[2024-01-24 12:52:21,813] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:21,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:21,815] [INFO] DQC Reference Directory: /var/lib/cwl/stgac98b208-f7fc-4234-9d90-955bac80b9f7/dqc_reference
[2024-01-24 12:52:23,049] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:23,050] [INFO] Task started: Prodigal
[2024-01-24 12:52:23,050] [INFO] Running command: gunzip -c /var/lib/cwl/stga82a4504-a9ab-4398-9779-9315938c5656/GCF_030160955.1_ASM3016095v1_genomic.fna.gz | prodigal -d GCF_030160955.1_ASM3016095v1_genomic.fna/cds.fna -a GCF_030160955.1_ASM3016095v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:38,029] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:38,030] [INFO] Task started: HMMsearch
[2024-01-24 12:52:38,030] [INFO] Running command: hmmsearch --tblout GCF_030160955.1_ASM3016095v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac98b208-f7fc-4234-9d90-955bac80b9f7/dqc_reference/reference_markers.hmm GCF_030160955.1_ASM3016095v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:38,333] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:38,334] [INFO] Found 6/6 markers.
[2024-01-24 12:52:38,381] [INFO] Query marker FASTA was written to GCF_030160955.1_ASM3016095v1_genomic.fna/markers.fasta
[2024-01-24 12:52:38,381] [INFO] Task started: Blastn
[2024-01-24 12:52:38,382] [INFO] Running command: blastn -query GCF_030160955.1_ASM3016095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac98b208-f7fc-4234-9d90-955bac80b9f7/dqc_reference/reference_markers.fasta -out GCF_030160955.1_ASM3016095v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:39,477] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:39,480] [INFO] Selected 9 target genomes.
[2024-01-24 12:52:39,480] [INFO] Target genome list was writen to GCF_030160955.1_ASM3016095v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:39,511] [INFO] Task started: fastANI
[2024-01-24 12:52:39,512] [INFO] Running command: fastANI --query /var/lib/cwl/stga82a4504-a9ab-4398-9779-9315938c5656/GCF_030160955.1_ASM3016095v1_genomic.fna.gz --refList GCF_030160955.1_ASM3016095v1_genomic.fna/target_genomes.txt --output GCF_030160955.1_ASM3016095v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:54,545] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:54,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac98b208-f7fc-4234-9d90-955bac80b9f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:54,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac98b208-f7fc-4234-9d90-955bac80b9f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:54,562] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:52:54,563] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:52:54,563] [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 gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	99.935	1759	1909	95	conclusive
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	91.1108	1452	1909	95	below_threshold
Methylobacterium radiodurans	strain=17Sr1-43	GCA_003173735.1	2202828	2202828	type	True	90.4829	1414	1909	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	86.1818	1265	1909	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	86.1268	1206	1909	95	below_threshold
Methylobacterium symbioticum	strain=SB0023/3	GCA_902141845.1	2584084	2584084	type	True	85.5019	1189	1909	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	83.5209	1030	1909	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	82.5692	1111	1909	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	82.3542	1042	1909	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:54,565] [INFO] DFAST Taxonomy check result was written to GCF_030160955.1_ASM3016095v1_genomic.fna/tc_result.tsv
[2024-01-24 12:52:54,565] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:54,565] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:54,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac98b208-f7fc-4234-9d90-955bac80b9f7/dqc_reference/checkm_data
[2024-01-24 12:52:54,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:54,626] [INFO] Task started: CheckM
[2024-01-24 12:52:54,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160955.1_ASM3016095v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160955.1_ASM3016095v1_genomic.fna/checkm_input GCF_030160955.1_ASM3016095v1_genomic.fna/checkm_result
[2024-01-24 12:53:40,806] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:40,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:40,830] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:40,831] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:40,831] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160955.1_ASM3016095v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:40,832] [INFO] Task started: Blastn
[2024-01-24 12:53:40,832] [INFO] Running command: blastn -query GCF_030160955.1_ASM3016095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac98b208-f7fc-4234-9d90-955bac80b9f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160955.1_ASM3016095v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:42,994] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:42,998] [INFO] Selected 14 target genomes.
[2024-01-24 12:53:42,998] [INFO] Target genome list was writen to GCF_030160955.1_ASM3016095v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:43,018] [INFO] Task started: fastANI
[2024-01-24 12:53:43,018] [INFO] Running command: fastANI --query /var/lib/cwl/stga82a4504-a9ab-4398-9779-9315938c5656/GCF_030160955.1_ASM3016095v1_genomic.fna.gz --refList GCF_030160955.1_ASM3016095v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160955.1_ASM3016095v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:05,965] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:05,980] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:54:05,980] [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_003173735.1	s__Methylobacterium radiodurans	90.494	1412	1909	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	86.2023	1262	1909	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	85.5115	1186	1909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992195.1	s__Methylobacterium oxalidis	83.5073	1048	1909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039875.1	s__Methylobacterium sp008039875	83.2008	1046	1909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCF_002355515.1	s__Methylobacterium populi_A	83.169	1071	1909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003096615.1	s__Methylobacterium organophilum	83.0957	1152	1909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.99	98.85	0.91	0.88	18	-
GCF_900112625.1	s__Methylobacterium sp900112625	82.9336	1119	1909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCA_002778835.1	s__Methylobacterium sp002778835	82.8364	916	1909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.93	99.92	0.96	0.96	4	-
GCF_009806555.1	s__Methylobacterium sp009806555	82.82	1089	1909	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	82.5834	1044	1909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.87	97.76	0.88	0.86	7	-
GCF_000364445.2	s__Methylobacterium mesophilicum	82.4185	1089	1909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103195.1	s__Methylobacterium sp900103195	82.2787	1082	1909	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
GCF_000022085.1	s__Methylobacterium nodulans	80.6254	932	1909	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 12:54:05,982] [INFO] GTDB search result was written to GCF_030160955.1_ASM3016095v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:05,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:05,986] [INFO] DFAST_QC result json was written to GCF_030160955.1_ASM3016095v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:05,986] [INFO] DFAST_QC completed!
[2024-01-24 12:54:05,986] [INFO] Total running time: 0h1m44s