[2023-03-19 04:43:18,706] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,706] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d5b6626-d85a-4a14-9fc5-9dc886c29811/dqc_reference
[2023-03-19 04:43:19,873] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,873] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,873] [INFO] Running command: cat /var/lib/cwl/stgb1e675b8-cd84-4f8e-ba13-ab06f4f2509e/OceanDNA-b23944.fa | prodigal -d OceanDNA-b23944/cds.fna -a OceanDNA-b23944/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:36,440] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:36,441] [INFO] Task started: HMMsearch
[2023-03-19 04:43:36,441] [INFO] Running command: hmmsearch --tblout OceanDNA-b23944/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d5b6626-d85a-4a14-9fc5-9dc886c29811/dqc_reference/reference_markers.hmm OceanDNA-b23944/protein.faa > /dev/null
[2023-03-19 04:43:36,625] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:36,626] [INFO] Found 6/6 markers.
[2023-03-19 04:43:36,641] [INFO] Query marker FASTA was written to OceanDNA-b23944/markers.fasta
[2023-03-19 04:43:36,641] [INFO] Task started: Blastn
[2023-03-19 04:43:36,641] [INFO] Running command: blastn -query OceanDNA-b23944/markers.fasta -db /var/lib/cwl/stg4d5b6626-d85a-4a14-9fc5-9dc886c29811/dqc_reference/reference_markers.fasta -out OceanDNA-b23944/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:37,405] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:37,405] [INFO] Selected 17 target genomes.
[2023-03-19 04:43:37,406] [INFO] Target genome list was writen to OceanDNA-b23944/target_genomes.txt
[2023-03-19 04:43:37,415] [INFO] Task started: fastANI
[2023-03-19 04:43:37,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1e675b8-cd84-4f8e-ba13-ab06f4f2509e/OceanDNA-b23944.fa --refList OceanDNA-b23944/target_genomes.txt --output OceanDNA-b23944/fastani_result.tsv --threads 1
[2023-03-19 04:43:47,876] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:47,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d5b6626-d85a-4a14-9fc5-9dc886c29811/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:47,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d5b6626-d85a-4a14-9fc5-9dc886c29811/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:47,886] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:43:47,886] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:43:47,886] [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 salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	84.4681	658	858	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	78.849	395	858	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	78.4618	363	858	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	76.9866	161	858	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	76.7779	135	858	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	76.7741	139	858	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	76.757	141	858	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	76.6561	152	858	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	76.6312	155	858	95	below_threshold
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	76.3763	55	858	95	below_threshold
Woodsholea maritima	strain=DSM 17123	GCA_000382325.1	240237	240237	type	True	76.1805	68	858	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	76.1499	50	858	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	76.0667	55	858	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.7662	57	858	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.5014	90	858	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	75.4728	87	858	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:43:47,886] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23944/tc_result.tsv
[2023-03-19 04:43:47,886] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:47,887] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:47,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d5b6626-d85a-4a14-9fc5-9dc886c29811/dqc_reference/checkm_data
[2023-03-19 04:43:47,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:47,954] [INFO] Task started: CheckM
[2023-03-19 04:43:47,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23944/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23944/checkm_input OceanDNA-b23944/checkm_result
[2023-03-19 04:44:30,388] [INFO] Task succeeded: CheckM
[2023-03-19 04:44:30,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:44:30,390] [INFO] ===== Completeness check finished =====
[2023-03-19 04:44:30,390] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:44:30,390] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23944/markers.fasta)
[2023-03-19 04:44:30,392] [INFO] Task started: Blastn
[2023-03-19 04:44:30,392] [INFO] Running command: blastn -query OceanDNA-b23944/markers.fasta -db /var/lib/cwl/stg4d5b6626-d85a-4a14-9fc5-9dc886c29811/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23944/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:44:31,845] [INFO] Task succeeded: Blastn
[2023-03-19 04:44:31,845] [INFO] Selected 9 target genomes.
[2023-03-19 04:44:31,845] [INFO] Target genome list was writen to OceanDNA-b23944/target_genomes_gtdb.txt
[2023-03-19 04:44:31,892] [INFO] Task started: fastANI
[2023-03-19 04:44:31,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1e675b8-cd84-4f8e-ba13-ab06f4f2509e/OceanDNA-b23944.fa --refList OceanDNA-b23944/target_genomes_gtdb.txt --output OceanDNA-b23944/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:44:37,264] [INFO] Task succeeded: fastANI
[2023-03-19 04:44:37,271] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:44:37,271] [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
GCF_900103475.1	s__Maricaulis salignorans	84.4681	658	858	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	78.849	395	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCA_015665295.1	s__Maricaulis sp015665295	78.6628	360	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642925.1	s__Maricaulis sp017642925	78.6535	395	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014745.1	s__Maricaulis maris_A	78.5322	381	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCF_005871165.1	s__Maricaulis sp005871165	78.4727	362	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707795.1	s__Maricaulis sp002707795	78.4394	271	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCA_905480005.1	s__Maricaulis sp905480005	78.3001	325	858	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	78.2812	373	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:44:37,271] [INFO] GTDB search result was written to OceanDNA-b23944/result_gtdb.tsv
[2023-03-19 04:44:37,271] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:44:37,272] [INFO] DFAST_QC result json was written to OceanDNA-b23944/dqc_result.json
[2023-03-19 04:44:37,273] [INFO] DFAST_QC completed!
[2023-03-19 04:44:37,273] [INFO] Total running time: 0h1m19s