[2024-01-24 11:26:28,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg681f31f5-4d59-4014-aa9b-871836681418/dqc_reference
[2024-01-24 11:26:29,341] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,342] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,342] [INFO] Running command: gunzip -c /var/lib/cwl/stg859d687f-0bfa-4d57-a181-65c82e80a856/GCF_030160995.1_ASM3016099v1_genomic.fna.gz | prodigal -d GCF_030160995.1_ASM3016099v1_genomic.fna/cds.fna -a GCF_030160995.1_ASM3016099v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:46,429] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:46,430] [INFO] Task started: HMMsearch
[2024-01-24 11:26:46,430] [INFO] Running command: hmmsearch --tblout GCF_030160995.1_ASM3016099v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg681f31f5-4d59-4014-aa9b-871836681418/dqc_reference/reference_markers.hmm GCF_030160995.1_ASM3016099v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:46,807] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:46,808] [INFO] Found 6/6 markers.
[2024-01-24 11:26:46,858] [INFO] Query marker FASTA was written to GCF_030160995.1_ASM3016099v1_genomic.fna/markers.fasta
[2024-01-24 11:26:46,858] [INFO] Task started: Blastn
[2024-01-24 11:26:46,859] [INFO] Running command: blastn -query GCF_030160995.1_ASM3016099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg681f31f5-4d59-4014-aa9b-871836681418/dqc_reference/reference_markers.fasta -out GCF_030160995.1_ASM3016099v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:47,898] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:47,903] [INFO] Selected 14 target genomes.
[2024-01-24 11:26:47,903] [INFO] Target genome list was writen to GCF_030160995.1_ASM3016099v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:47,920] [INFO] Task started: fastANI
[2024-01-24 11:26:47,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg859d687f-0bfa-4d57-a181-65c82e80a856/GCF_030160995.1_ASM3016099v1_genomic.fna.gz --refList GCF_030160995.1_ASM3016099v1_genomic.fna/target_genomes.txt --output GCF_030160995.1_ASM3016099v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:08,352] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:08,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg681f31f5-4d59-4014-aa9b-871836681418/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:08,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg681f31f5-4d59-4014-aa9b-871836681418/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:08,369] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:08,370] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:08,370] [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 oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	99.9377	1895	2063	95	conclusive
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	99.8916	1891	2063	95	conclusive
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	88.0728	1579	2063	95	below_threshold
Methylobacterium segetis	strain=17J42-1	GCA_004348265.1	2488750	2488750	type	True	87.7184	1353	2063	95	below_threshold
Methylobacterium soli	strain=YIM 48816	GCA_008806385.1	553447	553447	type	True	84.0064	1256	2063	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	83.8778	1073	2063	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	83.8109	960	2063	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	83.7301	1095	2063	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	83.3659	1069	2063	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	82.8149	1034	2063	95	below_threshold
Afifella aestuarii	strain=JA968	GCA_004023665.1	1909496	1909496	type	True	76.0907	189	2063	95	below_threshold
Actinopolyspora mortivallis	strain=HS-1	GCA_000384035.1	33906	33906	type	True	75.0414	79	2063	95	below_threshold
Saccharomonospora viridis	strain=DSM 43017	GCA_000023865.1	1852	1852	type	True	74.839	77	2063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:08,380] [INFO] DFAST Taxonomy check result was written to GCF_030160995.1_ASM3016099v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:08,380] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:08,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:08,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg681f31f5-4d59-4014-aa9b-871836681418/dqc_reference/checkm_data
[2024-01-24 11:27:08,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:08,443] [INFO] Task started: CheckM
[2024-01-24 11:27:08,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160995.1_ASM3016099v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160995.1_ASM3016099v1_genomic.fna/checkm_input GCF_030160995.1_ASM3016099v1_genomic.fna/checkm_result
[2024-01-24 11:27:59,827] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:59,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:59,849] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:59,849] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:59,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160995.1_ASM3016099v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:59,850] [INFO] Task started: Blastn
[2024-01-24 11:27:59,850] [INFO] Running command: blastn -query GCF_030160995.1_ASM3016099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg681f31f5-4d59-4014-aa9b-871836681418/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160995.1_ASM3016099v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:01,728] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:01,733] [INFO] Selected 14 target genomes.
[2024-01-24 11:28:01,733] [INFO] Target genome list was writen to GCF_030160995.1_ASM3016099v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:01,745] [INFO] Task started: fastANI
[2024-01-24 11:28:01,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg859d687f-0bfa-4d57-a181-65c82e80a856/GCF_030160995.1_ASM3016099v1_genomic.fna.gz --refList GCF_030160995.1_ASM3016099v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160995.1_ASM3016099v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:21,567] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:21,585] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:21,585] [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_007992195.1	s__Methylobacterium oxalidis	99.8916	1891	2063	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_003173715.1	s__Methylobacterium durans	88.0624	1579	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348265.1	s__Methylobacterium segetis	87.7217	1354	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806345.1	s__Methylobacterium sp008806345	84.6525	1187	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806385.1	s__Methylobacterium soli	84.0181	1256	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141855.1	s__Methylobacterium dankookense	83.8836	1142	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002778835.1	s__Methylobacterium sp002778835	83.5801	946	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.93	99.92	0.96	0.96	4	-
GCF_003173735.1	s__Methylobacterium radiodurans	83.5333	1085	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141845.1	s__Methylobacterium symbioticum	83.1891	1047	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040045.1	s__Methylobacterium sp008040045	82.8026	1012	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.17	0.85	0.85	3	-
GCF_900112625.1	s__Methylobacterium sp900112625	82.0974	1055	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_003697185.1	s__Methylobacterium brachiatum	81.6563	1003	2063	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.08	95.77	0.85	0.80	4	-
GCA_015709595.1	s__CAADGA01 sp900696425	74.9385	85	2063	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__CAADGA01	95.0	99.08	99.08	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:21,589] [INFO] GTDB search result was written to GCF_030160995.1_ASM3016099v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:21,590] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:21,596] [INFO] DFAST_QC result json was written to GCF_030160995.1_ASM3016099v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:21,596] [INFO] DFAST_QC completed!
[2024-01-24 11:28:21,596] [INFO] Total running time: 0h1m54s