[2024-01-25 17:50:35,604] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:35,605] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:35,605] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cd8aeec-4bb0-40f3-9430-032a30e0a2dc/dqc_reference
[2024-01-25 17:50:36,779] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:36,780] [INFO] Task started: Prodigal
[2024-01-25 17:50:36,780] [INFO] Running command: gunzip -c /var/lib/cwl/stga2362d03-1ab3-4f0f-bd9d-459916b60d05/GCF_003284585.1_ASM328458v1_genomic.fna.gz | prodigal -d GCF_003284585.1_ASM328458v1_genomic.fna/cds.fna -a GCF_003284585.1_ASM328458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:45,379] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:45,379] [INFO] Task started: HMMsearch
[2024-01-25 17:50:45,379] [INFO] Running command: hmmsearch --tblout GCF_003284585.1_ASM328458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cd8aeec-4bb0-40f3-9430-032a30e0a2dc/dqc_reference/reference_markers.hmm GCF_003284585.1_ASM328458v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:45,612] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:45,613] [INFO] Found 6/6 markers.
[2024-01-25 17:50:45,644] [INFO] Query marker FASTA was written to GCF_003284585.1_ASM328458v1_genomic.fna/markers.fasta
[2024-01-25 17:50:45,645] [INFO] Task started: Blastn
[2024-01-25 17:50:45,645] [INFO] Running command: blastn -query GCF_003284585.1_ASM328458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cd8aeec-4bb0-40f3-9430-032a30e0a2dc/dqc_reference/reference_markers.fasta -out GCF_003284585.1_ASM328458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:46,215] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:46,219] [INFO] Selected 29 target genomes.
[2024-01-25 17:50:46,219] [INFO] Target genome list was writen to GCF_003284585.1_ASM328458v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:46,248] [INFO] Task started: fastANI
[2024-01-25 17:50:46,248] [INFO] Running command: fastANI --query /var/lib/cwl/stga2362d03-1ab3-4f0f-bd9d-459916b60d05/GCF_003284585.1_ASM328458v1_genomic.fna.gz --refList GCF_003284585.1_ASM328458v1_genomic.fna/target_genomes.txt --output GCF_003284585.1_ASM328458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:04,396] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:04,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cd8aeec-4bb0-40f3-9430-032a30e0a2dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:04,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cd8aeec-4bb0-40f3-9430-032a30e0a2dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:04,402] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:51:04,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:04,402] [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
Nitrincola tibetensis	strain=xg18	GCA_003284585.1	2219697	2219697	type	True	100.0	1309	1310	95	conclusive
Nitrincola schmidtii	strain=NCAIM B.02626	GCA_008973715.1	1730894	1730894	type	True	78.6418	157	1310	95	below_threshold
Nitrincola tapanii	strain=MEB193	GCA_008368715.1	1708751	1708751	type	True	78.5638	135	1310	95	below_threshold
Nitrincola iocasae	strain=KXZD1103	GCA_008727795.1	2614693	2614693	type	True	78.4726	162	1310	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	77.9345	157	1310	95	below_threshold
Neptunomonas concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	76.8748	55	1310	95	below_threshold
Neptunomonas concharum	strain=JCM17730	GCA_008630635.1	1031538	1031538	type	True	76.8633	55	1310	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:04,404] [INFO] DFAST Taxonomy check result was written to GCF_003284585.1_ASM328458v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:04,404] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:04,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:04,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cd8aeec-4bb0-40f3-9430-032a30e0a2dc/dqc_reference/checkm_data
[2024-01-25 17:51:04,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:04,453] [INFO] Task started: CheckM
[2024-01-25 17:51:04,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003284585.1_ASM328458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003284585.1_ASM328458v1_genomic.fna/checkm_input GCF_003284585.1_ASM328458v1_genomic.fna/checkm_result
[2024-01-25 17:51:33,625] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:33,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:33,650] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:33,650] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:33,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003284585.1_ASM328458v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:33,651] [INFO] Task started: Blastn
[2024-01-25 17:51:33,651] [INFO] Running command: blastn -query GCF_003284585.1_ASM328458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cd8aeec-4bb0-40f3-9430-032a30e0a2dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_003284585.1_ASM328458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:34,506] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:34,509] [INFO] Selected 22 target genomes.
[2024-01-25 17:51:34,509] [INFO] Target genome list was writen to GCF_003284585.1_ASM328458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:34,529] [INFO] Task started: fastANI
[2024-01-25 17:51:34,529] [INFO] Running command: fastANI --query /var/lib/cwl/stga2362d03-1ab3-4f0f-bd9d-459916b60d05/GCF_003284585.1_ASM328458v1_genomic.fna.gz --refList GCF_003284585.1_ASM328458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003284585.1_ASM328458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:48,278] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:48,285] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:48,285] [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_003284585.1	s__Nitrincola tibetensis	100.0	1309	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009821115.1	s__Nitrincola alkalisediminis	88.7483	1103	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	99.09	99.09	0.91	0.91	2	-
GCF_008973715.1	s__Nitrincola schmidtii	78.694	154	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008368715.1	s__Nitrincola tapanii	78.6361	132	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727795.1	s__Nitrincola sp008727795	78.5043	160	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691225.1	s__Nitrincola lacisaponensis	77.9126	158	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007125745.1	s__Nitrincola sp007125745	77.8828	102	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693685.1	s__Nitrincola sp007693685	77.5942	137	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:48,286] [INFO] GTDB search result was written to GCF_003284585.1_ASM328458v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:48,287] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:48,289] [INFO] DFAST_QC result json was written to GCF_003284585.1_ASM328458v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:48,289] [INFO] DFAST_QC completed!
[2024-01-25 17:51:48,289] [INFO] Total running time: 0h1m13s