[2023-03-18 09:58:36,586] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:58:36,586] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:58:36,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b2ca6d6-8c65-4cab-9879-b0a3a439325d/dqc_reference
[2023-03-18 09:58:38,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:58:38,404] [INFO] Task started: Prodigal
[2023-03-18 09:58:38,404] [INFO] Running command: cat /var/lib/cwl/stgc4ac99bf-744c-48a5-b4f3-55355c157678/OceanDNA-b26414.fa | prodigal -d OceanDNA-b26414/cds.fna -a OceanDNA-b26414/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:58:49,665] [INFO] Task succeeded: Prodigal
[2023-03-18 09:58:49,666] [INFO] Task started: HMMsearch
[2023-03-18 09:58:49,666] [INFO] Running command: hmmsearch --tblout OceanDNA-b26414/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b2ca6d6-8c65-4cab-9879-b0a3a439325d/dqc_reference/reference_markers.hmm OceanDNA-b26414/protein.faa > /dev/null
[2023-03-18 09:58:49,834] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:58:49,835] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc4ac99bf-744c-48a5-b4f3-55355c157678/OceanDNA-b26414.fa]
[2023-03-18 09:58:49,850] [INFO] Query marker FASTA was written to OceanDNA-b26414/markers.fasta
[2023-03-18 09:58:49,853] [INFO] Task started: Blastn
[2023-03-18 09:58:49,853] [INFO] Running command: blastn -query OceanDNA-b26414/markers.fasta -db /var/lib/cwl/stg0b2ca6d6-8c65-4cab-9879-b0a3a439325d/dqc_reference/reference_markers.fasta -out OceanDNA-b26414/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:58:50,533] [INFO] Task succeeded: Blastn
[2023-03-18 09:58:50,534] [INFO] Selected 33 target genomes.
[2023-03-18 09:58:50,534] [INFO] Target genome list was writen to OceanDNA-b26414/target_genomes.txt
[2023-03-18 09:58:50,560] [INFO] Task started: fastANI
[2023-03-18 09:58:50,560] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4ac99bf-744c-48a5-b4f3-55355c157678/OceanDNA-b26414.fa --refList OceanDNA-b26414/target_genomes.txt --output OceanDNA-b26414/fastani_result.tsv --threads 1
[2023-03-18 09:59:17,451] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:17,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b2ca6d6-8c65-4cab-9879-b0a3a439325d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:59:17,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b2ca6d6-8c65-4cab-9879-b0a3a439325d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:59:17,459] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:59:17,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:59:17,460] [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	76.2598	72	600	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.0898	67	600	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.8496	51	600	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.7496	58	600	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.7231	60	600	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.689	56	600	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.6862	81	600	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.4942	60	600	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.3171	70	600	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.2265	64	600	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	75.167	51	600	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:59:17,460] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26414/tc_result.tsv
[2023-03-18 09:59:17,460] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:59:17,460] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:59:17,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b2ca6d6-8c65-4cab-9879-b0a3a439325d/dqc_reference/checkm_data
[2023-03-18 09:59:17,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:59:17,465] [INFO] Task started: CheckM
[2023-03-18 09:59:17,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26414/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26414/checkm_input OceanDNA-b26414/checkm_result
[2023-03-18 09:59:50,068] [INFO] Task succeeded: CheckM
[2023-03-18 09:59:50,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:59:50,070] [INFO] ===== Completeness check finished =====
[2023-03-18 09:59:50,070] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:59:50,071] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26414/markers.fasta)
[2023-03-18 09:59:50,072] [INFO] Task started: Blastn
[2023-03-18 09:59:50,072] [INFO] Running command: blastn -query OceanDNA-b26414/markers.fasta -db /var/lib/cwl/stg0b2ca6d6-8c65-4cab-9879-b0a3a439325d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26414/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:59:51,233] [INFO] Task succeeded: Blastn
[2023-03-18 09:59:51,234] [INFO] Selected 13 target genomes.
[2023-03-18 09:59:51,234] [INFO] Target genome list was writen to OceanDNA-b26414/target_genomes_gtdb.txt
[2023-03-18 09:59:51,246] [INFO] Task started: fastANI
[2023-03-18 09:59:51,246] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4ac99bf-744c-48a5-b4f3-55355c157678/OceanDNA-b26414.fa --refList OceanDNA-b26414/target_genomes_gtdb.txt --output OceanDNA-b26414/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:59:56,997] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:57,002] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:59:57,003] [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_002457745.1	s__UBA8309 sp002457745	84.9685	333	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522725.1	s__UBA8309 sp001627655	81.555	387	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_009920665.1	s__UBA8309 sp009920665	79.9806	362	600	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	79.9312	351	600	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	78.6294	175	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_002683535.1	s__UBA8309 sp002683535	77.6831	111	600	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	77.575	153	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780765.1	s__UBA8309 sp016780765	77.5597	179	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
--------------------------------------------------------------------------------
[2023-03-18 09:59:57,003] [INFO] GTDB search result was written to OceanDNA-b26414/result_gtdb.tsv
[2023-03-18 09:59:57,003] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:59:57,004] [INFO] DFAST_QC result json was written to OceanDNA-b26414/dqc_result.json
[2023-03-18 09:59:57,004] [INFO] DFAST_QC completed!
[2023-03-18 09:59:57,004] [INFO] Total running time: 0h1m20s