[2023-03-15 10:09:49,678] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:09:49,678] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:09:49,678] [INFO] DQC Reference Directory: /var/lib/cwl/stgb58fbb54-c36a-4563-bf77-6baa8dab7fa8/dqc_reference
[2023-03-15 10:09:51,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:09:51,537] [INFO] Task started: Prodigal
[2023-03-15 10:09:51,537] [INFO] Running command: cat /var/lib/cwl/stgb2358fc0-1c0c-4abe-bc5f-15ecbaa3a96d/OceanDNA-b31245.fa | prodigal -d OceanDNA-b31245/cds.fna -a OceanDNA-b31245/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:10:13,076] [INFO] Task succeeded: Prodigal
[2023-03-15 10:10:13,076] [INFO] Task started: HMMsearch
[2023-03-15 10:10:13,076] [INFO] Running command: hmmsearch --tblout OceanDNA-b31245/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb58fbb54-c36a-4563-bf77-6baa8dab7fa8/dqc_reference/reference_markers.hmm OceanDNA-b31245/protein.faa > /dev/null
[2023-03-15 10:10:13,285] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:10:13,286] [INFO] Found 6/6 markers.
[2023-03-15 10:10:13,308] [INFO] Query marker FASTA was written to OceanDNA-b31245/markers.fasta
[2023-03-15 10:10:13,308] [INFO] Task started: Blastn
[2023-03-15 10:10:13,308] [INFO] Running command: blastn -query OceanDNA-b31245/markers.fasta -db /var/lib/cwl/stgb58fbb54-c36a-4563-bf77-6baa8dab7fa8/dqc_reference/reference_markers.fasta -out OceanDNA-b31245/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:10:14,020] [INFO] Task succeeded: Blastn
[2023-03-15 10:10:14,021] [INFO] Selected 32 target genomes.
[2023-03-15 10:10:14,021] [INFO] Target genome list was writen to OceanDNA-b31245/target_genomes.txt
[2023-03-15 10:10:14,070] [INFO] Task started: fastANI
[2023-03-15 10:10:14,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2358fc0-1c0c-4abe-bc5f-15ecbaa3a96d/OceanDNA-b31245.fa --refList OceanDNA-b31245/target_genomes.txt --output OceanDNA-b31245/fastani_result.tsv --threads 1
[2023-03-15 10:10:38,310] [INFO] Task succeeded: fastANI
[2023-03-15 10:10:38,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb58fbb54-c36a-4563-bf77-6baa8dab7fa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:10:38,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb58fbb54-c36a-4563-bf77-6baa8dab7fa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:10:38,316] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:10:38,316] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:10:38,316] [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
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.731	70	1101	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.4904	50	1101	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.3225	56	1101	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.2588	53	1101	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.22	53	1101	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.193	55	1101	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.1251	55	1101	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:10:38,318] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31245/tc_result.tsv
[2023-03-15 10:10:38,318] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:10:38,318] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:10:38,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb58fbb54-c36a-4563-bf77-6baa8dab7fa8/dqc_reference/checkm_data
[2023-03-15 10:10:38,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:10:38,324] [INFO] Task started: CheckM
[2023-03-15 10:10:38,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31245/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31245/checkm_input OceanDNA-b31245/checkm_result
[2023-03-15 10:11:33,094] [INFO] Task succeeded: CheckM
[2023-03-15 10:11:33,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:11:33,105] [INFO] ===== Completeness check finished =====
[2023-03-15 10:11:33,105] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:11:33,106] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31245/markers.fasta)
[2023-03-15 10:11:33,107] [INFO] Task started: Blastn
[2023-03-15 10:11:33,107] [INFO] Running command: blastn -query OceanDNA-b31245/markers.fasta -db /var/lib/cwl/stgb58fbb54-c36a-4563-bf77-6baa8dab7fa8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31245/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:11:34,409] [INFO] Task succeeded: Blastn
[2023-03-15 10:11:34,412] [INFO] Selected 23 target genomes.
[2023-03-15 10:11:34,412] [INFO] Target genome list was writen to OceanDNA-b31245/target_genomes_gtdb.txt
[2023-03-15 10:11:35,178] [INFO] Task started: fastANI
[2023-03-15 10:11:35,178] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2358fc0-1c0c-4abe-bc5f-15ecbaa3a96d/OceanDNA-b31245.fa --refList OceanDNA-b31245/target_genomes_gtdb.txt --output OceanDNA-b31245/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:11:49,094] [INFO] Task succeeded: fastANI
[2023-03-15 10:11:49,103] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:11:49,103] [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_017857825.1	s__UBA4479 sp017857825	86.7244	714	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640505.1	s__UBA4479 sp017640505	77.2787	288	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.97	99.97	1.00	1.00	2	-
GCA_002389175.1	s__UBA4479 sp002389175	77.2329	127	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644185.1	s__UBA4479 sp017644185	77.1516	266	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706405.1	s__UBA1479 sp002706405	76.1559	85	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_002781745.1	s__UBA1479 sp002781745	76.0972	99	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696205.1	s__UBA1479 sp002696205	75.9702	103	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	75.9128	76	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_013204265.1	s__Casp-alpha2 sp013204265	75.8609	50	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015231605.1	s__JADGBG01 sp015231605	75.6503	51	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetovibrionaceae;g__JADGBG01	95.0	99.19	99.19	0.87	0.87	2	-
GCA_002869065.1	s__Rhodobium sp002869065	75.5641	53	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	75.193	55	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001295845.1	s__Rhodopseudomonas sp001295845	75.0014	61	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:11:49,106] [INFO] GTDB search result was written to OceanDNA-b31245/result_gtdb.tsv
[2023-03-15 10:11:49,108] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:11:49,112] [INFO] DFAST_QC result json was written to OceanDNA-b31245/dqc_result.json
[2023-03-15 10:11:49,112] [INFO] DFAST_QC completed!
[2023-03-15 10:11:49,112] [INFO] Total running time: 0h1m59s