[2023-03-17 04:15:14,695] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,695] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg56acfac4-ea99-495d-adf1-fdac50dcc39b/dqc_reference
[2023-03-17 04:15:16,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,101] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,102] [INFO] Running command: cat /var/lib/cwl/stg98380246-4874-4d05-8602-6e3272f64055/OceanDNA-b30957.fa | prodigal -d OceanDNA-b30957/cds.fna -a OceanDNA-b30957/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:29,124] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:29,125] [INFO] Task started: HMMsearch
[2023-03-17 04:15:29,125] [INFO] Running command: hmmsearch --tblout OceanDNA-b30957/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56acfac4-ea99-495d-adf1-fdac50dcc39b/dqc_reference/reference_markers.hmm OceanDNA-b30957/protein.faa > /dev/null
[2023-03-17 04:15:29,323] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:29,323] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg98380246-4874-4d05-8602-6e3272f64055/OceanDNA-b30957.fa]
[2023-03-17 04:15:29,340] [INFO] Query marker FASTA was written to OceanDNA-b30957/markers.fasta
[2023-03-17 04:15:29,340] [INFO] Task started: Blastn
[2023-03-17 04:15:29,341] [INFO] Running command: blastn -query OceanDNA-b30957/markers.fasta -db /var/lib/cwl/stg56acfac4-ea99-495d-adf1-fdac50dcc39b/dqc_reference/reference_markers.fasta -out OceanDNA-b30957/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:29,960] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:29,960] [INFO] Selected 17 target genomes.
[2023-03-17 04:15:29,961] [INFO] Target genome list was writen to OceanDNA-b30957/target_genomes.txt
[2023-03-17 04:15:29,969] [INFO] Task started: fastANI
[2023-03-17 04:15:29,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg98380246-4874-4d05-8602-6e3272f64055/OceanDNA-b30957.fa --refList OceanDNA-b30957/target_genomes.txt --output OceanDNA-b30957/fastani_result.tsv --threads 1
[2023-03-17 04:15:45,672] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:45,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56acfac4-ea99-495d-adf1-fdac50dcc39b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:45,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56acfac4-ea99-495d-adf1-fdac50dcc39b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:45,683] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:45,683] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:15:45,683] [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
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.665	172	689	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.6432	172	689	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.6144	154	689	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.521	150	689	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.5164	116	689	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.4738	80	689	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.4517	140	689	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.3881	130	689	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.3778	139	689	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.3557	140	689	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.234	122	689	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.991	124	689	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	75.9675	79	689	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.9	110	689	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.7916	107	689	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.7823	77	689	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	75.6357	115	689	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:45,683] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30957/tc_result.tsv
[2023-03-17 04:15:45,683] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:45,684] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:45,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56acfac4-ea99-495d-adf1-fdac50dcc39b/dqc_reference/checkm_data
[2023-03-17 04:15:45,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:45,691] [INFO] Task started: CheckM
[2023-03-17 04:15:45,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30957/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30957/checkm_input OceanDNA-b30957/checkm_result
[2023-03-17 04:16:20,863] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:20,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:20,866] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:20,867] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:20,867] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30957/markers.fasta)
[2023-03-17 04:16:20,867] [INFO] Task started: Blastn
[2023-03-17 04:16:20,867] [INFO] Running command: blastn -query OceanDNA-b30957/markers.fasta -db /var/lib/cwl/stg56acfac4-ea99-495d-adf1-fdac50dcc39b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30957/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:21,894] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:21,895] [INFO] Selected 6 target genomes.
[2023-03-17 04:16:21,895] [INFO] Target genome list was writen to OceanDNA-b30957/target_genomes_gtdb.txt
[2023-03-17 04:16:22,029] [INFO] Task started: fastANI
[2023-03-17 04:16:22,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg98380246-4874-4d05-8602-6e3272f64055/OceanDNA-b30957.fa --refList OceanDNA-b30957/target_genomes_gtdb.txt --output OceanDNA-b30957/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:26,338] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:26,343] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:16:26,343] [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_002325375.1	s__UBA1479 sp002325375	90.8761	625	689	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_002706405.1	s__UBA1479 sp002706405	88.1265	544	689	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	84.9912	541	689	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	82.8502	465	689	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_002433335.1	s__UBA1479 sp002433335	81.4968	468	689	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_002686255.1	s__Casp-alpha2 sp002686255	77.2792	164	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:26,343] [INFO] GTDB search result was written to OceanDNA-b30957/result_gtdb.tsv
[2023-03-17 04:16:26,344] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:26,345] [INFO] DFAST_QC result json was written to OceanDNA-b30957/dqc_result.json
[2023-03-17 04:16:26,345] [INFO] DFAST_QC completed!
[2023-03-17 04:16:26,345] [INFO] Total running time: 0h1m12s