929d7922ca1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:24,289] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:24,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:24,290] [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 dokdonensis	strain=DSM 23626	GCA_018394335.1	712036	712036	type	True	100.0	1374	1375	95	conclusive
Shewanella fodinae	strain=KCTC 22506	GCA_014651955.1	552357	552357	type	True	85.5494	1084	1375	95	below_threshold
Shewanella fodinae	strain=CCUG 57102	GCA_023349145.1	552357	552357	type	True	85.4651	1078	1375	95	below_threshold
Shewanella yunxiaonensis	strain=FJAT-54481	GCA_018223345.1	2829809	2829809	type	True	81.7502	765	1375	95	below_threshold
Shewanella cyperi	strain=FJAT-53720	GCA_017354985.1	2814292	2814292	type	True	79.4743	162	1375	95	below_threshold
Shewanella avicenniae	strain=FJAT-51800	GCA_017354945.1	2814294	2814294	type	True	78.6864	311	1375	95	below_threshold
Shewanella sediminis	strain=HAW-EB3	GCA_000018025.1	271097	271097	type	True	78.4146	104	1375	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	78.2233	256	1375	95	below_threshold
Shewanella indica	strain=KJW27	GCA_002836975.1	768528	768528	type	True	78.092	252	1375	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	77.9389	90	1375	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	77.7386	92	1375	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	77.7209	184	1375	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	77.2025	129	1375	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:24,291] [INFO] DFAST Taxonomy check result was written to GCF_018394335.1_ASM1839433v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:24,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:24,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:24,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e73dcab-2497-4d96-bb5f-1929d7922ca1/dqc_reference/checkm_data
[2024-01-24 14:47:24,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:24,341] [INFO] Task started: CheckM
[2024-01-24 14:47:24,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018394335.1_ASM1839433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018394335.1_ASM1839433v1_genomic.fna/checkm_input GCF_018394335.1_ASM1839433v1_genomic.fna/checkm_result
[2024-01-24 14:48:05,204] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:05,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:05,228] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:05,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:05,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018394335.1_ASM1839433v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:05,230] [INFO] Task started: Blastn
[2024-01-24 14:48:05,230] [INFO] Running command: blastn -query GCF_018394335.1_ASM1839433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e73dcab-2497-4d96-bb5f-1929d7922ca1/dqc_reference/reference_markers_gtdb.fasta -out GCF_018394335.1_ASM1839433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:06,465] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:06,471] [INFO] Selected 14 target genomes.
[2024-01-24 14:48:06,471] [INFO] Target genome list was writen to GCF_018394335.1_ASM1839433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:06,482] [INFO] Task started: fastANI
[2024-01-24 14:48:06,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgd67c47c3-c660-4fd8-9f3c-b91b6b7ae833/GCF_018394335.1_ASM1839433v1_genomic.fna.gz --refList GCF_018394335.1_ASM1839433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018394335.1_ASM1839433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:19,260] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:19,275] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:19,275] [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_018394335.1	s__Shewanella dokdonensis	100.0	1374	1375	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_014651955.1	s__Shewanella fodinae	85.5494	1084	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.57	97.13	0.90	0.90	3	-
GCF_018223345.1	s__Shewanella sp018223345	81.7114	762	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017354985.1	s__Shewanella sp017354985	79.5543	162	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_002966515.1	s__Shewanella sp002966515	78.7109	169	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCF_012911865.1	s__Shewanella sp012911865	78.6854	119	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017354945.1	s__Shewanella sp017354945	78.5485	310	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014885.1	s__Shewanella piezotolerans	78.4896	102	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018025.1	s__Shewanella sediminis	78.4274	104	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753795.1	s__Shewanella mangrovi	78.1162	346	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836975.1	s__Shewanella indica	78.0968	251	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	-
GCF_002836945.1	s__Shewanella chilikensis	78.0765	247	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:19,277] [INFO] GTDB search result was written to GCF_018394335.1_ASM1839433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:19,278] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:19,281] [INFO] DFAST_QC result json was written to GCF_018394335.1_ASM1839433v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:19,281] [INFO] DFAST_QC completed!
[2024-01-24 14:48:19,282] [INFO] Total running time: 0h1m23s