[2023-03-15 22:15:27,633] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:15:27,634] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:15:27,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg70f80954-947c-4424-bcbe-f341e72558f6/dqc_reference
[2023-03-15 22:15:29,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:15:29,361] [INFO] Task started: Prodigal
[2023-03-15 22:15:29,361] [INFO] Running command: cat /var/lib/cwl/stg1a98f1af-d46e-4e77-a2fd-8619ce780761/OceanDNA-b23949.fa | prodigal -d OceanDNA-b23949/cds.fna -a OceanDNA-b23949/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:15:41,036] [INFO] Task succeeded: Prodigal
[2023-03-15 22:15:41,037] [INFO] Task started: HMMsearch
[2023-03-15 22:15:41,037] [INFO] Running command: hmmsearch --tblout OceanDNA-b23949/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70f80954-947c-4424-bcbe-f341e72558f6/dqc_reference/reference_markers.hmm OceanDNA-b23949/protein.faa > /dev/null
[2023-03-15 22:15:41,224] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:15:41,224] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1a98f1af-d46e-4e77-a2fd-8619ce780761/OceanDNA-b23949.fa]
[2023-03-15 22:15:41,254] [INFO] Query marker FASTA was written to OceanDNA-b23949/markers.fasta
[2023-03-15 22:15:41,255] [INFO] Task started: Blastn
[2023-03-15 22:15:41,255] [INFO] Running command: blastn -query OceanDNA-b23949/markers.fasta -db /var/lib/cwl/stg70f80954-947c-4424-bcbe-f341e72558f6/dqc_reference/reference_markers.fasta -out OceanDNA-b23949/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:15:42,014] [INFO] Task succeeded: Blastn
[2023-03-15 22:15:42,018] [INFO] Selected 18 target genomes.
[2023-03-15 22:15:42,018] [INFO] Target genome list was writen to OceanDNA-b23949/target_genomes.txt
[2023-03-15 22:15:42,029] [INFO] Task started: fastANI
[2023-03-15 22:15:42,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a98f1af-d46e-4e77-a2fd-8619ce780761/OceanDNA-b23949.fa --refList OceanDNA-b23949/target_genomes.txt --output OceanDNA-b23949/fastani_result.tsv --threads 1
[2023-03-15 22:15:54,106] [INFO] Task succeeded: fastANI
[2023-03-15 22:15:54,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70f80954-947c-4424-bcbe-f341e72558f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:15:54,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70f80954-947c-4424-bcbe-f341e72558f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:15:54,116] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:15:54,116] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:15:54,116] [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	87.6971	571	634	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	80.408	412	634	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	78.6902	323	634	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	77.3184	116	634	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.272	140	634	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.272	140	634	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.2505	113	634	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	76.8758	66	634	95	below_threshold
Euryhalocaulis caribicus	strain=JL2009	GCA_000412185.1	1161401	1161401	type	True	76.5123	112	634	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	76.4653	55	634	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	76.0237	77	634	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	75.7909	71	634	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.7532	61	634	95	below_threshold
Breoghania corrubedonensis	strain=DSM 23382	GCA_003053845.1	665038	665038	type	True	75.5729	59	634	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.33	56	634	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:15:54,118] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23949/tc_result.tsv
[2023-03-15 22:15:54,121] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:15:54,121] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:15:54,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70f80954-947c-4424-bcbe-f341e72558f6/dqc_reference/checkm_data
[2023-03-15 22:15:54,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:15:54,127] [INFO] Task started: CheckM
[2023-03-15 22:15:54,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23949/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23949/checkm_input OceanDNA-b23949/checkm_result
[2023-03-15 22:16:35,532] [INFO] Task succeeded: CheckM
[2023-03-15 22:16:35,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:16:35,629] [INFO] ===== Completeness check finished =====
[2023-03-15 22:16:35,629] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:16:35,629] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23949/markers.fasta)
[2023-03-15 22:16:35,630] [INFO] Task started: Blastn
[2023-03-15 22:16:35,630] [INFO] Running command: blastn -query OceanDNA-b23949/markers.fasta -db /var/lib/cwl/stg70f80954-947c-4424-bcbe-f341e72558f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23949/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:16:37,006] [INFO] Task succeeded: Blastn
[2023-03-15 22:16:37,011] [INFO] Selected 9 target genomes.
[2023-03-15 22:16:37,011] [INFO] Target genome list was writen to OceanDNA-b23949/target_genomes_gtdb.txt
[2023-03-15 22:16:37,022] [INFO] Task started: fastANI
[2023-03-15 22:16:37,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a98f1af-d46e-4e77-a2fd-8619ce780761/OceanDNA-b23949.fa --refList OceanDNA-b23949/target_genomes_gtdb.txt --output OceanDNA-b23949/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:16:42,292] [INFO] Task succeeded: fastANI
[2023-03-15 22:16:42,299] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:16:42,299] [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_002694345.1	s__Maricaulis sp002694345	99.7403	494	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005871165.1	s__Maricaulis sp005871165	87.6971	571	634	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	87.3599	556	634	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	81.8361	475	634	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	81.3716	359	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCA_015665295.1	s__Maricaulis sp015665295	80.478	396	634	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	80.4042	412	634	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	80.2645	390	634	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	80.1453	369	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:16:42,302] [INFO] GTDB search result was written to OceanDNA-b23949/result_gtdb.tsv
[2023-03-15 22:16:42,306] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:16:42,311] [INFO] DFAST_QC result json was written to OceanDNA-b23949/dqc_result.json
[2023-03-15 22:16:42,311] [INFO] DFAST_QC completed!
[2023-03-15 22:16:42,311] [INFO] Total running time: 0h1m15s