[2023-03-15 16:03:34,274] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:03:34,274] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:03:34,274] [INFO] DQC Reference Directory: /var/lib/cwl/stgf37d741b-6d87-4315-812d-c62e43643acc/dqc_reference
[2023-03-15 16:03:35,747] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:03:35,748] [INFO] Task started: Prodigal
[2023-03-15 16:03:35,748] [INFO] Running command: cat /var/lib/cwl/stg86ad9f54-8dc3-4a49-aba0-f1246ee4caf0/OceanDNA-b26387.fa | prodigal -d OceanDNA-b26387/cds.fna -a OceanDNA-b26387/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:03:46,849] [INFO] Task succeeded: Prodigal
[2023-03-15 16:03:46,850] [INFO] Task started: HMMsearch
[2023-03-15 16:03:46,850] [INFO] Running command: hmmsearch --tblout OceanDNA-b26387/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf37d741b-6d87-4315-812d-c62e43643acc/dqc_reference/reference_markers.hmm OceanDNA-b26387/protein.faa > /dev/null
[2023-03-15 16:03:47,021] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:03:47,021] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg86ad9f54-8dc3-4a49-aba0-f1246ee4caf0/OceanDNA-b26387.fa]
[2023-03-15 16:03:47,039] [INFO] Query marker FASTA was written to OceanDNA-b26387/markers.fasta
[2023-03-15 16:03:47,040] [INFO] Task started: Blastn
[2023-03-15 16:03:47,040] [INFO] Running command: blastn -query OceanDNA-b26387/markers.fasta -db /var/lib/cwl/stgf37d741b-6d87-4315-812d-c62e43643acc/dqc_reference/reference_markers.fasta -out OceanDNA-b26387/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:03:47,693] [INFO] Task succeeded: Blastn
[2023-03-15 16:03:47,694] [INFO] Selected 29 target genomes.
[2023-03-15 16:03:47,694] [INFO] Target genome list was writen to OceanDNA-b26387/target_genomes.txt
[2023-03-15 16:03:47,712] [INFO] Task started: fastANI
[2023-03-15 16:03:47,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ad9f54-8dc3-4a49-aba0-f1246ee4caf0/OceanDNA-b26387.fa --refList OceanDNA-b26387/target_genomes.txt --output OceanDNA-b26387/fastani_result.tsv --threads 1
[2023-03-15 16:04:08,142] [INFO] Task succeeded: fastANI
[2023-03-15 16:04:08,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf37d741b-6d87-4315-812d-c62e43643acc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:04:08,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf37d741b-6d87-4315-812d-c62e43643acc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:04:08,152] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:04:08,152] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:04:08,153] [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 indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.4715	78	582	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.4324	78	582	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.3345	85	582	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.2782	73	582	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.0428	73	582	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.0077	75	582	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.9761	91	582	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	75.7334	73	582	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.7085	83	582	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.6924	84	582	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	75.5926	59	582	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.5423	86	582	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	75.5086	72	582	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	75.395	86	582	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	75.2349	55	582	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:04:08,153] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26387/tc_result.tsv
[2023-03-15 16:04:08,153] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:04:08,153] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:04:08,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf37d741b-6d87-4315-812d-c62e43643acc/dqc_reference/checkm_data
[2023-03-15 16:04:08,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:04:08,198] [INFO] Task started: CheckM
[2023-03-15 16:04:08,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26387/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26387/checkm_input OceanDNA-b26387/checkm_result
[2023-03-15 16:04:40,074] [INFO] Task succeeded: CheckM
[2023-03-15 16:04:40,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:04:40,079] [INFO] ===== Completeness check finished =====
[2023-03-15 16:04:40,079] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:04:40,079] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26387/markers.fasta)
[2023-03-15 16:04:40,080] [INFO] Task started: Blastn
[2023-03-15 16:04:40,080] [INFO] Running command: blastn -query OceanDNA-b26387/markers.fasta -db /var/lib/cwl/stgf37d741b-6d87-4315-812d-c62e43643acc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26387/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:04:41,232] [INFO] Task succeeded: Blastn
[2023-03-15 16:04:41,234] [INFO] Selected 17 target genomes.
[2023-03-15 16:04:41,234] [INFO] Target genome list was writen to OceanDNA-b26387/target_genomes_gtdb.txt
[2023-03-15 16:04:41,253] [INFO] Task started: fastANI
[2023-03-15 16:04:41,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ad9f54-8dc3-4a49-aba0-f1246ee4caf0/OceanDNA-b26387.fa --refList OceanDNA-b26387/target_genomes_gtdb.txt --output OceanDNA-b26387/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:04:50,367] [INFO] Task succeeded: fastANI
[2023-03-15 16:04:50,374] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:04:50,375] [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	82.9826	415	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_002457745.1	s__UBA8309 sp002457745	81.4175	299	582	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	80.2221	368	582	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	80.2134	378	582	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	78.1737	168	582	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	77.5357	107	582	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	77.375	145	582	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	77.323	188	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
GCF_014195655.1	s__Angulomicrobium tetraedrale	75.6491	53	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103325.1	s__Mesorhizobium qingshengii	75.6126	60	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010725.1	s__Azospirillum lipoferum_B	75.4913	91	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019216885.1	s__Methylobacterium sp019216885	75.2889	55	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:04:50,375] [INFO] GTDB search result was written to OceanDNA-b26387/result_gtdb.tsv
[2023-03-15 16:04:50,375] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:04:50,377] [INFO] DFAST_QC result json was written to OceanDNA-b26387/dqc_result.json
[2023-03-15 16:04:50,377] [INFO] DFAST_QC completed!
[2023-03-15 16:04:50,378] [INFO] Total running time: 0h1m16s