[2023-03-15 22:48:49,185] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:48:49,185] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:48:49,185] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e917f15-2272-4151-8657-584a5f53ea77/dqc_reference
[2023-03-15 22:48:50,300] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:48:50,300] [INFO] Task started: Prodigal
[2023-03-15 22:48:50,300] [INFO] Running command: cat /var/lib/cwl/stg46296112-885f-4d4d-a48e-251d259699a2/OceanDNA-b32900.fa | prodigal -d OceanDNA-b32900/cds.fna -a OceanDNA-b32900/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:49:07,351] [INFO] Task succeeded: Prodigal
[2023-03-15 22:49:07,351] [INFO] Task started: HMMsearch
[2023-03-15 22:49:07,351] [INFO] Running command: hmmsearch --tblout OceanDNA-b32900/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e917f15-2272-4151-8657-584a5f53ea77/dqc_reference/reference_markers.hmm OceanDNA-b32900/protein.faa > /dev/null
[2023-03-15 22:49:07,532] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:49:07,533] [INFO] Found 6/6 markers.
[2023-03-15 22:49:07,552] [INFO] Query marker FASTA was written to OceanDNA-b32900/markers.fasta
[2023-03-15 22:49:07,553] [INFO] Task started: Blastn
[2023-03-15 22:49:07,554] [INFO] Running command: blastn -query OceanDNA-b32900/markers.fasta -db /var/lib/cwl/stg1e917f15-2272-4151-8657-584a5f53ea77/dqc_reference/reference_markers.fasta -out OceanDNA-b32900/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:49:08,222] [INFO] Task succeeded: Blastn
[2023-03-15 22:49:08,223] [INFO] Selected 31 target genomes.
[2023-03-15 22:49:08,223] [INFO] Target genome list was writen to OceanDNA-b32900/target_genomes.txt
[2023-03-15 22:49:08,253] [INFO] Task started: fastANI
[2023-03-15 22:49:08,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg46296112-885f-4d4d-a48e-251d259699a2/OceanDNA-b32900.fa --refList OceanDNA-b32900/target_genomes.txt --output OceanDNA-b32900/fastani_result.tsv --threads 1
[2023-03-15 22:49:28,365] [INFO] Task succeeded: fastANI
[2023-03-15 22:49:28,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e917f15-2272-4151-8657-584a5f53ea77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:49:28,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e917f15-2272-4151-8657-584a5f53ea77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:49:28,370] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:49:28,371] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:49:28,371] [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
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.9842	54	910	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.8567	50	910	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.8412	58	910	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.8228	65	910	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.5157	57	910	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.4631	56	910	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:49:28,371] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32900/tc_result.tsv
[2023-03-15 22:49:28,371] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:49:28,371] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:49:28,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e917f15-2272-4151-8657-584a5f53ea77/dqc_reference/checkm_data
[2023-03-15 22:49:28,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:49:28,376] [INFO] Task started: CheckM
[2023-03-15 22:49:28,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32900/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32900/checkm_input OceanDNA-b32900/checkm_result
[2023-03-15 22:50:14,067] [INFO] Task succeeded: CheckM
[2023-03-15 22:50:14,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:50:14,115] [INFO] ===== Completeness check finished =====
[2023-03-15 22:50:14,115] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:50:14,115] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32900/markers.fasta)
[2023-03-15 22:50:14,117] [INFO] Task started: Blastn
[2023-03-15 22:50:14,117] [INFO] Running command: blastn -query OceanDNA-b32900/markers.fasta -db /var/lib/cwl/stg1e917f15-2272-4151-8657-584a5f53ea77/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32900/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:50:15,333] [INFO] Task succeeded: Blastn
[2023-03-15 22:50:15,336] [INFO] Selected 25 target genomes.
[2023-03-15 22:50:15,336] [INFO] Target genome list was writen to OceanDNA-b32900/target_genomes_gtdb.txt
[2023-03-15 22:50:16,054] [INFO] Task started: fastANI
[2023-03-15 22:50:16,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg46296112-885f-4d4d-a48e-251d259699a2/OceanDNA-b32900.fa --refList OceanDNA-b32900/target_genomes_gtdb.txt --output OceanDNA-b32900/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:50:31,821] [INFO] Task succeeded: fastANI
[2023-03-15 22:50:31,826] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:50:31,826] [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_018666805.1	s__PTKB01 sp018666805	81.0682	629	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	-
GCA_002937555.1	s__PTKB01 sp002937555	78.505	332	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717225.1	s__PTKB01 sp002717225	76.6529	114	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	75.9842	54	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	75.8228	65	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706185.1	s__Roseomonas sp902706185	75.3459	51	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264455.2	s__Tistrella mobilis	75.2868	57	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Tistrellales;f__Tistrellaceae;g__Tistrella	95.0	96.38	95.97	0.88	0.84	5	-
--------------------------------------------------------------------------------
[2023-03-15 22:50:31,830] [INFO] GTDB search result was written to OceanDNA-b32900/result_gtdb.tsv
[2023-03-15 22:50:31,830] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:50:31,831] [INFO] DFAST_QC result json was written to OceanDNA-b32900/dqc_result.json
[2023-03-15 22:50:31,831] [INFO] DFAST_QC completed!
[2023-03-15 22:50:31,831] [INFO] Total running time: 0h1m43s