[2023-03-17 00:45:47,184] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,184] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,184] [INFO] DQC Reference Directory: /var/lib/cwl/stgefbd6aaa-73c2-4382-a95d-00e3c03471ea/dqc_reference
[2023-03-17 00:45:48,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,352] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,353] [INFO] Running command: cat /var/lib/cwl/stg76cc3143-af3f-4d58-98d7-dfb1878c04fa/OceanDNA-b24798.fa | prodigal -d OceanDNA-b24798/cds.fna -a OceanDNA-b24798/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:13,449] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:13,450] [INFO] Task started: HMMsearch
[2023-03-17 00:46:13,450] [INFO] Running command: hmmsearch --tblout OceanDNA-b24798/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefbd6aaa-73c2-4382-a95d-00e3c03471ea/dqc_reference/reference_markers.hmm OceanDNA-b24798/protein.faa > /dev/null
[2023-03-17 00:46:13,653] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:13,654] [INFO] Found 6/6 markers.
[2023-03-17 00:46:13,679] [INFO] Query marker FASTA was written to OceanDNA-b24798/markers.fasta
[2023-03-17 00:46:13,680] [INFO] Task started: Blastn
[2023-03-17 00:46:13,680] [INFO] Running command: blastn -query OceanDNA-b24798/markers.fasta -db /var/lib/cwl/stgefbd6aaa-73c2-4382-a95d-00e3c03471ea/dqc_reference/reference_markers.fasta -out OceanDNA-b24798/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:14,474] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:14,475] [INFO] Selected 14 target genomes.
[2023-03-17 00:46:14,475] [INFO] Target genome list was writen to OceanDNA-b24798/target_genomes.txt
[2023-03-17 00:46:14,485] [INFO] Task started: fastANI
[2023-03-17 00:46:14,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg76cc3143-af3f-4d58-98d7-dfb1878c04fa/OceanDNA-b24798.fa --refList OceanDNA-b24798/target_genomes.txt --output OceanDNA-b24798/fastani_result.tsv --threads 1
[2023-03-17 00:46:27,904] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:27,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefbd6aaa-73c2-4382-a95d-00e3c03471ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:27,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefbd6aaa-73c2-4382-a95d-00e3c03471ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:27,913] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:27,913] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:46:27,913] [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
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	86.6659	1128	1363	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	86.1758	1091	1363	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	81.6378	954	1363	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	81.3673	875	1363	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.4267	400	1363	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	77.1535	251	1363	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.1501	133	1363	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.0958	143	1363	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.0944	128	1363	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.9521	195	1363	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	75.9166	90	1363	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.9151	113	1363	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	75.8951	118	1363	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	75.8829	119	1363	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:46:27,914] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24798/tc_result.tsv
[2023-03-17 00:46:27,914] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:27,914] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:27,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefbd6aaa-73c2-4382-a95d-00e3c03471ea/dqc_reference/checkm_data
[2023-03-17 00:46:27,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:27,921] [INFO] Task started: CheckM
[2023-03-17 00:46:27,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24798/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24798/checkm_input OceanDNA-b24798/checkm_result
[2023-03-17 00:47:29,672] [INFO] Task succeeded: CheckM
[2023-03-17 00:47:29,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:47:29,675] [INFO] ===== Completeness check finished =====
[2023-03-17 00:47:29,676] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:47:29,676] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24798/markers.fasta)
[2023-03-17 00:47:29,677] [INFO] Task started: Blastn
[2023-03-17 00:47:29,677] [INFO] Running command: blastn -query OceanDNA-b24798/markers.fasta -db /var/lib/cwl/stgefbd6aaa-73c2-4382-a95d-00e3c03471ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24798/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:47:31,194] [INFO] Task succeeded: Blastn
[2023-03-17 00:47:31,195] [INFO] Selected 11 target genomes.
[2023-03-17 00:47:31,195] [INFO] Target genome list was writen to OceanDNA-b24798/target_genomes_gtdb.txt
[2023-03-17 00:47:31,409] [INFO] Task started: fastANI
[2023-03-17 00:47:31,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg76cc3143-af3f-4d58-98d7-dfb1878c04fa/OceanDNA-b24798.fa --refList OceanDNA-b24798/target_genomes_gtdb.txt --output OceanDNA-b24798/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:40,892] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:40,899] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:47:40,899] [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_000426505.1	s__Nisaea denitrificans	86.6465	1130	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904795.1	s__Nisaea nitritireducens	86.1825	1090	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	81.6418	914	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	81.6389	954	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	77.8415	367	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	77.4425	398	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203465.1	s__JABMNR01 sp013203465	77.0232	209	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JABMNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780745.1	s__JADHLJ01 sp016780745	76.8162	165	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JADHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961745.1	s__BRH-c57 sp000961745	76.2493	87	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__BRH-c57	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040035.1	s__Methylobacterium sp008040035	76.0715	93	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811235.1	s__Microvirga arabica	75.9196	90	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:47:40,899] [INFO] GTDB search result was written to OceanDNA-b24798/result_gtdb.tsv
[2023-03-17 00:47:40,899] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:40,901] [INFO] DFAST_QC result json was written to OceanDNA-b24798/dqc_result.json
[2023-03-17 00:47:40,901] [INFO] DFAST_QC completed!
[2023-03-17 00:47:40,901] [INFO] Total running time: 0h1m54s