[2024-01-24 13:40:42,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:42,283] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:42,283] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f178f13-2ddf-47f3-8338-77b250dd922f/dqc_reference
[2024-01-24 13:40:43,781] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:43,783] [INFO] Task started: Prodigal
[2024-01-24 13:40:43,783] [INFO] Running command: gunzip -c /var/lib/cwl/stg1924774e-d09a-4d39-adb1-0524b208d1b0/GCF_014199985.1_ASM1419998v1_genomic.fna.gz | prodigal -d GCF_014199985.1_ASM1419998v1_genomic.fna/cds.fna -a GCF_014199985.1_ASM1419998v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:59,876] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:59,877] [INFO] Task started: HMMsearch
[2024-01-24 13:40:59,877] [INFO] Running command: hmmsearch --tblout GCF_014199985.1_ASM1419998v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f178f13-2ddf-47f3-8338-77b250dd922f/dqc_reference/reference_markers.hmm GCF_014199985.1_ASM1419998v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:00,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:00,209] [INFO] Found 6/6 markers.
[2024-01-24 13:41:00,326] [INFO] Query marker FASTA was written to GCF_014199985.1_ASM1419998v1_genomic.fna/markers.fasta
[2024-01-24 13:41:00,327] [INFO] Task started: Blastn
[2024-01-24 13:41:00,327] [INFO] Running command: blastn -query GCF_014199985.1_ASM1419998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f178f13-2ddf-47f3-8338-77b250dd922f/dqc_reference/reference_markers.fasta -out GCF_014199985.1_ASM1419998v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:01,390] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:01,393] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:01,393] [INFO] Target genome list was writen to GCF_014199985.1_ASM1419998v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:01,398] [INFO] Task started: fastANI
[2024-01-24 13:41:01,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg1924774e-d09a-4d39-adb1-0524b208d1b0/GCF_014199985.1_ASM1419998v1_genomic.fna.gz --refList GCF_014199985.1_ASM1419998v1_genomic.fna/target_genomes.txt --output GCF_014199985.1_ASM1419998v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:20,286] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:20,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f178f13-2ddf-47f3-8338-77b250dd922f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:20,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f178f13-2ddf-47f3-8338-77b250dd922f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:20,310] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:20,311] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:20,311] [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
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	100.0	1931	1933	95	conclusive
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	90.9281	1143	1933	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	90.2913	1503	1933	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	88.9552	1479	1933	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	87.6783	1221	1933	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	85.3734	1236	1933	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	85.2816	1194	1933	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	84.7196	1209	1933	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	84.0146	1106	1933	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	81.3622	766	1933	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	76.2526	234	1933	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	76.2142	257	1933	95	below_threshold
Roseomonas vastitatis	strain=CPCC 101021	GCA_003604215.1	2307076	2307076	type	True	75.9691	268	1933	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	75.8537	297	1933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:20,313] [INFO] DFAST Taxonomy check result was written to GCF_014199985.1_ASM1419998v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:20,313] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:20,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:20,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f178f13-2ddf-47f3-8338-77b250dd922f/dqc_reference/checkm_data
[2024-01-24 13:41:20,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:20,382] [INFO] Task started: CheckM
[2024-01-24 13:41:20,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199985.1_ASM1419998v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199985.1_ASM1419998v1_genomic.fna/checkm_input GCF_014199985.1_ASM1419998v1_genomic.fna/checkm_result
[2024-01-24 13:42:11,333] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:11,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:11,355] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:11,355] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:11,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199985.1_ASM1419998v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:11,356] [INFO] Task started: Blastn
[2024-01-24 13:42:11,356] [INFO] Running command: blastn -query GCF_014199985.1_ASM1419998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f178f13-2ddf-47f3-8338-77b250dd922f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199985.1_ASM1419998v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:13,228] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:13,231] [INFO] Selected 13 target genomes.
[2024-01-24 13:42:13,231] [INFO] Target genome list was writen to GCF_014199985.1_ASM1419998v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:13,245] [INFO] Task started: fastANI
[2024-01-24 13:42:13,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg1924774e-d09a-4d39-adb1-0524b208d1b0/GCF_014199985.1_ASM1419998v1_genomic.fna.gz --refList GCF_014199985.1_ASM1419998v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199985.1_ASM1419998v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:29,467] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:29,489] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:29,490] [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_014199985.1	s__Methylobacterium rhodesianum	100.0	1931	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.84	98.11	0.88	0.84	5	conclusive
GCF_002355515.1	s__Methylobacterium populi_A	92.9745	1601	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111705.1	s__Methylobacterium sp003111705	89.9554	1478	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.28	97.28	0.88	0.88	3	-
GCA_014138645.1	s__Methylobacterium thiocyanatum	89.8576	1469	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.87	97.76	0.88	0.86	7	-
GCF_014191355.1	s__Methylobacterium sp014191355	89.7301	1440	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542815.1	s__Methylobacterium sp001542815	88.9757	1404	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.78	0.92	0.92	2	-
GCF_900234795.1	s__Methylobacterium extorquens	88.9634	1477	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.03	96.19	0.88	0.73	17	-
GCF_001423405.1	s__Methylobacterium sp001423405	88.8988	1405	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201865.1	s__Methylobacterium sp003201865	87.5397	1321	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000202835.1	s__Acidiphilium multivorum	76.2146	257	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	98.69	98.42	0.90	0.87	6	-
GCF_003604215.1	s__Roseomonas vastitatis	75.9676	270	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887635.2	s__Paroceanicella profunda	75.8472	298	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001856665.1	s__LPB0142 sp001856665	75.758	225	1933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142	95.0	98.52	98.52	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:29,492] [INFO] GTDB search result was written to GCF_014199985.1_ASM1419998v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:29,492] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:29,495] [INFO] DFAST_QC result json was written to GCF_014199985.1_ASM1419998v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:29,496] [INFO] DFAST_QC completed!
[2024-01-24 13:42:29,496] [INFO] Total running time: 0h1m47s