[2024-01-24 11:48:21,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d0dbf67-766c-4c45-8237-8b371c99007d/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,566] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,566] [INFO] Running command: gunzip -c /var/lib/cwl/stg959d3f6d-628c-4c08-9a2a-2856f1d8cfdc/GCF_007992215.1_ASM799221v1_genomic.fna.gz | prodigal -d GCF_007992215.1_ASM799221v1_genomic.fna/cds.fna -a GCF_007992215.1_ASM799221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:37,410] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:37,410] [INFO] Task started: HMMsearch
[2024-01-24 11:48:37,410] [INFO] Running command: hmmsearch --tblout GCF_007992215.1_ASM799221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d0dbf67-766c-4c45-8237-8b371c99007d/dqc_reference/reference_markers.hmm GCF_007992215.1_ASM799221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:37,694] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:37,695] [INFO] Found 6/6 markers.
[2024-01-24 11:48:37,735] [INFO] Query marker FASTA was written to GCF_007992215.1_ASM799221v1_genomic.fna/markers.fasta
[2024-01-24 11:48:37,736] [INFO] Task started: Blastn
[2024-01-24 11:48:37,736] [INFO] Running command: blastn -query GCF_007992215.1_ASM799221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d0dbf67-766c-4c45-8237-8b371c99007d/dqc_reference/reference_markers.fasta -out GCF_007992215.1_ASM799221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:38,775] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:38,777] [INFO] Selected 12 target genomes.
[2024-01-24 11:48:38,778] [INFO] Target genome list was writen to GCF_007992215.1_ASM799221v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:38,783] [INFO] Task started: fastANI
[2024-01-24 11:48:38,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg959d3f6d-628c-4c08-9a2a-2856f1d8cfdc/GCF_007992215.1_ASM799221v1_genomic.fna.gz --refList GCF_007992215.1_ASM799221v1_genomic.fna/target_genomes.txt --output GCF_007992215.1_ASM799221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:48:52,565] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:52,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d0dbf67-766c-4c45-8237-8b371c99007d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:48:52,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d0dbf67-766c-4c45-8237-8b371c99007d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:48:52,576] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:48:52,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:48:52,577] [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 gnaphalii	strain=NBRC 107716	GCA_007992215.1	1010610	1010610	type	True	100.0	1535	1539	95	conclusive
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	99.957	1462	1539	95	conclusive
Methylobacterium brachythecii	strain=DSM 24105	GCA_014196345.1	1176177	1176177	type	True	86.8735	1156	1539	95	below_threshold
Methylobacterium haplocladii	strain=DSM 24195	GCA_022179265.1	1176176	1176176	type	True	84.0062	940	1539	95	below_threshold
Methylobacterium haplocladii	strain=NBRC 107714	GCA_007992175.1	1176176	1176176	type	True	83.9977	960	1539	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	81.5669	681	1539	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	81.4414	833	1539	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	81.3689	839	1539	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	80.9442	713	1539	95	below_threshold
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	80.601	811	1539	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	80.5334	664	1539	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	80.3335	794	1539	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:48:52,579] [INFO] DFAST Taxonomy check result was written to GCF_007992215.1_ASM799221v1_genomic.fna/tc_result.tsv
[2024-01-24 11:48:52,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:48:52,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:48:52,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d0dbf67-766c-4c45-8237-8b371c99007d/dqc_reference/checkm_data
[2024-01-24 11:48:52,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:48:52,625] [INFO] Task started: CheckM
[2024-01-24 11:48:52,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992215.1_ASM799221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992215.1_ASM799221v1_genomic.fna/checkm_input GCF_007992215.1_ASM799221v1_genomic.fna/checkm_result
[2024-01-24 11:49:31,928] [INFO] Task succeeded: CheckM
[2024-01-24 11:49:31,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:49:31,946] [INFO] ===== Completeness check finished =====
[2024-01-24 11:49:31,947] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:49:31,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992215.1_ASM799221v1_genomic.fna/markers.fasta)
[2024-01-24 11:49:31,948] [INFO] Task started: Blastn
[2024-01-24 11:49:31,948] [INFO] Running command: blastn -query GCF_007992215.1_ASM799221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d0dbf67-766c-4c45-8237-8b371c99007d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992215.1_ASM799221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:49:34,018] [INFO] Task succeeded: Blastn
[2024-01-24 11:49:34,022] [INFO] Selected 12 target genomes.
[2024-01-24 11:49:34,023] [INFO] Target genome list was writen to GCF_007992215.1_ASM799221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:49:34,032] [INFO] Task started: fastANI
[2024-01-24 11:49:34,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg959d3f6d-628c-4c08-9a2a-2856f1d8cfdc/GCF_007992215.1_ASM799221v1_genomic.fna.gz --refList GCF_007992215.1_ASM799221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992215.1_ASM799221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:49:48,214] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:48,226] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:49:48,226] [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_007992215.1	s__Methylobacterium gnaphalii	100.0	1535	1539	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_014196345.1	s__Methylobacterium brachythecii	86.8986	1153	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040035.1	s__Methylobacterium sp008040035	84.1257	932	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992175.1	s__Methylobacterium haplocladii	83.9908	960	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201865.1	s__Methylobacterium sp003201865	81.4395	811	1539	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	81.2876	839	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.78	0.92	0.92	2	-
GCF_014845115.1	s__Methylobacterium zatmanii	81.2222	756	1539	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	80.9394	786	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCA_002778835.1	s__Methylobacterium sp002778835	80.9093	728	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.93	99.92	0.96	0.96	4	-
GCF_900112625.1	s__Methylobacterium sp900112625	80.3728	779	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_009806555.1	s__Methylobacterium sp009806555	80.3335	728	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422815.1	s__Methylobacterium sp001422815	79.683	720	1539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.57	97.58	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:49:48,228] [INFO] GTDB search result was written to GCF_007992215.1_ASM799221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:49:48,228] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:49:48,231] [INFO] DFAST_QC result json was written to GCF_007992215.1_ASM799221v1_genomic.fna/dqc_result.json
[2024-01-24 11:49:48,232] [INFO] DFAST_QC completed!
[2024-01-24 11:49:48,232] [INFO] Total running time: 0h1m27s