[2023-03-15 10:21:47,929] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:47,929] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:47,929] [INFO] DQC Reference Directory: /var/lib/cwl/stge66d63bd-65de-4b9b-bfb5-7b2806f10ab3/dqc_reference
[2023-03-15 10:21:49,054] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:49,054] [INFO] Task started: Prodigal
[2023-03-15 10:21:49,054] [INFO] Running command: cat /var/lib/cwl/stgc1940155-35ee-4534-adf1-6633d41003cb/OceanDNA-b26667.fa | prodigal -d OceanDNA-b26667/cds.fna -a OceanDNA-b26667/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:22:25,122] [INFO] Task succeeded: Prodigal
[2023-03-15 10:22:25,122] [INFO] Task started: HMMsearch
[2023-03-15 10:22:25,122] [INFO] Running command: hmmsearch --tblout OceanDNA-b26667/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge66d63bd-65de-4b9b-bfb5-7b2806f10ab3/dqc_reference/reference_markers.hmm OceanDNA-b26667/protein.faa > /dev/null
[2023-03-15 10:22:25,388] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:22:25,388] [INFO] Found 6/6 markers.
[2023-03-15 10:22:25,429] [INFO] Query marker FASTA was written to OceanDNA-b26667/markers.fasta
[2023-03-15 10:22:25,429] [INFO] Task started: Blastn
[2023-03-15 10:22:25,429] [INFO] Running command: blastn -query OceanDNA-b26667/markers.fasta -db /var/lib/cwl/stge66d63bd-65de-4b9b-bfb5-7b2806f10ab3/dqc_reference/reference_markers.fasta -out OceanDNA-b26667/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:26,418] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:26,418] [INFO] Selected 9 target genomes.
[2023-03-15 10:22:26,419] [INFO] Target genome list was writen to OceanDNA-b26667/target_genomes.txt
[2023-03-15 10:22:26,424] [INFO] Task started: fastANI
[2023-03-15 10:22:26,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1940155-35ee-4534-adf1-6633d41003cb/OceanDNA-b26667.fa --refList OceanDNA-b26667/target_genomes.txt --output OceanDNA-b26667/fastani_result.tsv --threads 1
[2023-03-15 10:22:40,092] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:40,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge66d63bd-65de-4b9b-bfb5-7b2806f10ab3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:22:40,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge66d63bd-65de-4b9b-bfb5-7b2806f10ab3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:22:40,099] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:22:40,100] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:22:40,100] [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 tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	88.4832	1377	2027	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	88.3683	1395	2027	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	88.0573	1278	2027	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	87.8775	1331	2027	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	87.578	1271	2027	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_900113465.1	418223	418223	suspected-type	True	87.5203	1260	2027	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	87.0426	1285	2027	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	86.0398	1163	2027	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	82.6269	908	2027	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:22:40,100] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26667/tc_result.tsv
[2023-03-15 10:22:40,100] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:22:40,100] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:22:40,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge66d63bd-65de-4b9b-bfb5-7b2806f10ab3/dqc_reference/checkm_data
[2023-03-15 10:22:40,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:22:40,108] [INFO] Task started: CheckM
[2023-03-15 10:22:40,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26667/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26667/checkm_input OceanDNA-b26667/checkm_result
[2023-03-15 10:24:05,222] [INFO] Task succeeded: CheckM
[2023-03-15 10:24:05,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:24:05,226] [INFO] ===== Completeness check finished =====
[2023-03-15 10:24:05,226] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:24:05,226] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26667/markers.fasta)
[2023-03-15 10:24:05,228] [INFO] Task started: Blastn
[2023-03-15 10:24:05,228] [INFO] Running command: blastn -query OceanDNA-b26667/markers.fasta -db /var/lib/cwl/stge66d63bd-65de-4b9b-bfb5-7b2806f10ab3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26667/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:24:07,210] [INFO] Task succeeded: Blastn
[2023-03-15 10:24:07,210] [INFO] Selected 9 target genomes.
[2023-03-15 10:24:07,210] [INFO] Target genome list was writen to OceanDNA-b26667/target_genomes_gtdb.txt
[2023-03-15 10:24:07,651] [INFO] Task started: fastANI
[2023-03-15 10:24:07,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1940155-35ee-4534-adf1-6633d41003cb/OceanDNA-b26667.fa --refList OceanDNA-b26667/target_genomes_gtdb.txt --output OceanDNA-b26667/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:24:22,131] [INFO] Task succeeded: fastANI
[2023-03-15 10:24:22,137] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:24:22,138] [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
GCA_003096615.1	s__Methylobacterium organophilum	88.634	1359	2027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.99	98.85	0.91	0.88	18	-
GCF_014873335.1	s__Methylobacterium sp014873335	88.3385	1323	2027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009806555.1	s__Methylobacterium sp009806555	88.0016	1300	2027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833295.1	s__Methylobacterium sp017833295	87.9704	1350	2027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112625.1	s__Methylobacterium sp900112625	87.9063	1297	2027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_014138435.1	s__Methylobacterium fujisawaense	87.746	1277	2027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.82	98.73	0.93	0.90	12	-
GCF_900103195.1	s__Methylobacterium sp900103195	87.4476	1286	2027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
GCF_000364445.2	s__Methylobacterium mesophilicum	87.3949	1325	2027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697185.1	s__Methylobacterium brachiatum	86.4706	1251	2027	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.08	95.77	0.85	0.80	4	-
--------------------------------------------------------------------------------
[2023-03-15 10:24:22,138] [INFO] GTDB search result was written to OceanDNA-b26667/result_gtdb.tsv
[2023-03-15 10:24:22,138] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:24:22,139] [INFO] DFAST_QC result json was written to OceanDNA-b26667/dqc_result.json
[2023-03-15 10:24:22,139] [INFO] DFAST_QC completed!
[2023-03-15 10:24:22,139] [INFO] Total running time: 0h2m34s