[2024-01-24 14:05:53,144] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,149] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg0372bdec-41be-4bbd-b29d-1f2475c4b56b/dqc_reference
[2024-01-24 14:05:54,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:54,488] [INFO] Task started: Prodigal
[2024-01-24 14:05:54,489] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe92638e-6c27-46d5-b8b4-745b8d9292e6/GCF_019703875.1_ASM1970387v1_genomic.fna.gz | prodigal -d GCF_019703875.1_ASM1970387v1_genomic.fna/cds.fna -a GCF_019703875.1_ASM1970387v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:03,038] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:03,038] [INFO] Task started: HMMsearch
[2024-01-24 14:06:03,038] [INFO] Running command: hmmsearch --tblout GCF_019703875.1_ASM1970387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0372bdec-41be-4bbd-b29d-1f2475c4b56b/dqc_reference/reference_markers.hmm GCF_019703875.1_ASM1970387v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:03,329] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:03,330] [INFO] Found 6/6 markers.
[2024-01-24 14:06:03,359] [INFO] Query marker FASTA was written to GCF_019703875.1_ASM1970387v1_genomic.fna/markers.fasta
[2024-01-24 14:06:03,360] [INFO] Task started: Blastn
[2024-01-24 14:06:03,360] [INFO] Running command: blastn -query GCF_019703875.1_ASM1970387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0372bdec-41be-4bbd-b29d-1f2475c4b56b/dqc_reference/reference_markers.fasta -out GCF_019703875.1_ASM1970387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:04,080] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:04,083] [INFO] Selected 15 target genomes.
[2024-01-24 14:06:04,083] [INFO] Target genome list was writen to GCF_019703875.1_ASM1970387v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:04,135] [INFO] Task started: fastANI
[2024-01-24 14:06:04,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe92638e-6c27-46d5-b8b4-745b8d9292e6/GCF_019703875.1_ASM1970387v1_genomic.fna.gz --refList GCF_019703875.1_ASM1970387v1_genomic.fna/target_genomes.txt --output GCF_019703875.1_ASM1970387v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:12,471] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:12,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0372bdec-41be-4bbd-b29d-1f2475c4b56b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:12,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0372bdec-41be-4bbd-b29d-1f2475c4b56b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:12,482] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:12,482] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:12,482] [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
Methyloradius palustris	strain=Zm11	GCA_019703875.1	2778876	2778876	type	True	100.0	932	933	95	conclusive
Methylobacillus flagellatus	strain=KT	GCA_000013705.1	405	405	type	True	77.7107	70	933	95	below_threshold
Methylobacillus gramineus	strain=VKM B-2591	GCA_020532675.1	755169	755169	type	True	77.4263	114	933	95	below_threshold
Methylovorus menthalis	strain=VKM B-2663	GCA_020523625.1	1002227	1002227	type	True	77.3457	151	933	95	below_threshold
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	77.3335	90	933	95	below_threshold
Methylovorus glucosotrophus	strain=DSM 6874	GCA_009858335.1	266009	266009	type	True	77.2527	167	933	95	below_threshold
Methylovorus mays	strain=VKM B-2221	GCA_020531915.1	184077	184077	type	True	77.123	162	933	95	below_threshold
Methylotenera oryzisoli	strain=La3113	GCA_004661485.1	2080758	2080758	type	True	76.9925	88	933	95	below_threshold
Methylotenera mobilis	strain=JLW8	GCA_000023705.1	359408	359408	type	True	76.894	104	933	95	below_threshold
Methylobacillus arboreus	strain=VKM B-2590	GCA_020532725.1	755170	755170	type	True	76.8628	103	933	95	below_threshold
Methylophilus methylotrophus	strain=ATCC 53528	GCA_000378225.1	17	17	type	True	76.7298	89	933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:12,484] [INFO] DFAST Taxonomy check result was written to GCF_019703875.1_ASM1970387v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:12,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:12,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:12,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0372bdec-41be-4bbd-b29d-1f2475c4b56b/dqc_reference/checkm_data
[2024-01-24 14:06:12,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:12,516] [INFO] Task started: CheckM
[2024-01-24 14:06:12,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019703875.1_ASM1970387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019703875.1_ASM1970387v1_genomic.fna/checkm_input GCF_019703875.1_ASM1970387v1_genomic.fna/checkm_result
[2024-01-24 14:06:43,935] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:43,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:43,971] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:43,972] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:43,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019703875.1_ASM1970387v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:43,973] [INFO] Task started: Blastn
[2024-01-24 14:06:43,973] [INFO] Running command: blastn -query GCF_019703875.1_ASM1970387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0372bdec-41be-4bbd-b29d-1f2475c4b56b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019703875.1_ASM1970387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:44,974] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:44,978] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:44,978] [INFO] Target genome list was writen to GCF_019703875.1_ASM1970387v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:45,009] [INFO] Task started: fastANI
[2024-01-24 14:06:45,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe92638e-6c27-46d5-b8b4-745b8d9292e6/GCF_019703875.1_ASM1970387v1_genomic.fna.gz --refList GCF_019703875.1_ASM1970387v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019703875.1_ASM1970387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:54,165] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:54,183] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:06:54,183] [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_001648895.1	s__MM1 sp001648895	78.1167	191	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__MM1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953015.1	s__Methylopumilus_A turicensis	78.0242	89	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013705.1	s__Methylobacillus flagellatus	77.6875	70	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	97.96	97.96	0.89	0.89	2	-
GCA_903909015.1	s__Methylopumilus_A sp903909015	77.6509	55	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	98.79	98.38	0.84	0.83	5	-
GCA_902168195.1	s__CABHOJ01 sp902168195	77.3869	54	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__CABHOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730115.1	s__Pseudomethylobacillus aquaticus	77.3664	89	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903899965.1	s__Methylopumilus_A sp903899965	77.3154	89	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	98.90	98.39	0.92	0.86	12	-
GCF_009858335.1	s__Methylovorus glucosotrophus	77.2355	168	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylovorus	95.0	97.11	97.01	0.92	0.92	3	-
GCA_002281815.1	s__Methylotenera sp002281815	77.2182	79	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	99.58	99.54	0.87	0.85	3	-
GCF_006363955.1	s__Methylophilus medardicus	77.1499	64	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	100.00	100.00	1.00	1.00	3	-
GCA_000525025.1	s__Methylophilus sp000525025	77.0508	93	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	98.40	98.39	0.92	0.91	3	-
GCF_000617925.1	s__Methylobacillus glycogenes	76.9894	128	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004661485.1	s__Methylotenera sp004661485	76.9635	89	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187985.1	s__Methylobacillus rhizosphaerae	76.9416	91	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023705.1	s__Methylotenera mobilis	76.9199	102	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880825.1	s__JADGRN01 sp017880825	76.7771	66	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__JADGRN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378225.1	s__Methylophilus methylotrophus	76.7262	88	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	96.53	96.51	0.88	0.88	3	-
GCA_001803395.1	s__Methylotenera sp001803395	76.6334	82	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842285.1	s__Methylotenera sp002842285	76.6055	61	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870995.1	s__Methylopumilus_A sp903870995	76.4363	79	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	99.94	99.94	0.97	0.96	3	-
GCA_002281475.1	s__Methylophilus sp002281475	76.3611	61	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	99.39	99.39	0.85	0.85	2	-
GCA_001464125.1	s__Methylophilus sp001464125	76.2088	79	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:54,185] [INFO] GTDB search result was written to GCF_019703875.1_ASM1970387v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:54,185] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:54,189] [INFO] DFAST_QC result json was written to GCF_019703875.1_ASM1970387v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:54,189] [INFO] DFAST_QC completed!
[2024-01-24 14:06:54,190] [INFO] Total running time: 0h1m1s