[2024-01-24 12:31:57,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:57,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:57,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg2de1aa5e-50ac-4018-ba5b-3eb2be4f8ca6/dqc_reference
[2024-01-24 12:31:58,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:58,778] [INFO] Task started: Prodigal
[2024-01-24 12:31:58,778] [INFO] Running command: gunzip -c /var/lib/cwl/stg72b029b7-6c6e-444f-9a8f-2ef298f603d5/GCF_000422965.1_ASM42296v1_genomic.fna.gz | prodigal -d GCF_000422965.1_ASM42296v1_genomic.fna/cds.fna -a GCF_000422965.1_ASM42296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:14,782] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:14,782] [INFO] Task started: HMMsearch
[2024-01-24 12:32:14,783] [INFO] Running command: hmmsearch --tblout GCF_000422965.1_ASM42296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2de1aa5e-50ac-4018-ba5b-3eb2be4f8ca6/dqc_reference/reference_markers.hmm GCF_000422965.1_ASM42296v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:15,097] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:15,099] [INFO] Found 6/6 markers.
[2024-01-24 12:32:15,141] [INFO] Query marker FASTA was written to GCF_000422965.1_ASM42296v1_genomic.fna/markers.fasta
[2024-01-24 12:32:15,142] [INFO] Task started: Blastn
[2024-01-24 12:32:15,142] [INFO] Running command: blastn -query GCF_000422965.1_ASM42296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2de1aa5e-50ac-4018-ba5b-3eb2be4f8ca6/dqc_reference/reference_markers.fasta -out GCF_000422965.1_ASM42296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:16,154] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:16,159] [INFO] Selected 11 target genomes.
[2024-01-24 12:32:16,159] [INFO] Target genome list was writen to GCF_000422965.1_ASM42296v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:16,164] [INFO] Task started: fastANI
[2024-01-24 12:32:16,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg72b029b7-6c6e-444f-9a8f-2ef298f603d5/GCF_000422965.1_ASM42296v1_genomic.fna.gz --refList GCF_000422965.1_ASM42296v1_genomic.fna/target_genomes.txt --output GCF_000422965.1_ASM42296v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:27,589] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:27,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2de1aa5e-50ac-4018-ba5b-3eb2be4f8ca6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:27,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2de1aa5e-50ac-4018-ba5b-3eb2be4f8ca6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:27,599] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:27,600] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:27,600] [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
Pleomorphomonas oryzae	strain=DSM 16300	GCA_000422965.1	261934	261934	type	True	100.0	1722	1724	95	conclusive
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	86.8277	1237	1724	95	below_threshold
Pleomorphomonas diazotrophica	strain=R5-392	GCA_002844595.1	1166257	1166257	type	True	85.7788	1237	1724	95	below_threshold
Pleomorphomonas diazotrophica	strain=R5-392	GCA_900114935.1	1166257	1166257	type	True	85.7621	1224	1724	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	84.7855	1048	1724	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.2681	412	1724	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.0326	204	1724	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.8551	164	1724	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	76.5592	186	1724	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.4598	194	1724	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	76.423	207	1724	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:27,602] [INFO] DFAST Taxonomy check result was written to GCF_000422965.1_ASM42296v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:27,603] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:27,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:27,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2de1aa5e-50ac-4018-ba5b-3eb2be4f8ca6/dqc_reference/checkm_data
[2024-01-24 12:32:27,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:27,664] [INFO] Task started: CheckM
[2024-01-24 12:32:27,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422965.1_ASM42296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422965.1_ASM42296v1_genomic.fna/checkm_input GCF_000422965.1_ASM42296v1_genomic.fna/checkm_result
[2024-01-24 12:33:14,391] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:14,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:14,418] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:14,418] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:14,419] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422965.1_ASM42296v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:14,419] [INFO] Task started: Blastn
[2024-01-24 12:33:14,419] [INFO] Running command: blastn -query GCF_000422965.1_ASM42296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2de1aa5e-50ac-4018-ba5b-3eb2be4f8ca6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422965.1_ASM42296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:16,355] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:16,359] [INFO] Selected 8 target genomes.
[2024-01-24 12:33:16,360] [INFO] Target genome list was writen to GCF_000422965.1_ASM42296v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:16,366] [INFO] Task started: fastANI
[2024-01-24 12:33:16,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg72b029b7-6c6e-444f-9a8f-2ef298f603d5/GCF_000422965.1_ASM42296v1_genomic.fna.gz --refList GCF_000422965.1_ASM42296v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422965.1_ASM42296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:27,198] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:27,206] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:27,206] [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_000422965.1	s__Pleomorphomonas oryzae	100.0	1722	1724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011759535.1	s__Pleomorphomonas sp011759535	92.3944	1457	1724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018262505.1	s__Pleomorphomonas sp018262505	87.021	1232	1724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002770725.1	s__Pleomorphomonas carboxyditropha	86.8064	1240	1724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	98.10	98.10	0.89	0.89	2	-
GCF_002844595.1	s__Pleomorphomonas diazotrophica	85.766	1239	1724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018262575.1	s__Pleomorphomonas sp018262575	84.8427	1055	1724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425185.1	s__Pleomorphomonas koreensis	84.7469	1052	1724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	95.03	95.03	0.88	0.88	2	-
GCF_004366315.1	s__Pleomorphomonas sp004366315	84.4212	1244	1724	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:27,208] [INFO] GTDB search result was written to GCF_000422965.1_ASM42296v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:27,209] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:27,214] [INFO] DFAST_QC result json was written to GCF_000422965.1_ASM42296v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:27,214] [INFO] DFAST_QC completed!
[2024-01-24 12:33:27,214] [INFO] Total running time: 0h1m30s