[2023-03-14 11:14:12,763] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,764] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg6eba8131-4f94-4497-bab0-4e6ea8203c31/dqc_reference
[2023-03-14 11:14:14,233] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,234] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,234] [INFO] Running command: cat /var/lib/cwl/stg4a22975c-e0a5-4995-8248-2f7e83deebf3/OceanDNA-b26664.fa | prodigal -d OceanDNA-b26664/cds.fna -a OceanDNA-b26664/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:28,130] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:28,130] [INFO] Task started: HMMsearch
[2023-03-14 11:14:28,130] [INFO] Running command: hmmsearch --tblout OceanDNA-b26664/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6eba8131-4f94-4497-bab0-4e6ea8203c31/dqc_reference/reference_markers.hmm OceanDNA-b26664/protein.faa > /dev/null
[2023-03-14 11:14:28,409] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:28,409] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg4a22975c-e0a5-4995-8248-2f7e83deebf3/OceanDNA-b26664.fa]
[2023-03-14 11:14:28,426] [INFO] Query marker FASTA was written to OceanDNA-b26664/markers.fasta
[2023-03-14 11:14:28,427] [INFO] Task started: Blastn
[2023-03-14 11:14:28,427] [INFO] Running command: blastn -query OceanDNA-b26664/markers.fasta -db /var/lib/cwl/stg6eba8131-4f94-4497-bab0-4e6ea8203c31/dqc_reference/reference_markers.fasta -out OceanDNA-b26664/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:28,992] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:28,993] [INFO] Selected 13 target genomes.
[2023-03-14 11:14:28,994] [INFO] Target genome list was writen to OceanDNA-b26664/target_genomes.txt
[2023-03-14 11:14:29,005] [INFO] Task started: fastANI
[2023-03-14 11:14:29,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a22975c-e0a5-4995-8248-2f7e83deebf3/OceanDNA-b26664.fa --refList OceanDNA-b26664/target_genomes.txt --output OceanDNA-b26664/fastani_result.tsv --threads 1
[2023-03-14 11:14:43,317] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:43,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6eba8131-4f94-4497-bab0-4e6ea8203c31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:43,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6eba8131-4f94-4497-bab0-4e6ea8203c31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:43,327] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:43,327] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:14:43,328] [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
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	86.4824	657	773	95	below_threshold
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	82.8298	576	773	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	76.7446	313	773	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.6848	324	773	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	76.6329	344	773	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	76.5566	163	773	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	76.5302	253	773	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	76.4952	239	773	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	76.4392	312	773	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.4174	268	773	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.3513	264	773	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	76.3508	285	773	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	76.2324	256	773	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:43,328] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26664/tc_result.tsv
[2023-03-14 11:14:43,328] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:43,328] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:43,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6eba8131-4f94-4497-bab0-4e6ea8203c31/dqc_reference/checkm_data
[2023-03-14 11:14:43,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:43,341] [INFO] Task started: CheckM
[2023-03-14 11:14:43,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26664/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26664/checkm_input OceanDNA-b26664/checkm_result
[2023-03-14 11:15:19,876] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:19,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:19,879] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:19,879] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:19,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26664/markers.fasta)
[2023-03-14 11:15:19,880] [INFO] Task started: Blastn
[2023-03-14 11:15:19,881] [INFO] Running command: blastn -query OceanDNA-b26664/markers.fasta -db /var/lib/cwl/stg6eba8131-4f94-4497-bab0-4e6ea8203c31/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26664/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:20,656] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:20,656] [INFO] Selected 11 target genomes.
[2023-03-14 11:15:20,656] [INFO] Target genome list was writen to OceanDNA-b26664/target_genomes_gtdb.txt
[2023-03-14 11:15:20,672] [INFO] Task started: fastANI
[2023-03-14 11:15:20,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a22975c-e0a5-4995-8248-2f7e83deebf3/OceanDNA-b26664.fa --refList OceanDNA-b26664/target_genomes_gtdb.txt --output OceanDNA-b26664/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:29,772] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:29,779] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:15:29,779] [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_004137085.1	s__Lichenihabitans ramalinae	86.4516	659	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137685.1	s__Lichenihabitans minor	82.7838	580	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901457705.2	s__RH-AL1 sp901457705	76.6261	219	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__RH-AL1	95.0	99.94	99.94	0.99	0.99	3	-
GCF_002741015.1	s__Microvirga ossetica	76.5578	163	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716745.1	s__GCA-013693735 sp016716745	76.5416	247	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645695.1	s__Salinarimonas ramus	76.4604	242	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004323635.1	s__Lichenihabitans psoromatis	76.4369	188	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	97.95	97.95	0.93	0.93	2	-
GCA_016793505.1	s__GCA-013693735 sp016793505	76.4124	231	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903644085.1	s__Enterovirga sp903644085	76.4068	153	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Enterovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164915.1	s__Roseiarcus sp003164915	75.9744	153	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Roseiarcus	95.0	99.60	99.60	0.89	0.89	2	-
GCF_900114285.1	s__Methylocella palsarum	75.8117	69	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:29,779] [INFO] GTDB search result was written to OceanDNA-b26664/result_gtdb.tsv
[2023-03-14 11:15:29,779] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:29,780] [INFO] DFAST_QC result json was written to OceanDNA-b26664/dqc_result.json
[2023-03-14 11:15:29,781] [INFO] DFAST_QC completed!
[2023-03-14 11:15:29,781] [INFO] Total running time: 0h1m17s