[2024-01-24 14:54:56,492] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,494] [INFO] DQC Reference Directory: /var/lib/cwl/stgec970cf2-3a0f-4810-bd85-5252301f52ab/dqc_reference
[2024-01-24 14:54:57,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,925] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,926] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa0091e2-7c35-43d3-bb0f-52e88b5edf13/GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna.gz | prodigal -d GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/cds.fna -a GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:16,936] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:16,937] [INFO] Task started: HMMsearch
[2024-01-24 14:55:16,937] [INFO] Running command: hmmsearch --tblout GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec970cf2-3a0f-4810-bd85-5252301f52ab/dqc_reference/reference_markers.hmm GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:17,270] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:17,271] [INFO] Found 6/6 markers.
[2024-01-24 14:55:17,322] [INFO] Query marker FASTA was written to GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/markers.fasta
[2024-01-24 14:55:17,323] [INFO] Task started: Blastn
[2024-01-24 14:55:17,323] [INFO] Running command: blastn -query GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec970cf2-3a0f-4810-bd85-5252301f52ab/dqc_reference/reference_markers.fasta -out GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:18,451] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:18,455] [INFO] Selected 10 target genomes.
[2024-01-24 14:55:18,455] [INFO] Target genome list was writen to GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:18,477] [INFO] Task started: fastANI
[2024-01-24 14:55:18,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa0091e2-7c35-43d3-bb0f-52e88b5edf13/GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna.gz --refList GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/target_genomes.txt --output GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:34,198] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:34,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec970cf2-3a0f-4810-bd85-5252301f52ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:34,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec970cf2-3a0f-4810-bd85-5252301f52ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:34,208] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:34,209] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:34,209] [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 extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	100.0	1903	1905	95	conclusive
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	89.3588	1046	1905	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	89.0833	1430	1905	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	88.9726	1466	1905	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	87.0642	1163	1905	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	85.4775	1211	1905	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	85.2153	1209	1905	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	84.11	1189	1905	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	82.0188	1000	1905	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	81.4497	810	1905	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:34,211] [INFO] DFAST Taxonomy check result was written to GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:34,211] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:34,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:34,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec970cf2-3a0f-4810-bd85-5252301f52ab/dqc_reference/checkm_data
[2024-01-24 14:55:34,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:34,279] [INFO] Task started: CheckM
[2024-01-24 14:55:34,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/checkm_input GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/checkm_result
[2024-01-24 14:56:30,382] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:30,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:30,414] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:30,415] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:30,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:30,416] [INFO] Task started: Blastn
[2024-01-24 14:56:30,416] [INFO] Running command: blastn -query GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec970cf2-3a0f-4810-bd85-5252301f52ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:32,712] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:32,717] [INFO] Selected 10 target genomes.
[2024-01-24 14:56:32,717] [INFO] Target genome list was writen to GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:32,733] [INFO] Task started: fastANI
[2024-01-24 14:56:32,734] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa0091e2-7c35-43d3-bb0f-52e88b5edf13/GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna.gz --refList GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:48,595] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:48,609] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:48,609] [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_900234795.1	s__Methylobacterium extorquens	100.0	1903	1905	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.03	96.19	0.88	0.73	17	conclusive
GCF_001542815.1	s__Methylobacterium sp001542815	94.2242	1492	1905	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.78	0.92	0.92	2	-
GCF_001423405.1	s__Methylobacterium sp001423405	93.3183	1497	1905	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014138645.1	s__Methylobacterium thiocyanatum	89.6517	1458	1905	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.87	97.76	0.88	0.86	7	-
GCF_002355515.1	s__Methylobacterium populi_A	89.3144	1465	1905	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191355.1	s__Methylobacterium sp014191355	89.2016	1473	1905	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	89.0088	1476	1905	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.28	97.28	0.88	0.88	3	-
GCF_014199985.1	s__Methylobacterium rhodesianum	88.9505	1469	1905	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.84	98.11	0.88	0.84	5	-
GCF_003201865.1	s__Methylobacterium sp003201865	87.939	1337	1905	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114375.1	s__Methylobacterium salsuginis	85.2064	1210	1905	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:48,611] [INFO] GTDB search result was written to GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:48,612] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:48,615] [INFO] DFAST_QC result json was written to GCF_900234795.1_TK0001_PRJEB23178_v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:48,615] [INFO] DFAST_QC completed!
[2024-01-24 14:56:48,615] [INFO] Total running time: 0h1m52s