[2024-01-24 12:06:12,901] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:12,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:12,904] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd01c9d0-1b22-40ce-bb37-e2ce28221c5c/dqc_reference
[2024-01-24 12:06:14,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:14,303] [INFO] Task started: Prodigal
[2024-01-24 12:06:14,304] [INFO] Running command: gunzip -c /var/lib/cwl/stg8138cd35-c521-4e07-ba95-f5e0ba316bc5/GCF_022179765.1_ASM2217976v1_genomic.fna.gz | prodigal -d GCF_022179765.1_ASM2217976v1_genomic.fna/cds.fna -a GCF_022179765.1_ASM2217976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:29,939] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:29,939] [INFO] Task started: HMMsearch
[2024-01-24 12:06:29,939] [INFO] Running command: hmmsearch --tblout GCF_022179765.1_ASM2217976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd01c9d0-1b22-40ce-bb37-e2ce28221c5c/dqc_reference/reference_markers.hmm GCF_022179765.1_ASM2217976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:30,308] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:30,309] [INFO] Found 6/6 markers.
[2024-01-24 12:06:30,366] [INFO] Query marker FASTA was written to GCF_022179765.1_ASM2217976v1_genomic.fna/markers.fasta
[2024-01-24 12:06:30,367] [INFO] Task started: Blastn
[2024-01-24 12:06:30,367] [INFO] Running command: blastn -query GCF_022179765.1_ASM2217976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd01c9d0-1b22-40ce-bb37-e2ce28221c5c/dqc_reference/reference_markers.fasta -out GCF_022179765.1_ASM2217976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:31,570] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:31,574] [INFO] Selected 10 target genomes.
[2024-01-24 12:06:31,575] [INFO] Target genome list was writen to GCF_022179765.1_ASM2217976v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:31,590] [INFO] Task started: fastANI
[2024-01-24 12:06:31,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg8138cd35-c521-4e07-ba95-f5e0ba316bc5/GCF_022179765.1_ASM2217976v1_genomic.fna.gz --refList GCF_022179765.1_ASM2217976v1_genomic.fna/target_genomes.txt --output GCF_022179765.1_ASM2217976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:45,625] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:45,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd01c9d0-1b22-40ce-bb37-e2ce28221c5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:45,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd01c9d0-1b22-40ce-bb37-e2ce28221c5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:45,635] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:45,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:45,635] [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 suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	100.0	1821	1824	95	conclusive
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	87.5216	1271	1824	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	87.3298	1309	1824	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	85.1313	902	1824	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	84.8813	1200	1824	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	84.7174	1217	1824	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	84.4893	1003	1824	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	84.2228	1197	1824	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	81.1329	728	1824	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	80.8208	770	1824	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:45,636] [INFO] DFAST Taxonomy check result was written to GCF_022179765.1_ASM2217976v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:45,637] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:45,637] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:45,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd01c9d0-1b22-40ce-bb37-e2ce28221c5c/dqc_reference/checkm_data
[2024-01-24 12:06:45,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:45,695] [INFO] Task started: CheckM
[2024-01-24 12:06:45,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022179765.1_ASM2217976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022179765.1_ASM2217976v1_genomic.fna/checkm_input GCF_022179765.1_ASM2217976v1_genomic.fna/checkm_result
[2024-01-24 12:07:32,530] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:32,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:32,559] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:32,559] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:32,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022179765.1_ASM2217976v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:32,560] [INFO] Task started: Blastn
[2024-01-24 12:07:32,560] [INFO] Running command: blastn -query GCF_022179765.1_ASM2217976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd01c9d0-1b22-40ce-bb37-e2ce28221c5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_022179765.1_ASM2217976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:34,643] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:34,646] [INFO] Selected 11 target genomes.
[2024-01-24 12:07:34,647] [INFO] Target genome list was writen to GCF_022179765.1_ASM2217976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:34,659] [INFO] Task started: fastANI
[2024-01-24 12:07:34,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg8138cd35-c521-4e07-ba95-f5e0ba316bc5/GCF_022179765.1_ASM2217976v1_genomic.fna.gz --refList GCF_022179765.1_ASM2217976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022179765.1_ASM2217976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:49,735] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:49,755] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:49,756] [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_005502455.1	s__Methylobacterium sp005502455	99.433	1564	1824	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_014199935.1	s__Methylobacterium rhodinum	87.5116	1272	1824	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	87.3633	1305	1824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425465.1	s__Methylobacterium sp001425465	87.1256	1292	1824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355515.1	s__Methylobacterium populi_A	84.9095	1219	1824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199985.1	s__Methylobacterium rhodesianum	84.7592	1212	1824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.84	98.11	0.88	0.84	5	-
GCA_014138645.1	s__Methylobacterium thiocyanatum	84.7205	1229	1824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.87	97.76	0.88	0.86	7	-
GCF_003201865.1	s__Methylobacterium sp003201865	84.5551	1141	1824	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	84.5024	1002	1824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423405.1	s__Methylobacterium sp001423405	84.3101	1145	1824	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	84.1657	1146	1824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.78	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:49,758] [INFO] GTDB search result was written to GCF_022179765.1_ASM2217976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:49,761] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:49,764] [INFO] DFAST_QC result json was written to GCF_022179765.1_ASM2217976v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:49,764] [INFO] DFAST_QC completed!
[2024-01-24 12:07:49,764] [INFO] Total running time: 0h1m37s