[2024-01-24 10:47:11,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d34724d-ef23-4963-afc1-d57c68c29696/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,944] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,945] [INFO] Running command: gunzip -c /var/lib/cwl/stgf14a7718-0eb3-4f3a-9b28-289c0e65ce9b/GCF_030160495.1_ASM3016049v1_genomic.fna.gz | prodigal -d GCF_030160495.1_ASM3016049v1_genomic.fna/cds.fna -a GCF_030160495.1_ASM3016049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:30,921] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:30,922] [INFO] Task started: HMMsearch
[2024-01-24 10:47:30,922] [INFO] Running command: hmmsearch --tblout GCF_030160495.1_ASM3016049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d34724d-ef23-4963-afc1-d57c68c29696/dqc_reference/reference_markers.hmm GCF_030160495.1_ASM3016049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:31,236] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:31,237] [INFO] Found 6/6 markers.
[2024-01-24 10:47:31,281] [INFO] Query marker FASTA was written to GCF_030160495.1_ASM3016049v1_genomic.fna/markers.fasta
[2024-01-24 10:47:31,281] [INFO] Task started: Blastn
[2024-01-24 10:47:31,282] [INFO] Running command: blastn -query GCF_030160495.1_ASM3016049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d34724d-ef23-4963-afc1-d57c68c29696/dqc_reference/reference_markers.fasta -out GCF_030160495.1_ASM3016049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:32,186] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:32,190] [INFO] Selected 9 target genomes.
[2024-01-24 10:47:32,190] [INFO] Target genome list was writen to GCF_030160495.1_ASM3016049v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:32,227] [INFO] Task started: fastANI
[2024-01-24 10:47:32,228] [INFO] Running command: fastANI --query /var/lib/cwl/stgf14a7718-0eb3-4f3a-9b28-289c0e65ce9b/GCF_030160495.1_ASM3016049v1_genomic.fna.gz --refList GCF_030160495.1_ASM3016049v1_genomic.fna/target_genomes.txt --output GCF_030160495.1_ASM3016049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:43,817] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:43,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d34724d-ef23-4963-afc1-d57c68c29696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:43,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d34724d-ef23-4963-afc1-d57c68c29696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:43,864] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:43,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:43,864] [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 decolorationis	strain=S12	GCA_000485795.1	256839	256839	type	True	99.9777	1572	1597	95	conclusive
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	92.4805	1352	1597	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	92.2135	1374	1597	95	below_threshold
Shewanella xiamenensis	strain=JCM 16212	GCA_014647135.1	332186	332186	type	True	89.854	1310	1597	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_000146165.2	70863	70863	type	True	86.6701	1273	1597	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_013267215.1	70863	70863	type	True	86.5761	1283	1597	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	81.4676	885	1597	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	81.4058	990	1597	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	80.4129	764	1597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:43,865] [INFO] DFAST Taxonomy check result was written to GCF_030160495.1_ASM3016049v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:43,869] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:43,869] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:43,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d34724d-ef23-4963-afc1-d57c68c29696/dqc_reference/checkm_data
[2024-01-24 10:47:43,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:43,931] [INFO] Task started: CheckM
[2024-01-24 10:47:43,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160495.1_ASM3016049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160495.1_ASM3016049v1_genomic.fna/checkm_input GCF_030160495.1_ASM3016049v1_genomic.fna/checkm_result
[2024-01-24 10:48:21,616] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:21,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:21,638] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:21,639] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:21,639] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160495.1_ASM3016049v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:21,640] [INFO] Task started: Blastn
[2024-01-24 10:48:21,640] [INFO] Running command: blastn -query GCF_030160495.1_ASM3016049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d34724d-ef23-4963-afc1-d57c68c29696/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160495.1_ASM3016049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:22,847] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:22,851] [INFO] Selected 6 target genomes.
[2024-01-24 10:48:22,852] [INFO] Target genome list was writen to GCF_030160495.1_ASM3016049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:22,857] [INFO] Task started: fastANI
[2024-01-24 10:48:22,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgf14a7718-0eb3-4f3a-9b28-289c0e65ce9b/GCF_030160495.1_ASM3016049v1_genomic.fna.gz --refList GCF_030160495.1_ASM3016049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160495.1_ASM3016049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:31,441] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:31,453] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:31,453] [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_000485795.1	s__Shewanella decolorationis	99.9777	1572	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.60	97.51	0.93	0.92	3	conclusive
GCF_000203935.1	s__Shewanella sp000203935	93.1187	1396	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_002216875.1	s__Shewanella bicestrii	92.6107	1357	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.51	96.32	0.89	0.87	4	-
GCF_000014665.1	s__Shewanella sp000014665	91.8319	1334	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
GCF_014647135.1	s__Shewanella xiamenensis	89.8474	1311	1597	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	86.6625	1273	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:31,455] [INFO] GTDB search result was written to GCF_030160495.1_ASM3016049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:31,455] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:31,458] [INFO] DFAST_QC result json was written to GCF_030160495.1_ASM3016049v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:31,458] [INFO] DFAST_QC completed!
[2024-01-24 10:48:31,458] [INFO] Total running time: 0h1m20s