[2024-01-24 10:47:23,556] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:23,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:23,559] [INFO] DQC Reference Directory: /var/lib/cwl/stgacacfb90-e1cc-4f3b-bd6f-b4d0e376e7b6/dqc_reference
[2024-01-24 10:47:26,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,183] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,183] [INFO] Running command: gunzip -c /var/lib/cwl/stg659b17e1-8316-4cb1-9332-e5ca38b872d8/GCF_030409715.1_ASM3040971v1_genomic.fna.gz | prodigal -d GCF_030409715.1_ASM3040971v1_genomic.fna/cds.fna -a GCF_030409715.1_ASM3040971v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:35,793] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:35,793] [INFO] Task started: HMMsearch
[2024-01-24 10:47:35,794] [INFO] Running command: hmmsearch --tblout GCF_030409715.1_ASM3040971v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacacfb90-e1cc-4f3b-bd6f-b4d0e376e7b6/dqc_reference/reference_markers.hmm GCF_030409715.1_ASM3040971v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:36,066] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:36,067] [INFO] Found 6/6 markers.
[2024-01-24 10:47:36,105] [INFO] Query marker FASTA was written to GCF_030409715.1_ASM3040971v1_genomic.fna/markers.fasta
[2024-01-24 10:47:36,106] [INFO] Task started: Blastn
[2024-01-24 10:47:36,106] [INFO] Running command: blastn -query GCF_030409715.1_ASM3040971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacacfb90-e1cc-4f3b-bd6f-b4d0e376e7b6/dqc_reference/reference_markers.fasta -out GCF_030409715.1_ASM3040971v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:36,798] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:36,803] [INFO] Selected 31 target genomes.
[2024-01-24 10:47:36,803] [INFO] Target genome list was writen to GCF_030409715.1_ASM3040971v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:36,848] [INFO] Task started: fastANI
[2024-01-24 10:47:36,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg659b17e1-8316-4cb1-9332-e5ca38b872d8/GCF_030409715.1_ASM3040971v1_genomic.fna.gz --refList GCF_030409715.1_ASM3040971v1_genomic.fna/target_genomes.txt --output GCF_030409715.1_ASM3040971v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:55,820] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:55,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacacfb90-e1cc-4f3b-bd6f-b4d0e376e7b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:55,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacacfb90-e1cc-4f3b-bd6f-b4d0e376e7b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:55,827] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:55,827] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:55,827] [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
Reinekea forsetii	strain=Hel1_31_D35	GCA_002795845.1	1336806	1336806	type	True	79.4819	71	1248	95	below_threshold
Reinekea blandensis	strain=MED297	GCA_000153185.1	374838	374838	type	True	78.8456	86	1248	95	below_threshold
Reinekea thalattae	strain=SSH23	GCA_008041945.1	2593301	2593301	type	True	77.9213	94	1248	95	below_threshold
Reinekea marinisedimentorum	strain=DSM 15388	GCA_004341165.1	230495	230495	type	True	77.8016	92	1248	95	below_threshold
Saccharospirillum alexandrii	strain=LZ-5	GCA_004000275.1	2448477	2448477	type	True	76.4439	50	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:55,829] [INFO] DFAST Taxonomy check result was written to GCF_030409715.1_ASM3040971v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:55,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:55,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:55,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacacfb90-e1cc-4f3b-bd6f-b4d0e376e7b6/dqc_reference/checkm_data
[2024-01-24 10:47:55,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:55,875] [INFO] Task started: CheckM
[2024-01-24 10:47:55,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409715.1_ASM3040971v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409715.1_ASM3040971v1_genomic.fna/checkm_input GCF_030409715.1_ASM3040971v1_genomic.fna/checkm_result
[2024-01-24 10:48:30,720] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:30,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:30,747] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:30,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:30,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409715.1_ASM3040971v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:30,748] [INFO] Task started: Blastn
[2024-01-24 10:48:30,749] [INFO] Running command: blastn -query GCF_030409715.1_ASM3040971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacacfb90-e1cc-4f3b-bd6f-b4d0e376e7b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409715.1_ASM3040971v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:31,858] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:31,863] [INFO] Selected 25 target genomes.
[2024-01-24 10:48:31,863] [INFO] Target genome list was writen to GCF_030409715.1_ASM3040971v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:31,927] [INFO] Task started: fastANI
[2024-01-24 10:48:31,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg659b17e1-8316-4cb1-9332-e5ca38b872d8/GCF_030409715.1_ASM3040971v1_genomic.fna.gz --refList GCF_030409715.1_ASM3040971v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409715.1_ASM3040971v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:48,229] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:48,239] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:48,240] [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_018860385.1	s__Reinekea forsetii_A	96.1608	1037	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000153185.1	s__Reinekea blandensis	78.6566	85	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008041945.1	s__Reinekea thalattae	77.9213	94	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341165.1	s__Reinekea marinisedimentorum	77.8016	92	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015687175.1	s__Reinekea sp015687175	77.6508	118	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:48,243] [INFO] GTDB search result was written to GCF_030409715.1_ASM3040971v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:48,243] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:48,247] [INFO] DFAST_QC result json was written to GCF_030409715.1_ASM3040971v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:48,247] [INFO] DFAST_QC completed!
[2024-01-24 10:48:48,247] [INFO] Total running time: 0h1m25s