[2024-01-24 13:40:35,065] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,067] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,067] [INFO] DQC Reference Directory: /var/lib/cwl/stgca1c5ed2-41ca-46b1-b213-e4a03153e59b/dqc_reference
[2024-01-24 13:40:36,404] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,405] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,406] [INFO] Running command: gunzip -c /var/lib/cwl/stg4053e6d4-643d-49ab-ba25-7e6cf9944483/GCF_030160975.1_ASM3016097v1_genomic.fna.gz | prodigal -d GCF_030160975.1_ASM3016097v1_genomic.fna/cds.fna -a GCF_030160975.1_ASM3016097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:48,258] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:48,258] [INFO] Task started: HMMsearch
[2024-01-24 13:40:48,258] [INFO] Running command: hmmsearch --tblout GCF_030160975.1_ASM3016097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca1c5ed2-41ca-46b1-b213-e4a03153e59b/dqc_reference/reference_markers.hmm GCF_030160975.1_ASM3016097v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:48,599] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:48,601] [INFO] Found 6/6 markers.
[2024-01-24 13:40:48,642] [INFO] Query marker FASTA was written to GCF_030160975.1_ASM3016097v1_genomic.fna/markers.fasta
[2024-01-24 13:40:48,642] [INFO] Task started: Blastn
[2024-01-24 13:40:48,642] [INFO] Running command: blastn -query GCF_030160975.1_ASM3016097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca1c5ed2-41ca-46b1-b213-e4a03153e59b/dqc_reference/reference_markers.fasta -out GCF_030160975.1_ASM3016097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:49,788] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:49,798] [INFO] Selected 12 target genomes.
[2024-01-24 13:40:49,798] [INFO] Target genome list was writen to GCF_030160975.1_ASM3016097v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:49,805] [INFO] Task started: fastANI
[2024-01-24 13:40:49,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg4053e6d4-643d-49ab-ba25-7e6cf9944483/GCF_030160975.1_ASM3016097v1_genomic.fna.gz --refList GCF_030160975.1_ASM3016097v1_genomic.fna/target_genomes.txt --output GCF_030160975.1_ASM3016097v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:04,375] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:04,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca1c5ed2-41ca-46b1-b213-e4a03153e59b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:04,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca1c5ed2-41ca-46b1-b213-e4a03153e59b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:04,388] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:04,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:04,388] [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 haplocladii	strain=NBRC 107714	GCA_007992175.1	1176176	1176176	type	True	99.9765	1359	1403	95	conclusive
Methylobacterium haplocladii	strain=DSM 24195	GCA_022179265.1	1176176	1176176	type	True	99.9498	1331	1403	95	conclusive
Methylobacterium brachythecii	strain=DSM 24105	GCA_014196345.1	1176177	1176177	type	True	84.5918	1003	1403	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	83.9315	881	1403	95	below_threshold
Methylobacterium gnaphalii	strain=NBRC 107716	GCA_007992215.1	1010610	1010610	type	True	83.8856	912	1403	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	82.1965	713	1403	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	81.982	872	1403	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	81.8169	864	1403	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	81.7904	838	1403	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	81.2289	740	1403	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_900113465.1	418223	418223	suspected-type	True	80.6222	754	1403	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	80.5876	769	1403	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:04,390] [INFO] DFAST Taxonomy check result was written to GCF_030160975.1_ASM3016097v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:04,391] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:04,391] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:04,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca1c5ed2-41ca-46b1-b213-e4a03153e59b/dqc_reference/checkm_data
[2024-01-24 13:41:04,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:04,444] [INFO] Task started: CheckM
[2024-01-24 13:41:04,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160975.1_ASM3016097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160975.1_ASM3016097v1_genomic.fna/checkm_input GCF_030160975.1_ASM3016097v1_genomic.fna/checkm_result
[2024-01-24 13:41:44,620] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:44,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,654] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:44,654] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:44,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160975.1_ASM3016097v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:44,656] [INFO] Task started: Blastn
[2024-01-24 13:41:44,656] [INFO] Running command: blastn -query GCF_030160975.1_ASM3016097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca1c5ed2-41ca-46b1-b213-e4a03153e59b/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160975.1_ASM3016097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:46,954] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:46,958] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:46,958] [INFO] Target genome list was writen to GCF_030160975.1_ASM3016097v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:46,969] [INFO] Task started: fastANI
[2024-01-24 13:41:46,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg4053e6d4-643d-49ab-ba25-7e6cf9944483/GCF_030160975.1_ASM3016097v1_genomic.fna.gz --refList GCF_030160975.1_ASM3016097v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160975.1_ASM3016097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:00,654] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:00,671] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:00,671] [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_007992175.1	s__Methylobacterium haplocladii	99.9765	1359	1403	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_008040035.1	s__Methylobacterium sp008040035	88.8232	1069	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196345.1	s__Methylobacterium brachythecii	84.604	1002	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992215.1	s__Methylobacterium gnaphalii	83.8974	910	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900234795.1	s__Methylobacterium extorquens	81.9833	870	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.03	96.19	0.88	0.73	17	-
GCF_008039875.1	s__Methylobacterium sp008039875	81.9668	833	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCF_008040045.1	s__Methylobacterium sp008040045	81.8206	819	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.17	0.85	0.85	3	-
GCF_003111705.1	s__Methylobacterium sp003111705	81.7607	874	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.28	97.28	0.88	0.88	3	-
GCF_001422885.1	s__Methylobacterium sp001422885	81.4445	795	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502455.1	s__Methylobacterium sp005502455	81.4143	808	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423265.1	s__Methylobacterium sp001423265	81.1101	741	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.73	0.95	0.94	3	-
GCF_014138435.1	s__Methylobacterium fujisawaense	80.7877	753	1403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.82	98.73	0.93	0.90	12	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:00,673] [INFO] GTDB search result was written to GCF_030160975.1_ASM3016097v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:00,673] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:00,676] [INFO] DFAST_QC result json was written to GCF_030160975.1_ASM3016097v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:00,677] [INFO] DFAST_QC completed!
[2024-01-24 13:42:00,677] [INFO] Total running time: 0h1m26s