[2024-01-24 12:06:33,257] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,259] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg01898cad-f6de-4c9d-96f3-5070d72e6c05/dqc_reference
[2024-01-24 12:06:34,552] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,553] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,553] [INFO] Running command: gunzip -c /var/lib/cwl/stgf69f6b09-d736-466f-b1db-e9bfac0b2ff1/GCF_012641745.1_ASM1264174v1_genomic.fna.gz | prodigal -d GCF_012641745.1_ASM1264174v1_genomic.fna/cds.fna -a GCF_012641745.1_ASM1264174v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:45,994] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:45,995] [INFO] Task started: HMMsearch
[2024-01-24 12:06:45,995] [INFO] Running command: hmmsearch --tblout GCF_012641745.1_ASM1264174v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01898cad-f6de-4c9d-96f3-5070d72e6c05/dqc_reference/reference_markers.hmm GCF_012641745.1_ASM1264174v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:46,327] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:46,328] [INFO] Found 6/6 markers.
[2024-01-24 12:06:46,372] [INFO] Query marker FASTA was written to GCF_012641745.1_ASM1264174v1_genomic.fna/markers.fasta
[2024-01-24 12:06:46,372] [INFO] Task started: Blastn
[2024-01-24 12:06:46,372] [INFO] Running command: blastn -query GCF_012641745.1_ASM1264174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01898cad-f6de-4c9d-96f3-5070d72e6c05/dqc_reference/reference_markers.fasta -out GCF_012641745.1_ASM1264174v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:47,120] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:47,124] [INFO] Selected 12 target genomes.
[2024-01-24 12:06:47,125] [INFO] Target genome list was writen to GCF_012641745.1_ASM1264174v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:47,131] [INFO] Task started: fastANI
[2024-01-24 12:06:47,131] [INFO] Running command: fastANI --query /var/lib/cwl/stgf69f6b09-d736-466f-b1db-e9bfac0b2ff1/GCF_012641745.1_ASM1264174v1_genomic.fna.gz --refList GCF_012641745.1_ASM1264174v1_genomic.fna/target_genomes.txt --output GCF_012641745.1_ASM1264174v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:59,774] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:59,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01898cad-f6de-4c9d-96f3-5070d72e6c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:59,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01898cad-f6de-4c9d-96f3-5070d72e6c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:59,793] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:06:59,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:59,793] [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
Pseudoalteromonas peptidolytica	strain=DSM 14001	GCA_012641745.1	61150	61150	type	True	100.0	1654	1657	95	conclusive
Pseudoalteromonas peptidolytica	strain=F12-50-A1	GCA_014858745.1	61150	61150	type	True	99.9926	1653	1657	95	conclusive
Pseudoalteromonas peptidolytica	strain=NBRC 101021	GCA_007989895.1	61150	61150	type	True	99.9013	1491	1657	95	conclusive
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	84.0697	966	1657	95	below_threshold
Pseudoalteromonas piscicida	strain=JCM 20779	GCA_000238315.4	43662	43662	type	True	83.6556	973	1657	95	below_threshold
Pseudoalteromonas piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	83.6488	965	1657	95	below_threshold
Pseudoalteromonas flavipulchra	strain=LMG 20361	GCA_014596995.1	137779	137779	suspected-type	True	83.5699	984	1657	95	below_threshold
Pseudoalteromonas flavipulchra	strain=NCIMB 2033	GCA_014858715.1	137779	137779	suspected-type	True	83.5215	1001	1657	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	77.2785	53	1657	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	76.5027	54	1657	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:59,795] [INFO] DFAST Taxonomy check result was written to GCF_012641745.1_ASM1264174v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:59,796] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:59,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:59,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01898cad-f6de-4c9d-96f3-5070d72e6c05/dqc_reference/checkm_data
[2024-01-24 12:06:59,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:59,846] [INFO] Task started: CheckM
[2024-01-24 12:06:59,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012641745.1_ASM1264174v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012641745.1_ASM1264174v1_genomic.fna/checkm_input GCF_012641745.1_ASM1264174v1_genomic.fna/checkm_result
[2024-01-24 12:07:37,346] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:37,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:37,369] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:37,370] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:37,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012641745.1_ASM1264174v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:37,371] [INFO] Task started: Blastn
[2024-01-24 12:07:37,371] [INFO] Running command: blastn -query GCF_012641745.1_ASM1264174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01898cad-f6de-4c9d-96f3-5070d72e6c05/dqc_reference/reference_markers_gtdb.fasta -out GCF_012641745.1_ASM1264174v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:38,469] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:38,473] [INFO] Selected 9 target genomes.
[2024-01-24 12:07:38,474] [INFO] Target genome list was writen to GCF_012641745.1_ASM1264174v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:38,481] [INFO] Task started: fastANI
[2024-01-24 12:07:38,481] [INFO] Running command: fastANI --query /var/lib/cwl/stgf69f6b09-d736-466f-b1db-e9bfac0b2ff1/GCF_012641745.1_ASM1264174v1_genomic.fna.gz --refList GCF_012641745.1_ASM1264174v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012641745.1_ASM1264174v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:51,190] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:51,203] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:51,203] [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_012641745.1	s__Pseudoalteromonas peptidolytica	100.0	1654	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.11	98.10	0.96	0.91	6	conclusive
GCF_005886535.1	s__Pseudoalteromonas sp005886535	83.9156	919	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002208135.1	s__Pseudoalteromonas piscicida_A	83.8139	982	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.45	98.90	0.97	0.95	3	-
GCF_002289345.1	s__Pseudoalteromonas sp002289345	83.7926	918	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.3013	N/A	N/A	N/A	N/A	1	-
GCF_000238315.3	s__Pseudoalteromonas piscicida	83.7262	966	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0982	97.60	97.35	0.90	0.88	13	-
GCF_002850255.1	s__Pseudoalteromonas sp002850255	83.6458	959	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.4968	98.33	98.31	0.92	0.91	5	-
GCA_000814665.1	s__Pseudoalteromonas elyakovii	83.6118	986	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0982	98.47	97.40	0.94	0.89	9	-
GCF_016695175.1	s__Pseudoalteromonas sp002591815	83.6085	974	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6666	100.00	100.00	1.00	1.00	2	-
GCF_002744175.1	s__Pseudoalteromonas piscicida_B	82.8292	938	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:51,204] [INFO] GTDB search result was written to GCF_012641745.1_ASM1264174v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:51,205] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:51,208] [INFO] DFAST_QC result json was written to GCF_012641745.1_ASM1264174v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:51,208] [INFO] DFAST_QC completed!
[2024-01-24 12:07:51,208] [INFO] Total running time: 0h1m18s