[2024-01-24 12:31:50,636] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:50,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:50,639] [INFO] DQC Reference Directory: /var/lib/cwl/stga136d454-b695-4922-a1fc-f90db48250c4/dqc_reference
[2024-01-24 12:31:51,967] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:51,968] [INFO] Task started: Prodigal
[2024-01-24 12:31:51,968] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e3588a4-1ec1-469c-9348-2e5ce6cf5438/GCF_004341165.1_ASM434116v1_genomic.fna.gz | prodigal -d GCF_004341165.1_ASM434116v1_genomic.fna/cds.fna -a GCF_004341165.1_ASM434116v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:02,676] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:02,677] [INFO] Task started: HMMsearch
[2024-01-24 12:32:02,677] [INFO] Running command: hmmsearch --tblout GCF_004341165.1_ASM434116v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga136d454-b695-4922-a1fc-f90db48250c4/dqc_reference/reference_markers.hmm GCF_004341165.1_ASM434116v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:02,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:02,949] [INFO] Found 6/6 markers.
[2024-01-24 12:32:02,990] [INFO] Query marker FASTA was written to GCF_004341165.1_ASM434116v1_genomic.fna/markers.fasta
[2024-01-24 12:32:02,990] [INFO] Task started: Blastn
[2024-01-24 12:32:02,991] [INFO] Running command: blastn -query GCF_004341165.1_ASM434116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga136d454-b695-4922-a1fc-f90db48250c4/dqc_reference/reference_markers.fasta -out GCF_004341165.1_ASM434116v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:03,745] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:03,749] [INFO] Selected 25 target genomes.
[2024-01-24 12:32:03,749] [INFO] Target genome list was writen to GCF_004341165.1_ASM434116v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:03,779] [INFO] Task started: fastANI
[2024-01-24 12:32:03,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e3588a4-1ec1-469c-9348-2e5ce6cf5438/GCF_004341165.1_ASM434116v1_genomic.fna.gz --refList GCF_004341165.1_ASM434116v1_genomic.fna/target_genomes.txt --output GCF_004341165.1_ASM434116v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:20,628] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:20,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga136d454-b695-4922-a1fc-f90db48250c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:20,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga136d454-b695-4922-a1fc-f90db48250c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:20,642] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:20,642] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:20,643] [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 marinisedimentorum	strain=DSM 15388	GCA_004341165.1	230495	230495	type	True	100.0	1376	1378	95	conclusive
Reinekea thalattae	strain=SSH23	GCA_008041945.1	2593301	2593301	type	True	78.2539	193	1378	95	below_threshold
Reinekea blandensis	strain=MED297	GCA_000153185.1	374838	374838	type	True	77.7385	164	1378	95	below_threshold
Saccharospirillum alexandrii	strain=LZ-5	GCA_004000275.1	2448477	2448477	type	True	76.8747	104	1378	95	below_threshold
Saccharospirillum impatiens	strain=DSM 12546	GCA_000423605.1	169438	169438	type	True	76.8031	83	1378	95	below_threshold
Reinekea forsetii	strain=Hel1_31_D35	GCA_002795845.1	1336806	1336806	type	True	76.7925	95	1378	95	below_threshold
Saccharospirillum mangrovi	strain=HK-33	GCA_003367315.1	2161747	2161747	type	True	76.5	121	1378	95	below_threshold
Saccharospirillum mangrovi	strain=HK-33	GCA_003054775.1	2161747	2161747	type	True	76.4004	119	1378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:20,644] [INFO] DFAST Taxonomy check result was written to GCF_004341165.1_ASM434116v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:20,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:20,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:20,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga136d454-b695-4922-a1fc-f90db48250c4/dqc_reference/checkm_data
[2024-01-24 12:32:20,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:20,689] [INFO] Task started: CheckM
[2024-01-24 12:32:20,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004341165.1_ASM434116v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004341165.1_ASM434116v1_genomic.fna/checkm_input GCF_004341165.1_ASM434116v1_genomic.fna/checkm_result
[2024-01-24 12:32:57,052] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:57,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:57,077] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:57,078] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:57,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004341165.1_ASM434116v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:57,079] [INFO] Task started: Blastn
[2024-01-24 12:32:57,079] [INFO] Running command: blastn -query GCF_004341165.1_ASM434116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga136d454-b695-4922-a1fc-f90db48250c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_004341165.1_ASM434116v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:58,246] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:58,249] [INFO] Selected 19 target genomes.
[2024-01-24 12:32:58,249] [INFO] Target genome list was writen to GCF_004341165.1_ASM434116v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:58,263] [INFO] Task started: fastANI
[2024-01-24 12:32:58,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e3588a4-1ec1-469c-9348-2e5ce6cf5438/GCF_004341165.1_ASM434116v1_genomic.fna.gz --refList GCF_004341165.1_ASM434116v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004341165.1_ASM434116v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:11,158] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:11,176] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:11,176] [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_004341165.1	s__Reinekea marinisedimentorum	100.0	1376	1378	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_008041945.1	s__Reinekea thalattae	78.2539	193	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153185.1	s__Reinekea blandensis	77.7473	165	1378	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	77.611	134	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860385.1	s__Reinekea forsetii_A	77.3631	87	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000275.1	s__Saccharospirillum alexandrii	76.8747	104	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423605.1	s__Saccharospirillum impatiens	76.8033	82	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402545.1	s__Saccharospirillum sp018402545	76.8031	96	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795845.1	s__Reinekea forsetii	76.7904	96	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	99.43	98.93	0.96	0.91	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:11,178] [INFO] GTDB search result was written to GCF_004341165.1_ASM434116v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:11,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:11,183] [INFO] DFAST_QC result json was written to GCF_004341165.1_ASM434116v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:11,183] [INFO] DFAST_QC completed!
[2024-01-24 12:33:11,183] [INFO] Total running time: 0h1m21s