[2024-01-25 18:00:21,048] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:21,056] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:21,056] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e90b44a-d898-4999-a552-23d3310450bb/dqc_reference
[2024-01-25 18:00:22,219] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:22,219] [INFO] Task started: Prodigal
[2024-01-25 18:00:22,219] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ce4511d-ef9d-4dec-9b93-21bf41b17235/GCF_016834455.1_ASM1683445v1_genomic.fna.gz | prodigal -d GCF_016834455.1_ASM1683445v1_genomic.fna/cds.fna -a GCF_016834455.1_ASM1683445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:33,891] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:33,891] [INFO] Task started: HMMsearch
[2024-01-25 18:00:33,891] [INFO] Running command: hmmsearch --tblout GCF_016834455.1_ASM1683445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e90b44a-d898-4999-a552-23d3310450bb/dqc_reference/reference_markers.hmm GCF_016834455.1_ASM1683445v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:34,213] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:34,214] [INFO] Found 6/6 markers.
[2024-01-25 18:00:34,248] [INFO] Query marker FASTA was written to GCF_016834455.1_ASM1683445v1_genomic.fna/markers.fasta
[2024-01-25 18:00:34,249] [INFO] Task started: Blastn
[2024-01-25 18:00:34,249] [INFO] Running command: blastn -query GCF_016834455.1_ASM1683445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e90b44a-d898-4999-a552-23d3310450bb/dqc_reference/reference_markers.fasta -out GCF_016834455.1_ASM1683445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:35,036] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:35,040] [INFO] Selected 8 target genomes.
[2024-01-25 18:00:35,040] [INFO] Target genome list was writen to GCF_016834455.1_ASM1683445v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:35,044] [INFO] Task started: fastANI
[2024-01-25 18:00:35,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ce4511d-ef9d-4dec-9b93-21bf41b17235/GCF_016834455.1_ASM1683445v1_genomic.fna.gz --refList GCF_016834455.1_ASM1683445v1_genomic.fna/target_genomes.txt --output GCF_016834455.1_ASM1683445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:00:42,735] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:42,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e90b44a-d898-4999-a552-23d3310450bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:00:42,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e90b44a-d898-4999-a552-23d3310450bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:00:42,742] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:00:42,742] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:00:42,742] [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 litorisediminis	strain=SMK1-12	GCA_016834455.1	1173586	1173586	type	True	100.0	1410	1412	95	conclusive
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	99.9738	1372	1412	95	conclusive
Shewanella amazonensis	strain=SB2B	GCA_000015245.1	60478	60478	type	True	89.3536	1258	1412	95	below_threshold
Shewanella khirikhana	strain=TH2012	GCA_003957745.1	1965282	1965282	type	True	84.2675	1062	1412	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	82.4991	921	1412	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	78.6068	315	1412	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.3279	64	1412	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.237	62	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:00:42,743] [INFO] DFAST Taxonomy check result was written to GCF_016834455.1_ASM1683445v1_genomic.fna/tc_result.tsv
[2024-01-25 18:00:42,744] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:00:42,744] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:00:42,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e90b44a-d898-4999-a552-23d3310450bb/dqc_reference/checkm_data
[2024-01-25 18:00:42,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:00:42,786] [INFO] Task started: CheckM
[2024-01-25 18:00:42,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016834455.1_ASM1683445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016834455.1_ASM1683445v1_genomic.fna/checkm_input GCF_016834455.1_ASM1683445v1_genomic.fna/checkm_result
[2024-01-25 18:01:19,985] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:19,986] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:20,003] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:20,004] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:20,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016834455.1_ASM1683445v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:20,004] [INFO] Task started: Blastn
[2024-01-25 18:01:20,004] [INFO] Running command: blastn -query GCF_016834455.1_ASM1683445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e90b44a-d898-4999-a552-23d3310450bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_016834455.1_ASM1683445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:21,305] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:21,308] [INFO] Selected 8 target genomes.
[2024-01-25 18:01:21,308] [INFO] Target genome list was writen to GCF_016834455.1_ASM1683445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:21,314] [INFO] Task started: fastANI
[2024-01-25 18:01:21,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ce4511d-ef9d-4dec-9b93-21bf41b17235/GCF_016834455.1_ASM1683445v1_genomic.fna.gz --refList GCF_016834455.1_ASM1683445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016834455.1_ASM1683445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:29,484] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:29,492] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:29,492] [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_016834455.1	s__Shewanella litorisediminis	100.0	1410	1412	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_000015245.1	s__Shewanella amazonensis	89.3536	1258	1412	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	84.2719	1062	1412	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	82.5014	921	1412	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	80.4707	600	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_002777975.1	s__Shewanella carassii	78.7074	399	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003353085.1	s__Shewanella corallii	78.5878	318	1412	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	78.4112	311	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:29,494] [INFO] GTDB search result was written to GCF_016834455.1_ASM1683445v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:29,505] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:29,508] [INFO] DFAST_QC result json was written to GCF_016834455.1_ASM1683445v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:29,508] [INFO] DFAST_QC completed!
[2024-01-25 18:01:29,508] [INFO] Total running time: 0h1m8s