[2024-01-24 14:12:47,107] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,109] [INFO] DQC Reference Directory: /var/lib/cwl/stgd78f8b0b-6acc-404b-bb93-2e689c56f31b/dqc_reference
[2024-01-24 14:12:48,324] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,325] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,326] [INFO] Running command: gunzip -c /var/lib/cwl/stg6403c61d-b086-4d33-8ced-7b132e4460f0/GCF_014656355.1_ASM1465635v1_genomic.fna.gz | prodigal -d GCF_014656355.1_ASM1465635v1_genomic.fna/cds.fna -a GCF_014656355.1_ASM1465635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:03,351] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:03,352] [INFO] Task started: HMMsearch
[2024-01-24 14:13:03,352] [INFO] Running command: hmmsearch --tblout GCF_014656355.1_ASM1465635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd78f8b0b-6acc-404b-bb93-2e689c56f31b/dqc_reference/reference_markers.hmm GCF_014656355.1_ASM1465635v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:03,633] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:03,634] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6403c61d-b086-4d33-8ced-7b132e4460f0/GCF_014656355.1_ASM1465635v1_genomic.fna.gz]
[2024-01-24 14:13:03,678] [INFO] Query marker FASTA was written to GCF_014656355.1_ASM1465635v1_genomic.fna/markers.fasta
[2024-01-24 14:13:03,678] [INFO] Task started: Blastn
[2024-01-24 14:13:03,679] [INFO] Running command: blastn -query GCF_014656355.1_ASM1465635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd78f8b0b-6acc-404b-bb93-2e689c56f31b/dqc_reference/reference_markers.fasta -out GCF_014656355.1_ASM1465635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:04,534] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:04,537] [INFO] Selected 19 target genomes.
[2024-01-24 14:13:04,538] [INFO] Target genome list was writen to GCF_014656355.1_ASM1465635v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:04,547] [INFO] Task started: fastANI
[2024-01-24 14:13:04,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg6403c61d-b086-4d33-8ced-7b132e4460f0/GCF_014656355.1_ASM1465635v1_genomic.fna.gz --refList GCF_014656355.1_ASM1465635v1_genomic.fna/target_genomes.txt --output GCF_014656355.1_ASM1465635v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:21,815] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:21,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd78f8b0b-6acc-404b-bb93-2e689c56f31b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:21,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd78f8b0b-6acc-404b-bb93-2e689c56f31b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:21,835] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:21,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:21,836] [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
Camelimonas fluminis	strain=KCTC 42282	GCA_014656355.1	1576911	1576911	type	True	100.0	1637	1643	95	conclusive
Camelimonas lactis	strain=DSM 22958	GCA_004342915.1	659006	659006	type	True	88.9458	1166	1643	95	below_threshold
Chelatococcus reniformis	strain=CGMCC 1.12919	GCA_014640075.1	1494448	1494448	type	True	78.6602	557	1643	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	77.9247	303	1643	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.8951	314	1643	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	77.8164	265	1643	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	77.4748	277	1643	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	77.4641	332	1643	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	77.3493	286	1643	95	below_threshold
Saliniramus fredricksonii	strain=HL-109	GCA_900094735.1	1653334	1653334	type	True	77.2811	193	1643	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	77.2289	270	1643	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	77.1853	293	1643	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	77.1682	336	1643	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	77.1407	295	1643	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	77.0283	294	1643	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	76.9835	286	1643	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	76.9709	245	1643	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	76.9706	304	1643	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	76.8351	306	1643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:21,837] [INFO] DFAST Taxonomy check result was written to GCF_014656355.1_ASM1465635v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:21,838] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:21,838] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:21,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd78f8b0b-6acc-404b-bb93-2e689c56f31b/dqc_reference/checkm_data
[2024-01-24 14:13:21,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:21,889] [INFO] Task started: CheckM
[2024-01-24 14:13:21,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656355.1_ASM1465635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656355.1_ASM1465635v1_genomic.fna/checkm_input GCF_014656355.1_ASM1465635v1_genomic.fna/checkm_result
[2024-01-24 14:14:09,880] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:09,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:09,903] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:09,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:09,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656355.1_ASM1465635v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:09,904] [INFO] Task started: Blastn
[2024-01-24 14:14:09,904] [INFO] Running command: blastn -query GCF_014656355.1_ASM1465635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd78f8b0b-6acc-404b-bb93-2e689c56f31b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656355.1_ASM1465635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:11,567] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:11,570] [INFO] Selected 16 target genomes.
[2024-01-24 14:14:11,570] [INFO] Target genome list was writen to GCF_014656355.1_ASM1465635v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:11,594] [INFO] Task started: fastANI
[2024-01-24 14:14:11,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg6403c61d-b086-4d33-8ced-7b132e4460f0/GCF_014656355.1_ASM1465635v1_genomic.fna.gz --refList GCF_014656355.1_ASM1465635v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656355.1_ASM1465635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:27,129] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:27,147] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:27,147] [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_014656355.1	s__Camelimonas fluminis	100.0	1637	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Camelimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004342915.1	s__Camelimonas lactis	88.9458	1166	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Camelimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640075.1	s__Camelimonas reniformis	78.6679	556	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Camelimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201415.1	s__Chelatococcus_A composti	77.9151	304	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.84	99.53	0.99	0.98	4	-
GCF_009363855.1	s__Microvirga thermotolerans	77.8845	247	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016892765.1	s__Microvirga sp016892765	77.6591	237	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350535.1	s__Microvirga subterranea	77.4639	278	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217615.1	s__Methylobacterium sp003217615	77.4145	283	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014645695.1	s__Salinarimonas ramus	77.2583	267	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199985.1	s__Methylobacterium rhodesianum	77.2379	288	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.84	98.11	0.88	0.84	5	-
GCF_000429045.1	s__Salinarimonas rosea	77.2042	291	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043955.1	s__Methylobacterium tarhaniae	77.1771	334	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003567055.1	s__Salinarimonas sp003567055	77.0355	129	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103445.1	s__Methylobacterium phyllostachyos	76.9948	262	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137085.1	s__Lichenihabitans ramalinae	76.9715	245	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003096615.1	s__Methylobacterium organophilum	76.8783	312	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.99	98.85	0.91	0.88	18	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:27,149] [INFO] GTDB search result was written to GCF_014656355.1_ASM1465635v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:27,149] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:27,154] [INFO] DFAST_QC result json was written to GCF_014656355.1_ASM1465635v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:27,154] [INFO] DFAST_QC completed!
[2024-01-24 14:14:27,154] [INFO] Total running time: 0h1m40s