[2024-01-24 12:21:51,442] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:51,444] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:51,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg53be28fd-d50b-42b4-b961-06076c778623/dqc_reference
[2024-01-24 12:21:52,648] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:52,648] [INFO] Task started: Prodigal
[2024-01-24 12:21:52,649] [INFO] Running command: gunzip -c /var/lib/cwl/stg96e8174f-4d87-40c5-843c-0f14e88f70e7/GCF_025583945.1_ASM2558394v1_genomic.fna.gz | prodigal -d GCF_025583945.1_ASM2558394v1_genomic.fna/cds.fna -a GCF_025583945.1_ASM2558394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:03,179] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:03,180] [INFO] Task started: HMMsearch
[2024-01-24 12:22:03,180] [INFO] Running command: hmmsearch --tblout GCF_025583945.1_ASM2558394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53be28fd-d50b-42b4-b961-06076c778623/dqc_reference/reference_markers.hmm GCF_025583945.1_ASM2558394v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:03,539] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:03,540] [INFO] Found 6/6 markers.
[2024-01-24 12:22:03,584] [INFO] Query marker FASTA was written to GCF_025583945.1_ASM2558394v1_genomic.fna/markers.fasta
[2024-01-24 12:22:03,585] [INFO] Task started: Blastn
[2024-01-24 12:22:03,585] [INFO] Running command: blastn -query GCF_025583945.1_ASM2558394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53be28fd-d50b-42b4-b961-06076c778623/dqc_reference/reference_markers.fasta -out GCF_025583945.1_ASM2558394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:04,268] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:04,271] [INFO] Selected 27 target genomes.
[2024-01-24 12:22:04,271] [INFO] Target genome list was writen to GCF_025583945.1_ASM2558394v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:04,401] [INFO] Task started: fastANI
[2024-01-24 12:22:04,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg96e8174f-4d87-40c5-843c-0f14e88f70e7/GCF_025583945.1_ASM2558394v1_genomic.fna.gz --refList GCF_025583945.1_ASM2558394v1_genomic.fna/target_genomes.txt --output GCF_025583945.1_ASM2558394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:21,194] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:21,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53be28fd-d50b-42b4-b961-06076c778623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:21,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53be28fd-d50b-42b4-b961-06076c778623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:21,204] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:21,204] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:21,204] [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
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	77.8918	351	1478	95	below_threshold
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	77.1119	160	1478	95	below_threshold
Methylosarcina fibrata	strain=AML-C10	GCA_000372865.1	105972	105972	type	True	77.0439	65	1478	95	below_threshold
Methylovulum miyakonense	strain=HT12	GCA_000384075.1	645578	645578	type	True	76.9294	131	1478	95	below_threshold
Methylovulum psychrotolerans	strain=Sph1	GCA_002923755.1	1704499	1704499	type	True	76.8414	119	1478	95	below_threshold
Methylicorpusculum oleiharenae	strain=XLMV4	GCA_009828925.2	1338687	1338687	type	True	76.7464	103	1478	95	below_threshold
Crenothrix polyspora		GCA_900163755.1	360316	360316	reftype	True	76.4305	141	1478	95	below_threshold
Methylocucumis oryzae	strain=Sn10-6	GCA_000963695.1	1632867	1632867	type	True	76.4128	82	1478	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:21,206] [INFO] DFAST Taxonomy check result was written to GCF_025583945.1_ASM2558394v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:21,207] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:21,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:21,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53be28fd-d50b-42b4-b961-06076c778623/dqc_reference/checkm_data
[2024-01-24 12:22:21,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:21,257] [INFO] Task started: CheckM
[2024-01-24 12:22:21,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025583945.1_ASM2558394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025583945.1_ASM2558394v1_genomic.fna/checkm_input GCF_025583945.1_ASM2558394v1_genomic.fna/checkm_result
[2024-01-24 12:22:59,590] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:59,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:59,615] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:59,616] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:59,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025583945.1_ASM2558394v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:59,616] [INFO] Task started: Blastn
[2024-01-24 12:22:59,617] [INFO] Running command: blastn -query GCF_025583945.1_ASM2558394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53be28fd-d50b-42b4-b961-06076c778623/dqc_reference/reference_markers_gtdb.fasta -out GCF_025583945.1_ASM2558394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:00,732] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:00,736] [INFO] Selected 13 target genomes.
[2024-01-24 12:23:00,736] [INFO] Target genome list was writen to GCF_025583945.1_ASM2558394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:00,799] [INFO] Task started: fastANI
[2024-01-24 12:23:00,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg96e8174f-4d87-40c5-843c-0f14e88f70e7/GCF_025583945.1_ASM2558394v1_genomic.fna.gz --refList GCF_025583945.1_ASM2558394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025583945.1_ASM2558394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:09,050] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:09,061] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:23:09,061] [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_903903365.1	s__KS41 sp903903365	82.273	582	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873045.1	s__KS41 sp903873045	82.1862	542	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839795.1	s__KS41 sp903839795	81.6717	525	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256705.1	s__KS41 sp002256705	81.2664	356	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256465.1	s__KS41 sp002256465	80.4836	278	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862125.1	s__KS41 sp002862125	79.3109	617	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003158415.1	s__KS41 sp003158415	79.1209	373	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903939355.1	s__KS41 sp903939355	78.3947	274	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.41	98.41	0.76	0.76	2	-
GCA_903908165.1	s__KS41 sp903908165	77.9787	305	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.39	98.42	0.88	0.71	10	-
GCA_903859415.1	s__KS41 sp903859415	77.8263	299	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.28	98.83	0.89	0.85	3	-
GCA_903866825.1	s__KS41 sp903866825	77.7489	276	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.82	99.82	0.85	0.85	2	-
GCA_003584895.1	s__KS41 sp003584895	77.6888	230	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.75	98.03	0.85	0.79	12	-
GCA_003584875.1	s__KS41 sp003584875	77.6735	221	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.94	98.69	0.84	0.76	9	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:09,063] [INFO] GTDB search result was written to GCF_025583945.1_ASM2558394v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:09,063] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:09,067] [INFO] DFAST_QC result json was written to GCF_025583945.1_ASM2558394v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:09,067] [INFO] DFAST_QC completed!
[2024-01-24 12:23:09,068] [INFO] Total running time: 0h1m18s