[2024-01-24 13:01:24,798] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:24,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:24,800] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcac9033-3d4c-4992-aa87-246d0b6ce24d/dqc_reference
[2024-01-24 13:01:26,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:26,102] [INFO] Task started: Prodigal
[2024-01-24 13:01:26,102] [INFO] Running command: gunzip -c /var/lib/cwl/stge18f0bef-4da4-4369-94a2-6bc152dbee91/GCF_007992195.1_ASM799219v1_genomic.fna.gz | prodigal -d GCF_007992195.1_ASM799219v1_genomic.fna/cds.fna -a GCF_007992195.1_ASM799219v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:41,967] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:41,967] [INFO] Task started: HMMsearch
[2024-01-24 13:01:41,967] [INFO] Running command: hmmsearch --tblout GCF_007992195.1_ASM799219v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcac9033-3d4c-4992-aa87-246d0b6ce24d/dqc_reference/reference_markers.hmm GCF_007992195.1_ASM799219v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:42,325] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:42,327] [INFO] Found 6/6 markers.
[2024-01-24 13:01:42,378] [INFO] Query marker FASTA was written to GCF_007992195.1_ASM799219v1_genomic.fna/markers.fasta
[2024-01-24 13:01:42,379] [INFO] Task started: Blastn
[2024-01-24 13:01:42,379] [INFO] Running command: blastn -query GCF_007992195.1_ASM799219v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcac9033-3d4c-4992-aa87-246d0b6ce24d/dqc_reference/reference_markers.fasta -out GCF_007992195.1_ASM799219v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:43,436] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:43,444] [INFO] Selected 14 target genomes.
[2024-01-24 13:01:43,445] [INFO] Target genome list was writen to GCF_007992195.1_ASM799219v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:43,458] [INFO] Task started: fastANI
[2024-01-24 13:01:43,458] [INFO] Running command: fastANI --query /var/lib/cwl/stge18f0bef-4da4-4369-94a2-6bc152dbee91/GCF_007992195.1_ASM799219v1_genomic.fna.gz --refList GCF_007992195.1_ASM799219v1_genomic.fna/target_genomes.txt --output GCF_007992195.1_ASM799219v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:01,215] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:01,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcac9033-3d4c-4992-aa87-246d0b6ce24d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:01,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcac9033-3d4c-4992-aa87-246d0b6ce24d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:01,232] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:01,233] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:01,233] [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=NBRC 107715	GCA_007992195.1	944322	944322	type	True	100.0	1920	1934	95	conclusive
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	99.9586	1863	1934	95	conclusive
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	87.9388	1502	1934	95	below_threshold
Methylobacterium segetis	strain=17J42-1	GCA_004348265.1	2488750	2488750	type	True	87.6938	1305	1934	95	below_threshold
Methylobacterium soli	strain=YIM 48816	GCA_008806385.1	553447	553447	type	True	84.0995	1186	1934	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	84.0326	1034	1934	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	83.7621	1057	1934	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	83.7548	930	1934	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	83.4702	1007	1934	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	82.8924	992	1934	95	below_threshold
Afifella aestuarii	strain=JA968	GCA_004023665.1	1909496	1909496	type	True	76.1333	173	1934	95	below_threshold
Actinopolyspora mortivallis	strain=HS-1	GCA_000384035.1	33906	33906	type	True	74.9883	78	1934	95	below_threshold
Saccharomonospora viridis	strain=DSM 43017	GCA_000023865.1	1852	1852	type	True	74.8305	82	1934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:01,235] [INFO] DFAST Taxonomy check result was written to GCF_007992195.1_ASM799219v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:01,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:01,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:01,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcac9033-3d4c-4992-aa87-246d0b6ce24d/dqc_reference/checkm_data
[2024-01-24 13:02:01,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:01,299] [INFO] Task started: CheckM
[2024-01-24 13:02:01,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992195.1_ASM799219v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992195.1_ASM799219v1_genomic.fna/checkm_input GCF_007992195.1_ASM799219v1_genomic.fna/checkm_result
[2024-01-24 13:02:46,853] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:46,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:46,884] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:46,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:46,885] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992195.1_ASM799219v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:46,885] [INFO] Task started: Blastn
[2024-01-24 13:02:46,885] [INFO] Running command: blastn -query GCF_007992195.1_ASM799219v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcac9033-3d4c-4992-aa87-246d0b6ce24d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992195.1_ASM799219v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:48,710] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:48,715] [INFO] Selected 14 target genomes.
[2024-01-24 13:02:48,715] [INFO] Target genome list was writen to GCF_007992195.1_ASM799219v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:48,726] [INFO] Task started: fastANI
[2024-01-24 13:02:48,726] [INFO] Running command: fastANI --query /var/lib/cwl/stge18f0bef-4da4-4369-94a2-6bc152dbee91/GCF_007992195.1_ASM799219v1_genomic.fna.gz --refList GCF_007992195.1_ASM799219v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992195.1_ASM799219v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:06,852] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:06,870] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:06,870] [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	100.0	1920	1934	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	87.9538	1502	1934	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	87.626	1311	1934	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	84.5812	1141	1934	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	84.0594	1193	1934	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	83.9625	1091	1934	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	83.5703	909	1934	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	83.5391	1041	1934	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	83.1452	1012	1934	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	82.8788	971	1934	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	82.0399	1022	1934	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	81.575	984	1934	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	74.9282	76	1934	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 13:03:06,872] [INFO] GTDB search result was written to GCF_007992195.1_ASM799219v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:06,872] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:06,875] [INFO] DFAST_QC result json was written to GCF_007992195.1_ASM799219v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:06,876] [INFO] DFAST_QC completed!
[2024-01-24 13:03:06,876] [INFO] Total running time: 0h1m42s