[2024-01-24 11:43:42,011] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg30d71206-6aa1-4ac0-8f09-47137de1a1d4/dqc_reference
[2024-01-24 11:43:43,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,379] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,379] [INFO] Running command: gunzip -c /var/lib/cwl/stgcaf13308-f07c-48fc-aa13-bd8e2423f3d5/GCF_025449215.1_ASM2544921v1_genomic.fna.gz | prodigal -d GCF_025449215.1_ASM2544921v1_genomic.fna/cds.fna -a GCF_025449215.1_ASM2544921v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:55,783] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:55,783] [INFO] Task started: HMMsearch
[2024-01-24 11:43:55,783] [INFO] Running command: hmmsearch --tblout GCF_025449215.1_ASM2544921v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30d71206-6aa1-4ac0-8f09-47137de1a1d4/dqc_reference/reference_markers.hmm GCF_025449215.1_ASM2544921v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:56,123] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:56,125] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcaf13308-f07c-48fc-aa13-bd8e2423f3d5/GCF_025449215.1_ASM2544921v1_genomic.fna.gz]
[2024-01-24 11:43:56,175] [INFO] Query marker FASTA was written to GCF_025449215.1_ASM2544921v1_genomic.fna/markers.fasta
[2024-01-24 11:43:56,176] [INFO] Task started: Blastn
[2024-01-24 11:43:56,176] [INFO] Running command: blastn -query GCF_025449215.1_ASM2544921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30d71206-6aa1-4ac0-8f09-47137de1a1d4/dqc_reference/reference_markers.fasta -out GCF_025449215.1_ASM2544921v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:57,077] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:57,080] [INFO] Selected 12 target genomes.
[2024-01-24 11:43:57,080] [INFO] Target genome list was writen to GCF_025449215.1_ASM2544921v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:57,085] [INFO] Task started: fastANI
[2024-01-24 11:43:57,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgcaf13308-f07c-48fc-aa13-bd8e2423f3d5/GCF_025449215.1_ASM2544921v1_genomic.fna.gz --refList GCF_025449215.1_ASM2544921v1_genomic.fna/target_genomes.txt --output GCF_025449215.1_ASM2544921v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:10,958] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:10,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30d71206-6aa1-4ac0-8f09-47137de1a1d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:10,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30d71206-6aa1-4ac0-8f09-47137de1a1d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:10,970] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:10,971] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:10,971] [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 seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	100.0	1582	1583	95	conclusive
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	99.7713	1534	1583	95	conclusive
Shewanella decolorationis	strain=S12	GCA_000485795.1	256839	256839	type	True	92.3083	1337	1583	95	below_threshold
Shewanella xiamenensis	strain=JCM 16212	GCA_014647135.1	332186	332186	type	True	89.1307	1268	1583	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_000146165.2	70863	70863	type	True	86.0735	1257	1583	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_013267215.1	70863	70863	type	True	86.0505	1279	1583	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	81.5401	357	1583	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	81.2016	899	1583	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	81.1309	987	1583	95	below_threshold
Shewanella loihica	strain=PV-4	GCA_000016065.1	359303	359303	type	True	80.0894	362	1583	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	80.0852	774	1583	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	79.4226	351	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:10,974] [INFO] DFAST Taxonomy check result was written to GCF_025449215.1_ASM2544921v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:10,975] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:10,975] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:10,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30d71206-6aa1-4ac0-8f09-47137de1a1d4/dqc_reference/checkm_data
[2024-01-24 11:44:10,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:11,045] [INFO] Task started: CheckM
[2024-01-24 11:44:11,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025449215.1_ASM2544921v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025449215.1_ASM2544921v1_genomic.fna/checkm_input GCF_025449215.1_ASM2544921v1_genomic.fna/checkm_result
[2024-01-24 11:44:51,922] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:51,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:51,945] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:51,946] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:51,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025449215.1_ASM2544921v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:51,947] [INFO] Task started: Blastn
[2024-01-24 11:44:51,947] [INFO] Running command: blastn -query GCF_025449215.1_ASM2544921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30d71206-6aa1-4ac0-8f09-47137de1a1d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_025449215.1_ASM2544921v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:53,077] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:53,081] [INFO] Selected 10 target genomes.
[2024-01-24 11:44:53,081] [INFO] Target genome list was writen to GCF_025449215.1_ASM2544921v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:53,087] [INFO] Task started: fastANI
[2024-01-24 11:44:53,088] [INFO] Running command: fastANI --query /var/lib/cwl/stgcaf13308-f07c-48fc-aa13-bd8e2423f3d5/GCF_025449215.1_ASM2544921v1_genomic.fna.gz --refList GCF_025449215.1_ASM2544921v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025449215.1_ASM2544921v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:04,557] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:04,576] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:45:04,576] [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_002216875.1	s__Shewanella bicestrii	96.32	1463	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.51	96.32	0.89	0.87	4	inconclusive
GCF_000014665.1	s__Shewanella sp000014665	95.104	1418	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	inconclusive
GCF_000203935.1	s__Shewanella sp000203935	94.2376	1449	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_000485795.1	s__Shewanella decolorationis	92.305	1338	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.60	97.51	0.93	0.92	3	-
GCF_014647135.1	s__Shewanella xiamenensis	89.1307	1268	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.56	97.34	0.92	0.88	25	-
GCF_000146165.2	s__Shewanella oneidensis	86.0947	1255	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002215585.1	s__Shewanella marisflavi	82.0255	362	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.20	98.16	0.93	0.93	3	-
GCF_000016065.1	s__Shewanella loihica	80.0758	360	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_000832025.1	s__Shewanella sp000832025	79.6481	336	1583	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	79.437	350	1583	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 11:45:04,578] [INFO] GTDB search result was written to GCF_025449215.1_ASM2544921v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:04,579] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:04,583] [INFO] DFAST_QC result json was written to GCF_025449215.1_ASM2544921v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:04,583] [INFO] DFAST_QC completed!
[2024-01-24 11:45:04,584] [INFO] Total running time: 0h1m23s