[2024-01-24 12:21:43,472] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:43,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:43,474] [INFO] DQC Reference Directory: /var/lib/cwl/stgef5dd35a-e6e2-493a-a291-4a90c90c29be/dqc_reference
[2024-01-24 12:21:44,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:44,805] [INFO] Task started: Prodigal
[2024-01-24 12:21:44,805] [INFO] Running command: gunzip -c /var/lib/cwl/stg144604c6-f872-46f3-8553-5787d2e603c7/GCF_000093025.1_ASM9302v1_genomic.fna.gz | prodigal -d GCF_000093025.1_ASM9302v1_genomic.fna/cds.fna -a GCF_000093025.1_ASM9302v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:52,538] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:52,538] [INFO] Task started: HMMsearch
[2024-01-24 12:21:52,538] [INFO] Running command: hmmsearch --tblout GCF_000093025.1_ASM9302v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef5dd35a-e6e2-493a-a291-4a90c90c29be/dqc_reference/reference_markers.hmm GCF_000093025.1_ASM9302v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:52,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:52,854] [INFO] Found 6/6 markers.
[2024-01-24 12:21:52,883] [INFO] Query marker FASTA was written to GCF_000093025.1_ASM9302v1_genomic.fna/markers.fasta
[2024-01-24 12:21:52,883] [INFO] Task started: Blastn
[2024-01-24 12:21:52,883] [INFO] Running command: blastn -query GCF_000093025.1_ASM9302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef5dd35a-e6e2-493a-a291-4a90c90c29be/dqc_reference/reference_markers.fasta -out GCF_000093025.1_ASM9302v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:53,551] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:53,555] [INFO] Selected 19 target genomes.
[2024-01-24 12:21:53,556] [INFO] Target genome list was writen to GCF_000093025.1_ASM9302v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:53,564] [INFO] Task started: fastANI
[2024-01-24 12:21:53,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg144604c6-f872-46f3-8553-5787d2e603c7/GCF_000093025.1_ASM9302v1_genomic.fna.gz --refList GCF_000093025.1_ASM9302v1_genomic.fna/target_genomes.txt --output GCF_000093025.1_ASM9302v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:03,018] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:03,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef5dd35a-e6e2-493a-a291-4a90c90c29be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:03,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef5dd35a-e6e2-493a-a291-4a90c90c29be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:03,025] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:03,025] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:03,025] [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
Methylotenera versatilis	strain=301	GCA_000093025.1	1055487	1055487	type	True	100.0	1018	1019	95	conclusive
Methylotenera mobilis	strain=JLW8	GCA_000023705.1	359408	359408	type	True	78.2931	210	1019	95	below_threshold
Methylotenera oryzisoli	strain=La3113	GCA_004661485.1	2080758	2080758	type	True	78.2331	226	1019	95	below_threshold
Methylophilus methylotrophus	strain=ATCC 53528	GCA_000378225.1	17	17	type	True	76.8421	64	1019	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:03,029] [INFO] DFAST Taxonomy check result was written to GCF_000093025.1_ASM9302v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:03,031] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:03,031] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:03,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef5dd35a-e6e2-493a-a291-4a90c90c29be/dqc_reference/checkm_data
[2024-01-24 12:22:03,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:03,070] [INFO] Task started: CheckM
[2024-01-24 12:22:03,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000093025.1_ASM9302v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000093025.1_ASM9302v1_genomic.fna/checkm_input GCF_000093025.1_ASM9302v1_genomic.fna/checkm_result
[2024-01-24 12:22:32,850] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:32,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:32,868] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:32,869] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:32,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000093025.1_ASM9302v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:32,870] [INFO] Task started: Blastn
[2024-01-24 12:22:32,870] [INFO] Running command: blastn -query GCF_000093025.1_ASM9302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef5dd35a-e6e2-493a-a291-4a90c90c29be/dqc_reference/reference_markers_gtdb.fasta -out GCF_000093025.1_ASM9302v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:33,971] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:33,986] [INFO] Selected 15 target genomes.
[2024-01-24 12:22:33,986] [INFO] Target genome list was writen to GCF_000093025.1_ASM9302v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:34,040] [INFO] Task started: fastANI
[2024-01-24 12:22:34,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg144604c6-f872-46f3-8553-5787d2e603c7/GCF_000093025.1_ASM9302v1_genomic.fna.gz --refList GCF_000093025.1_ASM9302v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000093025.1_ASM9302v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:41,513] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:41,527] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:41,527] [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_000093025.1	s__Methylotenera versatilis	100.0	1017	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013141425.1	s__Methylotenera sp013141425	79.694	357	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141075.1	s__Methylotenera sp013141075	79.6022	317	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	97.66	97.66	0.85	0.85	2	-
GCA_903833595.1	s__Methylotenera sp903833595	78.783	223	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	97.98	97.98	0.85	0.85	2	-
GCA_903846555.1	s__Methylotenera sp903846555	78.7673	265	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384255.1	s__Methylotenera mobilis_B	78.7631	228	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	98.82	98.20	0.90	0.84	5	-
GCA_009693255.1	s__Methylotenera sp009693255	78.7127	213	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	99.85	99.85	0.93	0.93	2	-
GCF_000744605.1	s__Methylotenera sp000744605	78.7051	223	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903854305.1	s__Methylotenera sp903854305	78.5985	239	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903926935.1	s__Methylotenera sp903926935	78.4749	234	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141495.1	s__Methylotenera sp013141495	78.2745	236	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	98.86	98.86	0.96	0.96	2	-
GCF_000799735.1	s__Methylotenera sp000799735	78.1873	132	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001803395.1	s__Methylotenera sp001803395	78.1728	237	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140755.1	s__Methylotenera sp013140755	77.9919	209	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005791685.1	s__Methylotenera sp005791685	77.3684	106	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	99.44	99.44	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:41,529] [INFO] GTDB search result was written to GCF_000093025.1_ASM9302v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:41,530] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:41,534] [INFO] DFAST_QC result json was written to GCF_000093025.1_ASM9302v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:41,535] [INFO] DFAST_QC completed!
[2024-01-24 12:22:41,535] [INFO] Total running time: 0h0m58s