[2024-01-24 14:19:15,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,180] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,181] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3789b7d-e502-4002-908b-ed3c955800b0/dqc_reference
[2024-01-24 14:19:16,412] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:16,413] [INFO] Task started: Prodigal
[2024-01-24 14:19:16,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg40f3b520-c243-4f24-b9e9-87d77f62c22a/GCF_009811675.1_ASM981167v1_genomic.fna.gz | prodigal -d GCF_009811675.1_ASM981167v1_genomic.fna/cds.fna -a GCF_009811675.1_ASM981167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:28,074] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:28,075] [INFO] Task started: HMMsearch
[2024-01-24 14:19:28,075] [INFO] Running command: hmmsearch --tblout GCF_009811675.1_ASM981167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3789b7d-e502-4002-908b-ed3c955800b0/dqc_reference/reference_markers.hmm GCF_009811675.1_ASM981167v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:28,386] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:28,388] [INFO] Found 6/6 markers.
[2024-01-24 14:19:28,432] [INFO] Query marker FASTA was written to GCF_009811675.1_ASM981167v1_genomic.fna/markers.fasta
[2024-01-24 14:19:28,432] [INFO] Task started: Blastn
[2024-01-24 14:19:28,432] [INFO] Running command: blastn -query GCF_009811675.1_ASM981167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3789b7d-e502-4002-908b-ed3c955800b0/dqc_reference/reference_markers.fasta -out GCF_009811675.1_ASM981167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:29,441] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:29,444] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:29,445] [INFO] Target genome list was writen to GCF_009811675.1_ASM981167v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:29,451] [INFO] Task started: fastANI
[2024-01-24 14:19:29,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg40f3b520-c243-4f24-b9e9-87d77f62c22a/GCF_009811675.1_ASM981167v1_genomic.fna.gz --refList GCF_009811675.1_ASM981167v1_genomic.fna/target_genomes.txt --output GCF_009811675.1_ASM981167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:45,383] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:45,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3789b7d-e502-4002-908b-ed3c955800b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:45,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3789b7d-e502-4002-908b-ed3c955800b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:45,396] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:45,396] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:45,396] [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
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	100.0	1435	1438	95	conclusive
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	99.9707	1223	1438	95	conclusive
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	83.7316	911	1438	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	83.6735	919	1438	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	79.3408	568	1438	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	79.0917	470	1438	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	79.0334	451	1438	95	below_threshold
Methylocystis heyeri	strain=H2	GCA_004802635.2	391905	391905	type	True	78.8481	493	1438	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	77.6753	363	1438	95	below_threshold
Methylocella silvestris	strain=BL2	GCA_000021745.1	199596	199596	type	True	77.4926	343	1438	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	76.7754	256	1438	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.692	319	1438	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.3626	317	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:45,404] [INFO] DFAST Taxonomy check result was written to GCF_009811675.1_ASM981167v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:45,407] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:45,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:45,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3789b7d-e502-4002-908b-ed3c955800b0/dqc_reference/checkm_data
[2024-01-24 14:19:45,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:45,516] [INFO] Task started: CheckM
[2024-01-24 14:19:45,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009811675.1_ASM981167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009811675.1_ASM981167v1_genomic.fna/checkm_input GCF_009811675.1_ASM981167v1_genomic.fna/checkm_result
[2024-01-24 14:20:29,956] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:29,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:29,979] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:29,979] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:29,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009811675.1_ASM981167v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:29,980] [INFO] Task started: Blastn
[2024-01-24 14:20:29,980] [INFO] Running command: blastn -query GCF_009811675.1_ASM981167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3789b7d-e502-4002-908b-ed3c955800b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_009811675.1_ASM981167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:31,931] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:31,933] [INFO] Selected 7 target genomes.
[2024-01-24 14:20:31,933] [INFO] Target genome list was writen to GCF_009811675.1_ASM981167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:31,940] [INFO] Task started: fastANI
[2024-01-24 14:20:31,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg40f3b520-c243-4f24-b9e9-87d77f62c22a/GCF_009811675.1_ASM981167v1_genomic.fna.gz --refList GCF_009811675.1_ASM981167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009811675.1_ASM981167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:40,552] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:40,563] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:40,564] [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_003113265.1	s__Methylosinus sporium	99.9707	1223	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	98.07	97.36	0.91	0.86	5	conclusive
GCF_000685825.1	s__Methylosinus sp000685825	91.2434	1116	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.04	98.49	0.94	0.91	4	-
GCF_009936375.1	s__Methylosinus sp009936375	91.2136	1130	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745215.1	s__Methylosinus sp000745215	90.9113	1086	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379125.1	s__Methylosinus sp000379125	90.7268	1085	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015709455.1	s__Methylosinus sp015709455	89.4144	1151	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811655.1	s__Methylosinus sp009811655	88.0608	971	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:40,566] [INFO] GTDB search result was written to GCF_009811675.1_ASM981167v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:40,566] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:40,570] [INFO] DFAST_QC result json was written to GCF_009811675.1_ASM981167v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:40,571] [INFO] DFAST_QC completed!
[2024-01-24 14:20:40,571] [INFO] Total running time: 0h1m25s