[2024-01-24 12:31:58,407] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,410] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,410] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc666738-e056-420b-9d30-40e799b6f4db/dqc_reference
[2024-01-24 12:31:59,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:59,858] [INFO] Task started: Prodigal
[2024-01-24 12:31:59,858] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bcff648-c3cc-486c-ae95-1e3f377fd801/GCF_022179065.1_ASM2217906v1_genomic.fna.gz | prodigal -d GCF_022179065.1_ASM2217906v1_genomic.fna/cds.fna -a GCF_022179065.1_ASM2217906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:13,286] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:13,286] [INFO] Task started: HMMsearch
[2024-01-24 12:32:13,286] [INFO] Running command: hmmsearch --tblout GCF_022179065.1_ASM2217906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc666738-e056-420b-9d30-40e799b6f4db/dqc_reference/reference_markers.hmm GCF_022179065.1_ASM2217906v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:13,622] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:13,624] [INFO] Found 6/6 markers.
[2024-01-24 12:32:13,669] [INFO] Query marker FASTA was written to GCF_022179065.1_ASM2217906v1_genomic.fna/markers.fasta
[2024-01-24 12:32:13,669] [INFO] Task started: Blastn
[2024-01-24 12:32:13,669] [INFO] Running command: blastn -query GCF_022179065.1_ASM2217906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc666738-e056-420b-9d30-40e799b6f4db/dqc_reference/reference_markers.fasta -out GCF_022179065.1_ASM2217906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:14,746] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:14,750] [INFO] Selected 11 target genomes.
[2024-01-24 12:32:14,750] [INFO] Target genome list was writen to GCF_022179065.1_ASM2217906v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:14,754] [INFO] Task started: fastANI
[2024-01-24 12:32:14,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bcff648-c3cc-486c-ae95-1e3f377fd801/GCF_022179065.1_ASM2217906v1_genomic.fna.gz --refList GCF_022179065.1_ASM2217906v1_genomic.fna/target_genomes.txt --output GCF_022179065.1_ASM2217906v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:28,189] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:28,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc666738-e056-420b-9d30-40e799b6f4db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:28,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc666738-e056-420b-9d30-40e799b6f4db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:28,199] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:28,200] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:28,200] [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 adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	100.0	1523	1527	95	conclusive
Methylobacterium gossipiicola	strain=Gh-105	GCA_900113485.1	582675	582675	type	True	88.4609	1123	1527	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	83.4566	973	1527	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	82.5665	923	1527	95	below_threshold
Methylobacterium bullatum	strain=LMG 24788	GCA_014845095.1	570505	570505	type	True	82.4567	856	1527	95	below_threshold
Methylobacterium marchantiae	strain=DSM 21328	GCA_022179405.1	600331	600331	type	True	82.2814	907	1527	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	81.8737	831	1527	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	81.5401	919	1527	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	81.4532	734	1527	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	81.1777	919	1527	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	80.2582	814	1527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:28,202] [INFO] DFAST Taxonomy check result was written to GCF_022179065.1_ASM2217906v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:28,203] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:28,203] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:28,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc666738-e056-420b-9d30-40e799b6f4db/dqc_reference/checkm_data
[2024-01-24 12:32:28,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:28,251] [INFO] Task started: CheckM
[2024-01-24 12:32:28,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022179065.1_ASM2217906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022179065.1_ASM2217906v1_genomic.fna/checkm_input GCF_022179065.1_ASM2217906v1_genomic.fna/checkm_result
[2024-01-24 12:33:10,139] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:10,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:10,162] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:10,163] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:10,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022179065.1_ASM2217906v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:10,164] [INFO] Task started: Blastn
[2024-01-24 12:33:10,164] [INFO] Running command: blastn -query GCF_022179065.1_ASM2217906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc666738-e056-420b-9d30-40e799b6f4db/dqc_reference/reference_markers_gtdb.fasta -out GCF_022179065.1_ASM2217906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:12,282] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:12,286] [INFO] Selected 11 target genomes.
[2024-01-24 12:33:12,286] [INFO] Target genome list was writen to GCF_022179065.1_ASM2217906v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:12,295] [INFO] Task started: fastANI
[2024-01-24 12:33:12,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bcff648-c3cc-486c-ae95-1e3f377fd801/GCF_022179065.1_ASM2217906v1_genomic.fna.gz --refList GCF_022179065.1_ASM2217906v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022179065.1_ASM2217906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:24,734] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:24,746] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:33:24,746] [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_900113485.1	s__Methylobacterium gossipiicola	88.4658	1123	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422375.1	s__Methylobacterium sp001422375	87.8002	1165	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.25	0.90	0.90	2	-
GCF_001423295.1	s__Methylobacterium sp001423295	87.0349	1151	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.75	98.70	0.92	0.92	5	-
GCF_001424705.1	s__Methylobacterium sp001424705	83.7713	1041	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.56	98.52	0.92	0.91	5	-
GCF_001422885.1	s__Methylobacterium sp001422885	83.6338	1027	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217615.1	s__Methylobacterium sp003217615	83.3831	1028	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010692745.1	s__Methylobacterium sp010692745	83.3451	972	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423085.1	s__Methylobacterium sp001423085	83.3221	1027	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.83	97.83	0.87	0.87	2	-
GCF_001423265.1	s__Methylobacterium sp001423265	82.4781	905	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.73	0.95	0.94	3	-
GCF_000372825.1	s__Methylobacterium sp000372825	82.3504	900	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004004555.2	s__Methylobacterium sp004004555	80.2777	810	1527	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 12:33:24,752] [INFO] GTDB search result was written to GCF_022179065.1_ASM2217906v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:24,752] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:24,756] [INFO] DFAST_QC result json was written to GCF_022179065.1_ASM2217906v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:24,756] [INFO] DFAST_QC completed!
[2024-01-24 12:33:24,756] [INFO] Total running time: 0h1m26s