[2023-03-16 07:34:40,570] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:34:40,571] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:34:40,571] [INFO] DQC Reference Directory: /var/lib/cwl/stg310ef27d-2d31-4eeb-9706-d2029cce475d/dqc_reference
[2023-03-16 07:34:42,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:34:42,228] [INFO] Task started: Prodigal
[2023-03-16 07:34:42,228] [INFO] Running command: cat /var/lib/cwl/stg575d74a1-5e84-427d-9cc7-79a4c35098ba/OceanDNA-b23946.fa | prodigal -d OceanDNA-b23946/cds.fna -a OceanDNA-b23946/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:35:02,004] [INFO] Task succeeded: Prodigal
[2023-03-16 07:35:02,004] [INFO] Task started: HMMsearch
[2023-03-16 07:35:02,004] [INFO] Running command: hmmsearch --tblout OceanDNA-b23946/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg310ef27d-2d31-4eeb-9706-d2029cce475d/dqc_reference/reference_markers.hmm OceanDNA-b23946/protein.faa > /dev/null
[2023-03-16 07:35:02,220] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:35:02,221] [INFO] Found 6/6 markers.
[2023-03-16 07:35:02,242] [INFO] Query marker FASTA was written to OceanDNA-b23946/markers.fasta
[2023-03-16 07:35:02,243] [INFO] Task started: Blastn
[2023-03-16 07:35:02,243] [INFO] Running command: blastn -query OceanDNA-b23946/markers.fasta -db /var/lib/cwl/stg310ef27d-2d31-4eeb-9706-d2029cce475d/dqc_reference/reference_markers.fasta -out OceanDNA-b23946/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:35:03,059] [INFO] Task succeeded: Blastn
[2023-03-16 07:35:03,060] [INFO] Selected 18 target genomes.
[2023-03-16 07:35:03,060] [INFO] Target genome list was writen to OceanDNA-b23946/target_genomes.txt
[2023-03-16 07:35:03,178] [INFO] Task started: fastANI
[2023-03-16 07:35:03,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg575d74a1-5e84-427d-9cc7-79a4c35098ba/OceanDNA-b23946.fa --refList OceanDNA-b23946/target_genomes.txt --output OceanDNA-b23946/fastani_result.tsv --threads 1
[2023-03-16 07:35:14,394] [INFO] Task succeeded: fastANI
[2023-03-16 07:35:14,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg310ef27d-2d31-4eeb-9706-d2029cce475d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:35:14,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg310ef27d-2d31-4eeb-9706-d2029cce475d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:35:14,405] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:35:14,405] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:35:14,405] [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
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	81.7804	671	1072	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	80.4501	613	1072	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	78.6133	489	1072	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.808	317	1072	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.6757	265	1072	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.6629	264	1072	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.6048	305	1072	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	77.3406	214	1072	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	77.231	217	1072	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.2189	212	1072	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	76.2759	90	1072	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	76.1156	81	1072	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.9406	79	1072	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	75.7631	139	1072	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.5883	106	1072	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	75.5705	107	1072	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.563	90	1072	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:35:14,405] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23946/tc_result.tsv
[2023-03-16 07:35:14,405] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:35:14,405] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:35:14,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg310ef27d-2d31-4eeb-9706-d2029cce475d/dqc_reference/checkm_data
[2023-03-16 07:35:14,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:35:14,411] [INFO] Task started: CheckM
[2023-03-16 07:35:14,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23946/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23946/checkm_input OceanDNA-b23946/checkm_result
[2023-03-16 07:36:05,121] [INFO] Task succeeded: CheckM
[2023-03-16 07:36:05,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:36:05,140] [INFO] ===== Completeness check finished =====
[2023-03-16 07:36:05,140] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:36:05,140] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23946/markers.fasta)
[2023-03-16 07:36:05,141] [INFO] Task started: Blastn
[2023-03-16 07:36:05,141] [INFO] Running command: blastn -query OceanDNA-b23946/markers.fasta -db /var/lib/cwl/stg310ef27d-2d31-4eeb-9706-d2029cce475d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23946/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:36:06,633] [INFO] Task succeeded: Blastn
[2023-03-16 07:36:06,638] [INFO] Selected 11 target genomes.
[2023-03-16 07:36:06,639] [INFO] Target genome list was writen to OceanDNA-b23946/target_genomes_gtdb.txt
[2023-03-16 07:36:07,191] [INFO] Task started: fastANI
[2023-03-16 07:36:07,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg575d74a1-5e84-427d-9cc7-79a4c35098ba/OceanDNA-b23946.fa --refList OceanDNA-b23946/target_genomes_gtdb.txt --output OceanDNA-b23946/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:36:14,847] [INFO] Task succeeded: fastANI
[2023-03-16 07:36:14,854] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:36:14,854] [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_002707795.1	s__Maricaulis sp002707795	93.7672	676	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCA_017642925.1	s__Maricaulis sp017642925	93.6005	971	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871165.1	s__Maricaulis sp005871165	81.7949	670	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694345.1	s__Maricaulis sp002694345	81.4	442	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016817355.1	s__Maricaulis parjimensis	81.3706	661	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665295.1	s__Maricaulis sp015665295	80.7043	580	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	80.4413	614	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_000014745.1	s__Maricaulis maris_A	80.2208	573	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCA_905480005.1	s__Maricaulis sp905480005	80.1245	512	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643475.1	s__Maricaulis sp017643475	78.706	408	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103475.1	s__Maricaulis salignorans	78.6	490	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:36:14,854] [INFO] GTDB search result was written to OceanDNA-b23946/result_gtdb.tsv
[2023-03-16 07:36:14,854] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:36:14,856] [INFO] DFAST_QC result json was written to OceanDNA-b23946/dqc_result.json
[2023-03-16 07:36:14,856] [INFO] DFAST_QC completed!
[2023-03-16 07:36:14,856] [INFO] Total running time: 0h1m34s