[2024-01-24 13:13:46,273] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:46,275] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:46,276] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d05d273-bcb1-4c91-946e-37e8041d1714/dqc_reference
[2024-01-24 13:13:47,590] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:47,591] [INFO] Task started: Prodigal
[2024-01-24 13:13:47,592] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1050fe1-06d9-4618-937b-ee487232acc9/GCF_030160935.1_ASM3016093v1_genomic.fna.gz | prodigal -d GCF_030160935.1_ASM3016093v1_genomic.fna/cds.fna -a GCF_030160935.1_ASM3016093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:00,621] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:00,621] [INFO] Task started: HMMsearch
[2024-01-24 13:14:00,621] [INFO] Running command: hmmsearch --tblout GCF_030160935.1_ASM3016093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d05d273-bcb1-4c91-946e-37e8041d1714/dqc_reference/reference_markers.hmm GCF_030160935.1_ASM3016093v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:00,920] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:00,922] [INFO] Found 6/6 markers.
[2024-01-24 13:14:00,967] [INFO] Query marker FASTA was written to GCF_030160935.1_ASM3016093v1_genomic.fna/markers.fasta
[2024-01-24 13:14:00,967] [INFO] Task started: Blastn
[2024-01-24 13:14:00,967] [INFO] Running command: blastn -query GCF_030160935.1_ASM3016093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d05d273-bcb1-4c91-946e-37e8041d1714/dqc_reference/reference_markers.fasta -out GCF_030160935.1_ASM3016093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:02,009] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:02,013] [INFO] Selected 12 target genomes.
[2024-01-24 13:14:02,014] [INFO] Target genome list was writen to GCF_030160935.1_ASM3016093v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:02,017] [INFO] Task started: fastANI
[2024-01-24 13:14:02,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1050fe1-06d9-4618-937b-ee487232acc9/GCF_030160935.1_ASM3016093v1_genomic.fna.gz --refList GCF_030160935.1_ASM3016093v1_genomic.fna/target_genomes.txt --output GCF_030160935.1_ASM3016093v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:15,238] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:15,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d05d273-bcb1-4c91-946e-37e8041d1714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:15,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d05d273-bcb1-4c91-946e-37e8041d1714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:15,251] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:14:15,251] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:15,251] [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
Methylobacterium gnaphalii	strain=NBRC 107716	GCA_007992215.1	1010610	1010610	type	True	99.9815	1472	1526	95	conclusive
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	99.9472	1414	1526	95	conclusive
Methylobacterium brachythecii	strain=DSM 24105	GCA_014196345.1	1176177	1176177	type	True	86.8089	1146	1526	95	below_threshold
Methylobacterium haplocladii	strain=NBRC 107714	GCA_007992175.1	1176176	1176176	type	True	83.9801	947	1526	95	below_threshold
Methylobacterium haplocladii	strain=DSM 24195	GCA_022179265.1	1176176	1176176	type	True	83.8879	919	1526	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	81.636	667	1526	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	81.345	824	1526	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	81.2895	851	1526	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	80.8496	720	1526	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	80.5454	649	1526	95	below_threshold
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	80.5246	805	1526	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	80.2852	787	1526	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:15,253] [INFO] DFAST Taxonomy check result was written to GCF_030160935.1_ASM3016093v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:15,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:15,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:15,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d05d273-bcb1-4c91-946e-37e8041d1714/dqc_reference/checkm_data
[2024-01-24 13:14:15,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:15,306] [INFO] Task started: CheckM
[2024-01-24 13:14:15,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160935.1_ASM3016093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160935.1_ASM3016093v1_genomic.fna/checkm_input GCF_030160935.1_ASM3016093v1_genomic.fna/checkm_result
[2024-01-24 13:14:55,688] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:55,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:55,711] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:55,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:55,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160935.1_ASM3016093v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:55,712] [INFO] Task started: Blastn
[2024-01-24 13:14:55,712] [INFO] Running command: blastn -query GCF_030160935.1_ASM3016093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d05d273-bcb1-4c91-946e-37e8041d1714/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160935.1_ASM3016093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:57,892] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:57,895] [INFO] Selected 12 target genomes.
[2024-01-24 13:14:57,895] [INFO] Target genome list was writen to GCF_030160935.1_ASM3016093v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:57,898] [INFO] Task started: fastANI
[2024-01-24 13:14:57,898] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1050fe1-06d9-4618-937b-ee487232acc9/GCF_030160935.1_ASM3016093v1_genomic.fna.gz --refList GCF_030160935.1_ASM3016093v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160935.1_ASM3016093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:11,015] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:11,029] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:11,029] [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_007992215.1	s__Methylobacterium gnaphalii	99.9815	1472	1526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014196345.1	s__Methylobacterium brachythecii	86.802	1147	1526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040035.1	s__Methylobacterium sp008040035	83.9988	932	1526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992175.1	s__Methylobacterium haplocladii	83.9774	947	1526	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	81.3377	822	1526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.78	0.92	0.92	2	-
GCF_003201865.1	s__Methylobacterium sp003201865	81.3249	821	1526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014845115.1	s__Methylobacterium zatmanii	81.2031	753	1526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039875.1	s__Methylobacterium sp008039875	80.9387	779	1526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCA_002778835.1	s__Methylobacterium sp002778835	80.8524	734	1526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.93	99.92	0.96	0.96	4	-
GCF_900112625.1	s__Methylobacterium sp900112625	80.384	773	1526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_009806555.1	s__Methylobacterium sp009806555	80.3192	729	1526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422815.1	s__Methylobacterium sp001422815	79.7444	708	1526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.57	97.58	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:11,031] [INFO] GTDB search result was written to GCF_030160935.1_ASM3016093v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:11,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:11,035] [INFO] DFAST_QC result json was written to GCF_030160935.1_ASM3016093v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:11,035] [INFO] DFAST_QC completed!
[2024-01-24 13:15:11,035] [INFO] Total running time: 0h1m25s