[2024-01-24 13:46:40,970] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:40,972] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:40,972] [INFO] DQC Reference Directory: /var/lib/cwl/stg781d0549-ac2d-4374-a7e0-584bba8ae9d0/dqc_reference
[2024-01-24 13:46:42,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:42,322] [INFO] Task started: Prodigal
[2024-01-24 13:46:42,323] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bb7284c-4a22-4add-beaf-6216e1881a11/GCF_014138645.1_ASM1413864v1_genomic.fna.gz | prodigal -d GCF_014138645.1_ASM1413864v1_genomic.fna/cds.fna -a GCF_014138645.1_ASM1413864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:58,607] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:58,608] [INFO] Task started: HMMsearch
[2024-01-24 13:46:58,608] [INFO] Running command: hmmsearch --tblout GCF_014138645.1_ASM1413864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg781d0549-ac2d-4374-a7e0-584bba8ae9d0/dqc_reference/reference_markers.hmm GCF_014138645.1_ASM1413864v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:58,925] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:58,927] [INFO] Found 6/6 markers.
[2024-01-24 13:46:58,978] [INFO] Query marker FASTA was written to GCF_014138645.1_ASM1413864v1_genomic.fna/markers.fasta
[2024-01-24 13:46:58,978] [INFO] Task started: Blastn
[2024-01-24 13:46:58,979] [INFO] Running command: blastn -query GCF_014138645.1_ASM1413864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg781d0549-ac2d-4374-a7e0-584bba8ae9d0/dqc_reference/reference_markers.fasta -out GCF_014138645.1_ASM1413864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:00,177] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:00,181] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:00,182] [INFO] Target genome list was writen to GCF_014138645.1_ASM1413864v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:00,215] [INFO] Task started: fastANI
[2024-01-24 13:47:00,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bb7284c-4a22-4add-beaf-6216e1881a11/GCF_014138645.1_ASM1413864v1_genomic.fna.gz --refList GCF_014138645.1_ASM1413864v1_genomic.fna/target_genomes.txt --output GCF_014138645.1_ASM1413864v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:15,243] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:15,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg781d0549-ac2d-4374-a7e0-584bba8ae9d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:15,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg781d0549-ac2d-4374-a7e0-584bba8ae9d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:15,255] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:47:15,256] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:47:15,256] [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 podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	89.8291	1058	1862	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	89.7358	1476	1862	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	89.6368	1449	1862	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	89.6289	1469	1862	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	87.7899	1159	1862	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	86.0121	1246	1862	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	85.9058	1219	1862	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	84.751	1219	1862	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	81.5636	847	1862	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	81.4096	970	1862	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:15,258] [INFO] DFAST Taxonomy check result was written to GCF_014138645.1_ASM1413864v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:15,258] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:15,258] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:15,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg781d0549-ac2d-4374-a7e0-584bba8ae9d0/dqc_reference/checkm_data
[2024-01-24 13:47:15,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:15,313] [INFO] Task started: CheckM
[2024-01-24 13:47:15,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014138645.1_ASM1413864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014138645.1_ASM1413864v1_genomic.fna/checkm_input GCF_014138645.1_ASM1413864v1_genomic.fna/checkm_result
[2024-01-24 13:48:03,159] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:03,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:03,178] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:03,178] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:03,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014138645.1_ASM1413864v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:03,179] [INFO] Task started: Blastn
[2024-01-24 13:48:03,180] [INFO] Running command: blastn -query GCF_014138645.1_ASM1413864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg781d0549-ac2d-4374-a7e0-584bba8ae9d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014138645.1_ASM1413864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:05,413] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:05,416] [INFO] Selected 9 target genomes.
[2024-01-24 13:48:05,416] [INFO] Target genome list was writen to GCF_014138645.1_ASM1413864v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:05,426] [INFO] Task started: fastANI
[2024-01-24 13:48:05,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bb7284c-4a22-4add-beaf-6216e1881a11/GCF_014138645.1_ASM1413864v1_genomic.fna.gz --refList GCF_014138645.1_ASM1413864v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014138645.1_ASM1413864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:19,543] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:19,559] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:19,559] [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
GCA_014138645.1	s__Methylobacterium thiocyanatum	100.0	1860	1862	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.87	97.76	0.88	0.86	7	conclusive
GCF_002355515.1	s__Methylobacterium populi_A	90.5046	1476	1862	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	89.7086	1479	1862	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.84	98.11	0.88	0.84	5	-
GCF_900234795.1	s__Methylobacterium extorquens	89.6445	1466	1862	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.03	96.19	0.88	0.73	17	-
GCF_001542815.1	s__Methylobacterium sp001542815	89.6192	1420	1862	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.78	0.92	0.92	2	-
GCF_003111705.1	s__Methylobacterium sp003111705	89.6017	1469	1862	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.28	97.28	0.88	0.88	3	-
GCF_001423405.1	s__Methylobacterium sp001423405	89.4982	1443	1862	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	89.2764	1409	1862	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	87.7742	1160	1862	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 13:48:19,560] [INFO] GTDB search result was written to GCF_014138645.1_ASM1413864v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:19,561] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:19,563] [INFO] DFAST_QC result json was written to GCF_014138645.1_ASM1413864v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:19,563] [INFO] DFAST_QC completed!
[2024-01-24 13:48:19,563] [INFO] Total running time: 0h1m39s