[2023-03-16 10:22:21,032] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:22:21,033] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:22:21,033] [INFO] DQC Reference Directory: /var/lib/cwl/stg957ab137-10d9-412e-8ea2-c5a7d466306d/dqc_reference
[2023-03-16 10:22:22,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:22:22,725] [INFO] Task started: Prodigal
[2023-03-16 10:22:22,725] [INFO] Running command: cat /var/lib/cwl/stg9d87e51c-3536-41f6-935f-7b6c5620d394/OceanDNA-b33104.fa | prodigal -d OceanDNA-b33104/cds.fna -a OceanDNA-b33104/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:22:54,844] [INFO] Task succeeded: Prodigal
[2023-03-16 10:22:54,844] [INFO] Task started: HMMsearch
[2023-03-16 10:22:54,845] [INFO] Running command: hmmsearch --tblout OceanDNA-b33104/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg957ab137-10d9-412e-8ea2-c5a7d466306d/dqc_reference/reference_markers.hmm OceanDNA-b33104/protein.faa > /dev/null
[2023-03-16 10:22:55,373] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:22:55,374] [INFO] Found 6/6 markers.
[2023-03-16 10:22:55,419] [INFO] Query marker FASTA was written to OceanDNA-b33104/markers.fasta
[2023-03-16 10:22:55,419] [INFO] Task started: Blastn
[2023-03-16 10:22:55,419] [INFO] Running command: blastn -query OceanDNA-b33104/markers.fasta -db /var/lib/cwl/stg957ab137-10d9-412e-8ea2-c5a7d466306d/dqc_reference/reference_markers.fasta -out OceanDNA-b33104/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:22:56,450] [INFO] Task succeeded: Blastn
[2023-03-16 10:22:56,451] [INFO] Selected 30 target genomes.
[2023-03-16 10:22:56,451] [INFO] Target genome list was writen to OceanDNA-b33104/target_genomes.txt
[2023-03-16 10:22:56,560] [INFO] Task started: fastANI
[2023-03-16 10:22:56,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d87e51c-3536-41f6-935f-7b6c5620d394/OceanDNA-b33104.fa --refList OceanDNA-b33104/target_genomes.txt --output OceanDNA-b33104/fastani_result.tsv --threads 1
[2023-03-16 10:23:18,231] [INFO] Task succeeded: fastANI
[2023-03-16 10:23:18,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg957ab137-10d9-412e-8ea2-c5a7d466306d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:23:18,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg957ab137-10d9-412e-8ea2-c5a7d466306d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:23:18,240] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:23:18,240] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:23:18,240] [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 sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.8531	57	1575	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.6734	60	1575	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.4325	67	1575	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.4091	62	1575	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.4061	65	1575	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.3951	66	1575	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.3687	67	1575	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:23:18,241] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33104/tc_result.tsv
[2023-03-16 10:23:18,241] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:23:18,241] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:23:18,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg957ab137-10d9-412e-8ea2-c5a7d466306d/dqc_reference/checkm_data
[2023-03-16 10:23:18,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:23:18,263] [INFO] Task started: CheckM
[2023-03-16 10:23:18,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33104/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33104/checkm_input OceanDNA-b33104/checkm_result
[2023-03-16 10:24:31,863] [INFO] Task succeeded: CheckM
[2023-03-16 10:24:31,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:24:31,867] [INFO] ===== Completeness check finished =====
[2023-03-16 10:24:31,867] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:24:31,867] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33104/markers.fasta)
[2023-03-16 10:24:31,868] [INFO] Task started: Blastn
[2023-03-16 10:24:31,868] [INFO] Running command: blastn -query OceanDNA-b33104/markers.fasta -db /var/lib/cwl/stg957ab137-10d9-412e-8ea2-c5a7d466306d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33104/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:24:33,193] [INFO] Task succeeded: Blastn
[2023-03-16 10:24:33,195] [INFO] Selected 25 target genomes.
[2023-03-16 10:24:33,195] [INFO] Target genome list was writen to OceanDNA-b33104/target_genomes_gtdb.txt
[2023-03-16 10:24:33,383] [INFO] Task started: fastANI
[2023-03-16 10:24:33,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d87e51c-3536-41f6-935f-7b6c5620d394/OceanDNA-b33104.fa --refList OceanDNA-b33104/target_genomes_gtdb.txt --output OceanDNA-b33104/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:24:56,333] [INFO] Task succeeded: fastANI
[2023-03-16 10:24:56,341] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:24:56,342] [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_002716125.1	s__UBA6544 sp002716125	99.7427	1429	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018665505.1	s__UBA6544 sp018665505	77.2876	319	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724555.1	s__UBA6544 sp002724555	76.8241	200	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434595.1	s__UBA6544 sp002434595	76.7554	143	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	75.6315	98	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	75.5939	61	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869285.1	s__SHVZ01 sp016869285	75.5726	53	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	75.4749	59	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	75.4091	62	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016201015.1	s__JACQDQ01 sp016201015	75.3954	52	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JACQDQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840595.1	s__Bin65 sp009840595	75.3587	55	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	98.91	96.90	0.94	0.92	4	-
GCF_008728855.1	s__Hypericibacter terrae	75.2486	52	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938675.2	s__Inquilinus sp005938675	75.0783	63	1575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:24:56,342] [INFO] GTDB search result was written to OceanDNA-b33104/result_gtdb.tsv
[2023-03-16 10:24:56,342] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:24:56,344] [INFO] DFAST_QC result json was written to OceanDNA-b33104/dqc_result.json
[2023-03-16 10:24:56,344] [INFO] DFAST_QC completed!
[2023-03-16 10:24:56,344] [INFO] Total running time: 0h2m35s