[2024-01-24 12:15:18,540] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg69d6a897-e3ae-4c0b-a6c8-6c5dc091af2a/dqc_reference
[2024-01-24 12:15:19,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:19,919] [INFO] Task started: Prodigal
[2024-01-24 12:15:19,919] [INFO] Running command: gunzip -c /var/lib/cwl/stg566f5d68-fd74-44a1-a879-53a8013d897f/GCF_019457615.1_ASM1945761v1_genomic.fna.gz | prodigal -d GCF_019457615.1_ASM1945761v1_genomic.fna/cds.fna -a GCF_019457615.1_ASM1945761v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:34,531] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:34,531] [INFO] Task started: HMMsearch
[2024-01-24 12:15:34,531] [INFO] Running command: hmmsearch --tblout GCF_019457615.1_ASM1945761v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69d6a897-e3ae-4c0b-a6c8-6c5dc091af2a/dqc_reference/reference_markers.hmm GCF_019457615.1_ASM1945761v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:34,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:34,789] [INFO] Found 6/6 markers.
[2024-01-24 12:15:34,828] [INFO] Query marker FASTA was written to GCF_019457615.1_ASM1945761v1_genomic.fna/markers.fasta
[2024-01-24 12:15:34,828] [INFO] Task started: Blastn
[2024-01-24 12:15:34,828] [INFO] Running command: blastn -query GCF_019457615.1_ASM1945761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69d6a897-e3ae-4c0b-a6c8-6c5dc091af2a/dqc_reference/reference_markers.fasta -out GCF_019457615.1_ASM1945761v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:35,710] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:35,713] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:35,713] [INFO] Target genome list was writen to GCF_019457615.1_ASM1945761v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:35,716] [INFO] Task started: fastANI
[2024-01-24 12:15:35,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg566f5d68-fd74-44a1-a879-53a8013d897f/GCF_019457615.1_ASM1945761v1_genomic.fna.gz --refList GCF_019457615.1_ASM1945761v1_genomic.fna/target_genomes.txt --output GCF_019457615.1_ASM1945761v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:43,696] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:43,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69d6a897-e3ae-4c0b-a6c8-6c5dc091af2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:43,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69d6a897-e3ae-4c0b-a6c8-6c5dc091af2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:43,703] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:43,704] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:43,704] [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 amazonensis	strain=SB2B	GCA_000015245.1	60478	60478	type	True	92.06	1351	1504	95	below_threshold
Shewanella litorisediminis	strain=SMK1-12	GCA_016834455.1	1173586	1173586	type	True	90.4968	1289	1504	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	90.3566	1269	1504	95	below_threshold
Shewanella khirikhana	strain=TH2012	GCA_003957745.1	1965282	1965282	type	True	84.9304	1083	1504	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	82.4768	929	1504	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	78.7965	406	1504	95	below_threshold
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	78.3291	345	1504	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	76.7854	57	1504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:43,714] [INFO] DFAST Taxonomy check result was written to GCF_019457615.1_ASM1945761v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:43,714] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:43,714] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:43,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69d6a897-e3ae-4c0b-a6c8-6c5dc091af2a/dqc_reference/checkm_data
[2024-01-24 12:15:43,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:43,758] [INFO] Task started: CheckM
[2024-01-24 12:15:43,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019457615.1_ASM1945761v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019457615.1_ASM1945761v1_genomic.fna/checkm_input GCF_019457615.1_ASM1945761v1_genomic.fna/checkm_result
[2024-01-24 12:16:25,480] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:25,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:25,524] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:25,524] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:25,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019457615.1_ASM1945761v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:25,525] [INFO] Task started: Blastn
[2024-01-24 12:16:25,525] [INFO] Running command: blastn -query GCF_019457615.1_ASM1945761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69d6a897-e3ae-4c0b-a6c8-6c5dc091af2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_019457615.1_ASM1945761v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:26,796] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:26,799] [INFO] Selected 7 target genomes.
[2024-01-24 12:16:26,799] [INFO] Target genome list was writen to GCF_019457615.1_ASM1945761v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:26,802] [INFO] Task started: fastANI
[2024-01-24 12:16:26,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg566f5d68-fd74-44a1-a879-53a8013d897f/GCF_019457615.1_ASM1945761v1_genomic.fna.gz --refList GCF_019457615.1_ASM1945761v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019457615.1_ASM1945761v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:34,342] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:34,349] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:16:34,349] [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_000015245.1	s__Shewanella amazonensis	92.0486	1352	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016834455.1	s__Shewanella litorisediminis	90.4812	1287	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957745.1	s__Shewanella khirikhana	84.9192	1084	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018596335.1	s__Shewanella sp018596335	82.4865	927	1504	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	80.2725	604	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_009183365.2	s__Shewanella algae	79.247	430	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
GCF_003353085.1	s__Shewanella corallii	78.7715	313	1504	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 12:16:34,351] [INFO] GTDB search result was written to GCF_019457615.1_ASM1945761v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:34,351] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:34,354] [INFO] DFAST_QC result json was written to GCF_019457615.1_ASM1945761v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:34,354] [INFO] DFAST_QC completed!
[2024-01-24 12:16:34,354] [INFO] Total running time: 0h1m16s