[2024-01-24 11:12:54,970] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:54,973] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:54,973] [INFO] DQC Reference Directory: /var/lib/cwl/stgca408ada-7553-4d14-8e03-14bcead9c431/dqc_reference
[2024-01-24 11:12:56,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:56,259] [INFO] Task started: Prodigal
[2024-01-24 11:12:56,259] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbe4e8af-3c24-48ec-9913-8630010fc805/GCF_016613415.1_ASM1661341v1_genomic.fna.gz | prodigal -d GCF_016613415.1_ASM1661341v1_genomic.fna/cds.fna -a GCF_016613415.1_ASM1661341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:13,615] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:13,616] [INFO] Task started: HMMsearch
[2024-01-24 11:13:13,616] [INFO] Running command: hmmsearch --tblout GCF_016613415.1_ASM1661341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca408ada-7553-4d14-8e03-14bcead9c431/dqc_reference/reference_markers.hmm GCF_016613415.1_ASM1661341v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:13,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:13,980] [INFO] Found 6/6 markers.
[2024-01-24 11:13:14,048] [INFO] Query marker FASTA was written to GCF_016613415.1_ASM1661341v1_genomic.fna/markers.fasta
[2024-01-24 11:13:14,049] [INFO] Task started: Blastn
[2024-01-24 11:13:14,049] [INFO] Running command: blastn -query GCF_016613415.1_ASM1661341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca408ada-7553-4d14-8e03-14bcead9c431/dqc_reference/reference_markers.fasta -out GCF_016613415.1_ASM1661341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:15,213] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:15,216] [INFO] Selected 13 target genomes.
[2024-01-24 11:13:15,216] [INFO] Target genome list was writen to GCF_016613415.1_ASM1661341v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:15,221] [INFO] Task started: fastANI
[2024-01-24 11:13:15,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbe4e8af-3c24-48ec-9913-8630010fc805/GCF_016613415.1_ASM1661341v1_genomic.fna.gz --refList GCF_016613415.1_ASM1661341v1_genomic.fna/target_genomes.txt --output GCF_016613415.1_ASM1661341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:42,781] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:42,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca408ada-7553-4d14-8e03-14bcead9c431/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:42,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca408ada-7553-4d14-8e03-14bcead9c431/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:42,793] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:42,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:42,794] [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 ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	100.0	2159	2172	95	conclusive
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	92.9945	1554	2172	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	90.455	1736	2172	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	90.4074	1618	2172	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	90.3664	1563	2172	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	90.3006	1440	2172	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	89.7644	1617	2172	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	89.7378	1440	2172	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	89.7297	1613	2172	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	89.6408	1590	2172	95	below_threshold
Methylobacterium aquaticum	strain=DSM 16371	GCA_001043915.1	270351	270351	type	True	88.9696	1473	2172	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	84.755	1386	2172	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	84.6852	1322	2172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:42,795] [INFO] DFAST Taxonomy check result was written to GCF_016613415.1_ASM1661341v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:42,796] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:42,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:42,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca408ada-7553-4d14-8e03-14bcead9c431/dqc_reference/checkm_data
[2024-01-24 11:13:42,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:42,861] [INFO] Task started: CheckM
[2024-01-24 11:13:42,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016613415.1_ASM1661341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016613415.1_ASM1661341v1_genomic.fna/checkm_input GCF_016613415.1_ASM1661341v1_genomic.fna/checkm_result
[2024-01-24 11:14:32,490] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:32,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:32,509] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:32,510] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:32,510] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016613415.1_ASM1661341v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:32,510] [INFO] Task started: Blastn
[2024-01-24 11:14:32,511] [INFO] Running command: blastn -query GCF_016613415.1_ASM1661341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca408ada-7553-4d14-8e03-14bcead9c431/dqc_reference/reference_markers_gtdb.fasta -out GCF_016613415.1_ASM1661341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:34,755] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:34,759] [INFO] Selected 12 target genomes.
[2024-01-24 11:14:34,760] [INFO] Target genome list was writen to GCF_016613415.1_ASM1661341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:34,781] [INFO] Task started: fastANI
[2024-01-24 11:14:34,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbe4e8af-3c24-48ec-9913-8630010fc805/GCF_016613415.1_ASM1661341v1_genomic.fna.gz --refList GCF_016613415.1_ASM1661341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016613415.1_ASM1661341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:01,563] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:01,581] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:01,581] [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_016613415.1	s__Methylobacterium ajmalii	100.0	2159	2172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.55	96.20	0.90	0.83	5	conclusive
GCF_001043895.1	s__Methylobacterium indicum	92.9969	1552	2172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.73	98.07	0.88	0.87	6	-
GCF_003058325.1	s__Methylobacterium currus	90.46	1737	2172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653715.1	s__Methylobacterium platani	90.399	1619	2172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.94	99.94	0.97	0.97	2	-
GCF_003173755.1	s__Methylobacterium terrae	90.356	1565	2172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016804325.1	s__Methylobacterium aquaticum_C	90.1745	1639	2172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043735.1	s__Methylobacterium sp011043735	90.155	1716	2172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019216885.1	s__Methylobacterium sp019216885	90.0379	1653	2172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173775.1	s__Methylobacterium sp003173775	90.0018	1600	2172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCF_006151805.1	s__Methylobacterium sp006151805	89.7631	1618	2172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043955.1	s__Methylobacterium tarhaniae	89.7371	1441	2172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745635.1	s__Methylobacterium sp004745635	89.6424	1590	2172	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 11:15:01,583] [INFO] GTDB search result was written to GCF_016613415.1_ASM1661341v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:01,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:01,589] [INFO] DFAST_QC result json was written to GCF_016613415.1_ASM1661341v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:01,589] [INFO] DFAST_QC completed!
[2024-01-24 11:15:01,589] [INFO] Total running time: 0h2m7s