[2024-01-25 18:58:20,562] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:20,564] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:20,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg61b7ce2d-528f-4cc7-ba15-59b27c886460/dqc_reference
[2024-01-25 18:58:21,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:21,740] [INFO] Task started: Prodigal
[2024-01-25 18:58:21,740] [INFO] Running command: gunzip -c /var/lib/cwl/stgb383ae6f-26a5-4ef3-b66b-270a5628f8a2/GCF_000385335.1_ASM38533v1_genomic.fna.gz | prodigal -d GCF_000385335.1_ASM38533v1_genomic.fna/cds.fna -a GCF_000385335.1_ASM38533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:33,036] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:33,037] [INFO] Task started: HMMsearch
[2024-01-25 18:58:33,037] [INFO] Running command: hmmsearch --tblout GCF_000385335.1_ASM38533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61b7ce2d-528f-4cc7-ba15-59b27c886460/dqc_reference/reference_markers.hmm GCF_000385335.1_ASM38533v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:33,265] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:33,266] [INFO] Found 6/6 markers.
[2024-01-25 18:58:33,301] [INFO] Query marker FASTA was written to GCF_000385335.1_ASM38533v1_genomic.fna/markers.fasta
[2024-01-25 18:58:33,301] [INFO] Task started: Blastn
[2024-01-25 18:58:33,302] [INFO] Running command: blastn -query GCF_000385335.1_ASM38533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b7ce2d-528f-4cc7-ba15-59b27c886460/dqc_reference/reference_markers.fasta -out GCF_000385335.1_ASM38533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:34,115] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:34,118] [INFO] Selected 18 target genomes.
[2024-01-25 18:58:34,118] [INFO] Target genome list was writen to GCF_000385335.1_ASM38533v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:34,137] [INFO] Task started: fastANI
[2024-01-25 18:58:34,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgb383ae6f-26a5-4ef3-b66b-270a5628f8a2/GCF_000385335.1_ASM38533v1_genomic.fna.gz --refList GCF_000385335.1_ASM38533v1_genomic.fna/target_genomes.txt --output GCF_000385335.1_ASM38533v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:49,047] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:49,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61b7ce2d-528f-4cc7-ba15-59b27c886460/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:49,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61b7ce2d-528f-4cc7-ba15-59b27c886460/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:49,058] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:58:49,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:49,059] [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
Methyloferula stellata	strain=AR4T	GCA_000385335.1	876270	876270	type	True	100.0	1411	1411	95	conclusive
Methylovirgula ligni	strain=BW863	GCA_004135935.1	569860	569860	type	True	78.1172	325	1411	95	below_threshold
Methylovirgula ligni	strain=BW863	GCA_003387225.1	569860	569860	type	True	78.0424	321	1411	95	below_threshold
Methylocapsa acidiphila	strain=B2	GCA_000427445.1	133552	133552	type	True	77.9856	326	1411	95	below_threshold
Methylocella silvestris	strain=BL2	GCA_000021745.1	199596	199596	type	True	77.9475	335	1411	95	below_threshold
Methylocapsa aurea	strain=KYG	GCA_000746085.1	663610	663610	type	True	77.8593	357	1411	95	below_threshold
Beijerinckia indica subsp. indica	strain=ATCC 9039	GCA_000019845.1	31994	533	type	True	77.8107	270	1411	95	below_threshold
Beijerinckia mobilis	strain=UQM 1969	GCA_000745425.1	231434	231434	type	True	77.4506	264	1411	95	below_threshold
Methylocapsa palsarum	strain=NE2	GCA_900114285.1	1612308	1612308	type	True	77.2953	262	1411	95	below_threshold
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	77.2882	216	1411	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	77.2225	201	1411	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	76.9347	219	1411	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	76.6033	136	1411	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	76.5388	170	1411	95	below_threshold
Rhizobium grahamii	strain=CCGE 502	GCA_000298315.2	1120045	1120045	type	True	76.499	87	1411	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	76.4823	133	1411	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	76.3272	123	1411	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.2997	170	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:49,060] [INFO] DFAST Taxonomy check result was written to GCF_000385335.1_ASM38533v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:49,060] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:49,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:49,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61b7ce2d-528f-4cc7-ba15-59b27c886460/dqc_reference/checkm_data
[2024-01-25 18:58:49,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:49,104] [INFO] Task started: CheckM
[2024-01-25 18:58:49,105] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000385335.1_ASM38533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000385335.1_ASM38533v1_genomic.fna/checkm_input GCF_000385335.1_ASM38533v1_genomic.fna/checkm_result
[2024-01-25 18:59:23,693] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:23,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:23,712] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:23,712] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:23,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000385335.1_ASM38533v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:23,713] [INFO] Task started: Blastn
[2024-01-25 18:59:23,713] [INFO] Running command: blastn -query GCF_000385335.1_ASM38533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b7ce2d-528f-4cc7-ba15-59b27c886460/dqc_reference/reference_markers_gtdb.fasta -out GCF_000385335.1_ASM38533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:25,321] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:25,324] [INFO] Selected 19 target genomes.
[2024-01-25 18:59:25,324] [INFO] Target genome list was writen to GCF_000385335.1_ASM38533v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:25,346] [INFO] Task started: fastANI
[2024-01-25 18:59:25,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgb383ae6f-26a5-4ef3-b66b-270a5628f8a2/GCF_000385335.1_ASM38533v1_genomic.fna.gz --refList GCF_000385335.1_ASM38533v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000385335.1_ASM38533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:40,038] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:40,051] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:40,051] [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_000385335.1	s__Methyloferula stellata	100.0	1411	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methyloferula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015655535.1	s__Methyloferula sp015655535	87.9837	857	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methyloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135935.1	s__Methylovirgula ligni	78.1255	325	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylovirgula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000427445.1	s__Methylocella acidiphila	78.0064	324	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901905185.1	s__Methylocella tundrae	77.9737	283	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	97.31	97.31	0.88	0.88	2	-
GCF_000021745.1	s__Methylocella silvestris	77.9444	336	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002891535.1	s__Methylocella silvestris_A	77.8896	295	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746085.1	s__Methylocella aurea	77.8377	360	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019845.1	s__Beijerinckia indica	77.7989	271	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Beijerinckia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015709455.1	s__Methylosinus sp015709455	77.5432	284	1411	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	77.4717	285	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685825.1	s__Methylosinus sp000685825	77.3731	304	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.04	98.49	0.94	0.91	4	-
GCF_000304315.1	s__Methylocystis sp000304315	77.3453	211	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003722355.1	s__Methylocystis hirsuta	77.3012	215	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	95.95	95.95	0.95	0.95	2	-
GCA_016869435.1	s__Methylocystis sp016869435	77.1604	202	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004564215.1	s__Methylocella sp004564215	77.0992	241	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898965.1	s__28-YEA-48 sp001898965	77.0814	235	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009720655.1	s__Rhodoblastus acidophilus_A	77.0217	174	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918155.1	s__28-YEA-48 sp903918155	76.8123	132	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:40,053] [INFO] GTDB search result was written to GCF_000385335.1_ASM38533v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:40,053] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:40,056] [INFO] DFAST_QC result json was written to GCF_000385335.1_ASM38533v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:40,057] [INFO] DFAST_QC completed!
[2024-01-25 18:59:40,057] [INFO] Total running time: 0h1m19s