[2023-03-19 02:16:59,657] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:16:59,657] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:16:59,658] [INFO] DQC Reference Directory: /var/lib/cwl/stg36fa86ba-f6ca-46b4-9249-7d024c8fc220/dqc_reference
[2023-03-19 02:17:00,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:17:00,762] [INFO] Task started: Prodigal
[2023-03-19 02:17:00,762] [INFO] Running command: cat /var/lib/cwl/stga91fd352-2041-4b5e-aeed-74688ba39813/OceanDNA-b31276.fa | prodigal -d OceanDNA-b31276/cds.fna -a OceanDNA-b31276/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:17:27,700] [INFO] Task succeeded: Prodigal
[2023-03-19 02:17:27,700] [INFO] Task started: HMMsearch
[2023-03-19 02:17:27,700] [INFO] Running command: hmmsearch --tblout OceanDNA-b31276/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36fa86ba-f6ca-46b4-9249-7d024c8fc220/dqc_reference/reference_markers.hmm OceanDNA-b31276/protein.faa > /dev/null
[2023-03-19 02:17:27,921] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:17:27,921] [INFO] Found 6/6 markers.
[2023-03-19 02:17:27,949] [INFO] Query marker FASTA was written to OceanDNA-b31276/markers.fasta
[2023-03-19 02:17:27,950] [INFO] Task started: Blastn
[2023-03-19 02:17:27,950] [INFO] Running command: blastn -query OceanDNA-b31276/markers.fasta -db /var/lib/cwl/stg36fa86ba-f6ca-46b4-9249-7d024c8fc220/dqc_reference/reference_markers.fasta -out OceanDNA-b31276/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:17:28,754] [INFO] Task succeeded: Blastn
[2023-03-19 02:17:28,755] [INFO] Selected 30 target genomes.
[2023-03-19 02:17:28,755] [INFO] Target genome list was writen to OceanDNA-b31276/target_genomes.txt
[2023-03-19 02:17:28,769] [INFO] Task started: fastANI
[2023-03-19 02:17:28,769] [INFO] Running command: fastANI --query /var/lib/cwl/stga91fd352-2041-4b5e-aeed-74688ba39813/OceanDNA-b31276.fa --refList OceanDNA-b31276/target_genomes.txt --output OceanDNA-b31276/fastani_result.tsv --threads 1
[2023-03-19 02:17:50,305] [INFO] Task succeeded: fastANI
[2023-03-19 02:17:50,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36fa86ba-f6ca-46b4-9249-7d024c8fc220/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:17:50,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36fa86ba-f6ca-46b4-9249-7d024c8fc220/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:17:50,320] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:17:50,320] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:17:50,321] [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
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	76.2485	161	1371	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.1921	110	1371	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.0993	138	1371	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.0797	128	1371	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.0691	182	1371	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.0546	130	1371	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.0456	160	1371	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	76.0391	98	1371	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.0333	142	1371	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.022	143	1371	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.0049	190	1371	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.9534	144	1371	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.9468	125	1371	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	75.9355	114	1371	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.9147	114	1371	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	75.8854	118	1371	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	75.8402	152	1371	95	below_threshold
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	75.737	77	1371	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	75.7129	80	1371	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	75.6399	62	1371	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	75.5626	71	1371	95	below_threshold
Albidovulum inexpectatum	strain=DSM 12048	GCA_002927635.1	196587	196587	type	True	75.5558	54	1371	95	below_threshold
Thalassospira marina	strain=CSC3H3	GCA_002844375.1	2048283	2048283	type	True	75.4596	50	1371	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	75.3629	70	1371	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	75.3081	67	1371	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	75.2967	71	1371	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:17:50,321] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31276/tc_result.tsv
[2023-03-19 02:17:50,321] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:17:50,321] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:17:50,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36fa86ba-f6ca-46b4-9249-7d024c8fc220/dqc_reference/checkm_data
[2023-03-19 02:17:50,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:17:50,477] [INFO] Task started: CheckM
[2023-03-19 02:17:50,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31276/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31276/checkm_input OceanDNA-b31276/checkm_result
[2023-03-19 02:18:57,037] [INFO] Task succeeded: CheckM
[2023-03-19 02:18:57,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:18:57,042] [INFO] ===== Completeness check finished =====
[2023-03-19 02:18:57,042] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:18:57,042] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31276/markers.fasta)
[2023-03-19 02:18:57,044] [INFO] Task started: Blastn
[2023-03-19 02:18:57,044] [INFO] Running command: blastn -query OceanDNA-b31276/markers.fasta -db /var/lib/cwl/stg36fa86ba-f6ca-46b4-9249-7d024c8fc220/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31276/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:18:58,576] [INFO] Task succeeded: Blastn
[2023-03-19 02:18:58,578] [INFO] Selected 18 target genomes.
[2023-03-19 02:18:58,578] [INFO] Target genome list was writen to OceanDNA-b31276/target_genomes_gtdb.txt
[2023-03-19 02:18:58,613] [INFO] Task started: fastANI
[2023-03-19 02:18:58,613] [INFO] Running command: fastANI --query /var/lib/cwl/stga91fd352-2041-4b5e-aeed-74688ba39813/OceanDNA-b31276.fa --refList OceanDNA-b31276/target_genomes_gtdb.txt --output OceanDNA-b31276/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:19:10,073] [INFO] Task succeeded: fastANI
[2023-03-19 02:19:10,082] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:19:10,082] [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_017640505.1	s__UBA4479 sp017640505	80.8317	771	1371	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_017644185.1	s__UBA4479 sp017644185	80.0492	740	1371	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_002325375.1	s__UBA1479 sp002325375	79.8866	275	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCA_002696205.1	s__UBA1479 sp002696205	78.1808	211	1371	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_002706405.1	s__UBA1479 sp002706405	78.0323	221	1371	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_017857825.1	s__UBA4479 sp017857825	77.4153	250	1371	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_002781745.1	s__UBA1479 sp002781745	76.9988	214	1371	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_016187325.1	s__JACPJY01 sp016187325	76.6485	161	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763915.1	s__Casp-alpha2 sp016763915	76.2037	89	1371	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_002389175.1	s__UBA4479 sp002389175	76.1598	131	1371	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_018648445.1	s__JABGRG01 sp018648445	75.9593	76	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JABGRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124335.1	s__Tagaea sp016124335	75.9492	88	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__Tagaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242505.1	s__Reyranella sp018242505	75.7328	93	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	75.4268	108	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:19:10,083] [INFO] GTDB search result was written to OceanDNA-b31276/result_gtdb.tsv
[2023-03-19 02:19:10,083] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:19:10,086] [INFO] DFAST_QC result json was written to OceanDNA-b31276/dqc_result.json
[2023-03-19 02:19:10,086] [INFO] DFAST_QC completed!
[2023-03-19 02:19:10,086] [INFO] Total running time: 0h2m10s