[2023-03-15 11:22:20,468] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:22:20,468] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:22:20,468] [INFO] DQC Reference Directory: /var/lib/cwl/stga53fbf51-e532-43f0-821b-417bee853182/dqc_reference
[2023-03-15 11:22:21,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:22:21,950] [INFO] Task started: Prodigal
[2023-03-15 11:22:21,951] [INFO] Running command: cat /var/lib/cwl/stg285a4e39-e6a3-4112-bc73-f1255563dba0/OceanDNA-b26561.fa | prodigal -d OceanDNA-b26561/cds.fna -a OceanDNA-b26561/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:22:29,838] [INFO] Task succeeded: Prodigal
[2023-03-15 11:22:29,838] [INFO] Task started: HMMsearch
[2023-03-15 11:22:29,838] [INFO] Running command: hmmsearch --tblout OceanDNA-b26561/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga53fbf51-e532-43f0-821b-417bee853182/dqc_reference/reference_markers.hmm OceanDNA-b26561/protein.faa > /dev/null
[2023-03-15 11:22:29,999] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:22:29,999] [INFO] Found 6/6 markers.
[2023-03-15 11:22:30,013] [INFO] Query marker FASTA was written to OceanDNA-b26561/markers.fasta
[2023-03-15 11:22:30,013] [INFO] Task started: Blastn
[2023-03-15 11:22:30,013] [INFO] Running command: blastn -query OceanDNA-b26561/markers.fasta -db /var/lib/cwl/stga53fbf51-e532-43f0-821b-417bee853182/dqc_reference/reference_markers.fasta -out OceanDNA-b26561/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:30,753] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:30,754] [INFO] Selected 34 target genomes.
[2023-03-15 11:22:30,754] [INFO] Target genome list was writen to OceanDNA-b26561/target_genomes.txt
[2023-03-15 11:22:30,775] [INFO] Task started: fastANI
[2023-03-15 11:22:30,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg285a4e39-e6a3-4112-bc73-f1255563dba0/OceanDNA-b26561.fa --refList OceanDNA-b26561/target_genomes.txt --output OceanDNA-b26561/fastani_result.tsv --threads 1
[2023-03-15 11:22:59,127] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:59,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga53fbf51-e532-43f0-821b-417bee853182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:22:59,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga53fbf51-e532-43f0-821b-417bee853182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:22:59,142] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:22:59,142] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:22:59,142] [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	76.9867	74	365	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.8093	76	365	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.7223	56	365	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.6808	57	365	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.6667	57	365	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	76.5929	55	365	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.5882	92	365	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	76.5621	56	365	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.5393	52	365	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	76.5312	58	365	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.4856	88	365	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.4754	82	365	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	76.4031	58	365	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.3668	63	365	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.2997	58	365	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	76.2711	59	365	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	76.2698	58	365	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	76.2618	51	365	95	below_threshold
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	76.0851	53	365	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	76.0662	53	365	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	76.0427	63	365	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	75.9863	57	365	95	below_threshold
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	75.89	51	365	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.8681	62	365	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	75.6513	63	365	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:22:59,142] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26561/tc_result.tsv
[2023-03-15 11:22:59,143] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:22:59,143] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:22:59,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga53fbf51-e532-43f0-821b-417bee853182/dqc_reference/checkm_data
[2023-03-15 11:22:59,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:22:59,491] [INFO] Task started: CheckM
[2023-03-15 11:22:59,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26561/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26561/checkm_input OceanDNA-b26561/checkm_result
[2023-03-15 11:23:24,472] [INFO] Task succeeded: CheckM
[2023-03-15 11:23:24,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:23:24,475] [INFO] ===== Completeness check finished =====
[2023-03-15 11:23:24,475] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:23:24,475] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26561/markers.fasta)
[2023-03-15 11:23:24,476] [INFO] Task started: Blastn
[2023-03-15 11:23:24,476] [INFO] Running command: blastn -query OceanDNA-b26561/markers.fasta -db /var/lib/cwl/stga53fbf51-e532-43f0-821b-417bee853182/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26561/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:23:25,864] [INFO] Task succeeded: Blastn
[2023-03-15 11:23:25,865] [INFO] Selected 16 target genomes.
[2023-03-15 11:23:25,865] [INFO] Target genome list was writen to OceanDNA-b26561/target_genomes_gtdb.txt
[2023-03-15 11:23:25,876] [INFO] Task started: fastANI
[2023-03-15 11:23:25,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg285a4e39-e6a3-4112-bc73-f1255563dba0/OceanDNA-b26561.fa --refList OceanDNA-b26561/target_genomes_gtdb.txt --output OceanDNA-b26561/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:23:32,819] [INFO] Task succeeded: fastANI
[2023-03-15 11:23:32,827] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:23:32,827] [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_011522725.1	s__UBA8309 sp001627655	98.9155	348	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	conclusive
GCA_002457745.1	s__UBA8309 sp002457745	81.4258	211	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920665.1	s__UBA8309 sp009920665	80.7951	253	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	80.7625	246	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213025.1	s__UBA8309 sp004213025	80.5625	146	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686685.1	s__UBA8309 sp002686685	79.631	121	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_016780765.1	s__UBA8309 sp016780765	78.2155	130	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
GCA_002683535.1	s__UBA8309 sp002683535	78.0599	93	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524735.1	s__UBA8309 sp011524735	77.5889	95	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017963645.1	s__Marivibrio halodurans	76.4324	57	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Marivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350085.1	s__Mesorhizobium metallidurans	76.04	54	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305815.1	s__Kaistia sp017305815	75.5845	53	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:23:32,827] [INFO] GTDB search result was written to OceanDNA-b26561/result_gtdb.tsv
[2023-03-15 11:23:32,827] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:23:32,829] [INFO] DFAST_QC result json was written to OceanDNA-b26561/dqc_result.json
[2023-03-15 11:23:32,829] [INFO] DFAST_QC completed!
[2023-03-15 11:23:32,829] [INFO] Total running time: 0h1m12s