[2024-01-25 19:41:20,759] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:20,762] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:20,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d1de49d-1195-48d4-9892-f856d1850094/dqc_reference
[2024-01-25 19:41:21,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:21,882] [INFO] Task started: Prodigal
[2024-01-25 19:41:21,882] [INFO] Running command: gunzip -c /var/lib/cwl/stgc43fb0d6-d36c-4df4-999b-6daba0c1d5eb/GCF_014647215.1_ASM1464721v1_genomic.fna.gz | prodigal -d GCF_014647215.1_ASM1464721v1_genomic.fna/cds.fna -a GCF_014647215.1_ASM1464721v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:41:29,278] [INFO] Task succeeded: Prodigal
[2024-01-25 19:41:29,278] [INFO] Task started: HMMsearch
[2024-01-25 19:41:29,278] [INFO] Running command: hmmsearch --tblout GCF_014647215.1_ASM1464721v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d1de49d-1195-48d4-9892-f856d1850094/dqc_reference/reference_markers.hmm GCF_014647215.1_ASM1464721v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:41:29,519] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:41:29,520] [INFO] Found 6/6 markers.
[2024-01-25 19:41:29,555] [INFO] Query marker FASTA was written to GCF_014647215.1_ASM1464721v1_genomic.fna/markers.fasta
[2024-01-25 19:41:29,555] [INFO] Task started: Blastn
[2024-01-25 19:41:29,555] [INFO] Running command: blastn -query GCF_014647215.1_ASM1464721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d1de49d-1195-48d4-9892-f856d1850094/dqc_reference/reference_markers.fasta -out GCF_014647215.1_ASM1464721v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:30,258] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:30,261] [INFO] Selected 17 target genomes.
[2024-01-25 19:41:30,261] [INFO] Target genome list was writen to GCF_014647215.1_ASM1464721v1_genomic.fna/target_genomes.txt
[2024-01-25 19:41:30,269] [INFO] Task started: fastANI
[2024-01-25 19:41:30,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgc43fb0d6-d36c-4df4-999b-6daba0c1d5eb/GCF_014647215.1_ASM1464721v1_genomic.fna.gz --refList GCF_014647215.1_ASM1464721v1_genomic.fna/target_genomes.txt --output GCF_014647215.1_ASM1464721v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:41:44,084] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:44,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d1de49d-1195-48d4-9892-f856d1850094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:41:44,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d1de49d-1195-48d4-9892-f856d1850094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:41:44,095] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:41:44,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:41:44,096] [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 aestuarii	strain=JCM 17801	GCA_014647215.1	1028752	1028752	type	True	100.0	1282	1282	95	conclusive
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	99.9942	1274	1282	95	conclusive
Shewanella glacialimarina	strain=TZS-4	GCA_020511155.1	2590884	2590884	type	True	81.7143	829	1282	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	79.7816	485	1282	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	79.7525	490	1282	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	79.6868	473	1282	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	79.624	463	1282	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	79.6027	470	1282	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	79.5552	485	1282	95	below_threshold
Shewanella livingstonensis	strain=LMG 19866	GCA_003855395.1	150120	150120	type	True	79.5039	472	1282	95	below_threshold
Shewanella ulleungensis	strain=JCM 32305	GCA_014648315.1	2282699	2282699	type	True	79.4849	465	1282	95	below_threshold
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	79.4766	467	1282	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	79.4171	478	1282	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	79.3486	467	1282	95	below_threshold
Shewanella polaris	strain=SM1901	GCA_006385555.1	2588449	2588449	type	True	79.1718	461	1282	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	78.624	371	1282	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	77.9918	188	1282	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:41:44,097] [INFO] DFAST Taxonomy check result was written to GCF_014647215.1_ASM1464721v1_genomic.fna/tc_result.tsv
[2024-01-25 19:41:44,098] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:41:44,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:41:44,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d1de49d-1195-48d4-9892-f856d1850094/dqc_reference/checkm_data
[2024-01-25 19:41:44,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:41:44,138] [INFO] Task started: CheckM
[2024-01-25 19:41:44,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647215.1_ASM1464721v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647215.1_ASM1464721v1_genomic.fna/checkm_input GCF_014647215.1_ASM1464721v1_genomic.fna/checkm_result
[2024-01-25 19:42:10,244] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:10,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:10,260] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:10,261] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:10,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647215.1_ASM1464721v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:10,262] [INFO] Task started: Blastn
[2024-01-25 19:42:10,262] [INFO] Running command: blastn -query GCF_014647215.1_ASM1464721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d1de49d-1195-48d4-9892-f856d1850094/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647215.1_ASM1464721v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:11,373] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:11,387] [INFO] Selected 14 target genomes.
[2024-01-25 19:42:11,387] [INFO] Target genome list was writen to GCF_014647215.1_ASM1464721v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:11,408] [INFO] Task started: fastANI
[2024-01-25 19:42:11,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgc43fb0d6-d36c-4df4-999b-6daba0c1d5eb/GCF_014647215.1_ASM1464721v1_genomic.fna.gz --refList GCF_014647215.1_ASM1464721v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647215.1_ASM1464721v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:24,001] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:24,012] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:42:24,012] [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_014647215.1	s__Shewanella aestuarii	100.0	1282	1282	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_011765625.1	s__Shewanella aestuarii_A	80.2283	623	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828585.1	s__Shewanella litoralis	79.7912	486	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014648295.1	s__Shewanella saliphila	79.6721	475	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_014641855.1	s__Shewanella inventionis	79.6163	490	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797125.1	s__Shewanella frigidimarina	79.5591	462	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_003855395.1	s__Shewanella livingstonensis	79.5165	471	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797885.1	s__Shewanella vesiculosa	79.4907	466	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	-
GCF_014648315.1	s__Shewanella ulleungensis	79.4877	467	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648035.1	s__Shewanella algicola	79.4346	481	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_010092445.1	s__Shewanella sp002836315	79.2659	481	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.47	98.34	0.91	0.90	4	-
GCF_006385555.1	s__Shewanella polaris	79.1763	460	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_001957135.1	s__Shewanella sp001957135	78.5365	392	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221465.1	s__Shewanella intestini	78.4871	336	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:24,013] [INFO] GTDB search result was written to GCF_014647215.1_ASM1464721v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:24,014] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:24,017] [INFO] DFAST_QC result json was written to GCF_014647215.1_ASM1464721v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:24,017] [INFO] DFAST_QC completed!
[2024-01-25 19:42:24,017] [INFO] Total running time: 0h1m3s