[2024-01-24 13:28:28,150] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:28,151] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:28,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg623ffad9-c02c-4ffc-9d7f-0fe31794dfac/dqc_reference
[2024-01-24 13:28:29,455] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:29,456] [INFO] Task started: Prodigal
[2024-01-24 13:28:29,456] [INFO] Running command: gunzip -c /var/lib/cwl/stg0944d2d6-10af-4054-b801-56920321c8f9/GCF_000013765.1_ASM1376v1_genomic.fna.gz | prodigal -d GCF_000013765.1_ASM1376v1_genomic.fna/cds.fna -a GCF_000013765.1_ASM1376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:41,033] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:41,033] [INFO] Task started: HMMsearch
[2024-01-24 13:28:41,034] [INFO] Running command: hmmsearch --tblout GCF_000013765.1_ASM1376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg623ffad9-c02c-4ffc-9d7f-0fe31794dfac/dqc_reference/reference_markers.hmm GCF_000013765.1_ASM1376v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:41,322] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:41,324] [INFO] Found 6/6 markers.
[2024-01-24 13:28:41,366] [INFO] Query marker FASTA was written to GCF_000013765.1_ASM1376v1_genomic.fna/markers.fasta
[2024-01-24 13:28:41,367] [INFO] Task started: Blastn
[2024-01-24 13:28:41,367] [INFO] Running command: blastn -query GCF_000013765.1_ASM1376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623ffad9-c02c-4ffc-9d7f-0fe31794dfac/dqc_reference/reference_markers.fasta -out GCF_000013765.1_ASM1376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:42,131] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:42,136] [INFO] Selected 25 target genomes.
[2024-01-24 13:28:42,136] [INFO] Target genome list was writen to GCF_000013765.1_ASM1376v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:42,151] [INFO] Task started: fastANI
[2024-01-24 13:28:42,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg0944d2d6-10af-4054-b801-56920321c8f9/GCF_000013765.1_ASM1376v1_genomic.fna.gz --refList GCF_000013765.1_ASM1376v1_genomic.fna/target_genomes.txt --output GCF_000013765.1_ASM1376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:01,126] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:01,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg623ffad9-c02c-4ffc-9d7f-0fe31794dfac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:01,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg623ffad9-c02c-4ffc-9d7f-0fe31794dfac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:01,148] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:01,148] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:01,149] [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 denitrificans	strain=OS217	GCA_000013765.1	192073	192073	type	True	100.0	1513	1515	95	conclusive
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	79.2538	313	1515	95	below_threshold
Shewanella polaris	strain=SM1901	GCA_006385555.1	2588449	2588449	type	True	79.0633	315	1515	95	below_threshold
Shewanella glacialimarina	strain=TZS-4	GCA_020511155.1	2590884	2590884	type	True	79.0194	317	1515	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	78.9241	334	1515	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	78.9053	333	1515	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_014647215.1	1028752	1028752	type	True	78.8966	292	1515	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	78.8961	291	1515	95	below_threshold
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	78.895	325	1515	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	78.8717	331	1515	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	78.8345	320	1515	95	below_threshold
Shewanella algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	78.7945	320	1515	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	78.789	332	1515	95	below_threshold
Shewanella glacialipiscicola	strain=T147	GCA_019655235.1	614069	614069	type	True	78.7425	237	1515	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	78.6926	278	1515	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	78.625	262	1515	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	78.5187	247	1515	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	78.502	257	1515	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	78.4747	299	1515	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	78.392	276	1515	95	below_threshold
Shewanella xiamenensis	strain=JCM 16212	GCA_014647135.1	332186	332186	type	True	78.1504	289	1515	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	78.0505	181	1515	95	below_threshold
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	77.787	211	1515	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	77.7591	211	1515	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	77.3575	161	1515	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:01,151] [INFO] DFAST Taxonomy check result was written to GCF_000013765.1_ASM1376v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:01,151] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:01,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:01,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg623ffad9-c02c-4ffc-9d7f-0fe31794dfac/dqc_reference/checkm_data
[2024-01-24 13:29:01,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:01,198] [INFO] Task started: CheckM
[2024-01-24 13:29:01,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000013765.1_ASM1376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000013765.1_ASM1376v1_genomic.fna/checkm_input GCF_000013765.1_ASM1376v1_genomic.fna/checkm_result
[2024-01-24 13:29:41,265] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:41,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:41,284] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:41,284] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:41,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000013765.1_ASM1376v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:41,285] [INFO] Task started: Blastn
[2024-01-24 13:29:41,285] [INFO] Running command: blastn -query GCF_000013765.1_ASM1376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623ffad9-c02c-4ffc-9d7f-0fe31794dfac/dqc_reference/reference_markers_gtdb.fasta -out GCF_000013765.1_ASM1376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:42,493] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:42,497] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:42,497] [INFO] Target genome list was writen to GCF_000013765.1_ASM1376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:42,520] [INFO] Task started: fastANI
[2024-01-24 13:29:42,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg0944d2d6-10af-4054-b801-56920321c8f9/GCF_000013765.1_ASM1376v1_genomic.fna.gz --refList GCF_000013765.1_ASM1376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000013765.1_ASM1376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:57,760] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:57,782] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:57,782] [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_000013765.1	s__Shewanella denitrificans	100.0	1513	1515	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_014163735.1	s__Shewanella sp014163735	86.1917	994	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002966515.1	s__Shewanella sp002966515	79.531	311	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCF_003797125.1	s__Shewanella frigidimarina	79.2936	306	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_014648315.1	s__Shewanella ulleungensis	78.9436	301	1515	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	78.936	335	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014641855.1	s__Shewanella inventionis	78.9218	323	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647215.1	s__Shewanella aestuarii	78.9042	293	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014665.1	s__Shewanella sp000014665	78.8959	294	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
GCF_007567505.1	s__Shewanella donghaensis	78.8784	251	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648295.1	s__Shewanella saliphila	78.8734	335	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_002216875.1	s__Shewanella bicestrii	78.8725	288	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.51	96.32	0.89	0.87	4	-
GCF_014648035.1	s__Shewanella algicola	78.8201	318	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_003957745.1	s__Shewanella khirikhana	78.769	179	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203935.1	s__Shewanella sp000203935	78.7533	287	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_900156405.1	s__Shewanella morhuae	78.5015	255	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_000217915.1	s__Shewanella sp000217915	78.3612	267	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019209865.1	s__Shewanella sp019209865	77.9564	168	1515	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 13:29:57,784] [INFO] GTDB search result was written to GCF_000013765.1_ASM1376v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:57,784] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:57,789] [INFO] DFAST_QC result json was written to GCF_000013765.1_ASM1376v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:57,789] [INFO] DFAST_QC completed!
[2024-01-24 13:29:57,789] [INFO] Total running time: 0h1m30s