[2023-03-14 11:33:34,917] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,918] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,918] [INFO] DQC Reference Directory: /var/lib/cwl/stga5489b0e-b604-44c5-8b2d-9c58dd92da14/dqc_reference
[2023-03-14 11:33:36,164] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,164] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,164] [INFO] Running command: cat /var/lib/cwl/stgfba88ea2-43e8-48f8-8331-63e1912797ce/OceanDNA-b23918.fa | prodigal -d OceanDNA-b23918/cds.fna -a OceanDNA-b23918/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:52,960] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:52,961] [INFO] Task started: HMMsearch
[2023-03-14 11:33:52,961] [INFO] Running command: hmmsearch --tblout OceanDNA-b23918/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5489b0e-b604-44c5-8b2d-9c58dd92da14/dqc_reference/reference_markers.hmm OceanDNA-b23918/protein.faa > /dev/null
[2023-03-14 11:33:53,165] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:53,165] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfba88ea2-43e8-48f8-8331-63e1912797ce/OceanDNA-b23918.fa]
[2023-03-14 11:33:53,183] [INFO] Query marker FASTA was written to OceanDNA-b23918/markers.fasta
[2023-03-14 11:33:53,183] [INFO] Task started: Blastn
[2023-03-14 11:33:53,183] [INFO] Running command: blastn -query OceanDNA-b23918/markers.fasta -db /var/lib/cwl/stga5489b0e-b604-44c5-8b2d-9c58dd92da14/dqc_reference/reference_markers.fasta -out OceanDNA-b23918/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:53,947] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:53,948] [INFO] Selected 14 target genomes.
[2023-03-14 11:33:53,949] [INFO] Target genome list was writen to OceanDNA-b23918/target_genomes.txt
[2023-03-14 11:33:53,956] [INFO] Task started: fastANI
[2023-03-14 11:33:53,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgfba88ea2-43e8-48f8-8331-63e1912797ce/OceanDNA-b23918.fa --refList OceanDNA-b23918/target_genomes.txt --output OceanDNA-b23918/fastani_result.tsv --threads 1
[2023-03-14 11:34:01,959] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:01,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5489b0e-b604-44c5-8b2d-9c58dd92da14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:01,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5489b0e-b604-44c5-8b2d-9c58dd92da14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:01,969] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:34:01,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:34:01,969] [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	86.536	707	868	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	78.6411	389	868	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	78.2877	366	868	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	76.8525	155	868	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	76.6746	107	868	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	76.5983	111	868	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	76.3866	127	868	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	76.3717	128	868	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.282	148	868	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	75.9185	152	868	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	75.9052	153	868	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	75.7708	63	868	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	75.7096	78	868	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.5428	72	868	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:34:01,970] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23918/tc_result.tsv
[2023-03-14 11:34:01,970] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:01,970] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:01,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5489b0e-b604-44c5-8b2d-9c58dd92da14/dqc_reference/checkm_data
[2023-03-14 11:34:01,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:02,027] [INFO] Task started: CheckM
[2023-03-14 11:34:02,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23918/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23918/checkm_input OceanDNA-b23918/checkm_result
[2023-03-14 11:34:45,813] [INFO] Task succeeded: CheckM
[2023-03-14 11:34:45,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:34:45,815] [INFO] ===== Completeness check finished =====
[2023-03-14 11:34:45,815] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:34:45,816] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23918/markers.fasta)
[2023-03-14 11:34:45,816] [INFO] Task started: Blastn
[2023-03-14 11:34:45,816] [INFO] Running command: blastn -query OceanDNA-b23918/markers.fasta -db /var/lib/cwl/stga5489b0e-b604-44c5-8b2d-9c58dd92da14/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23918/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:46,840] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:46,841] [INFO] Selected 8 target genomes.
[2023-03-14 11:34:46,841] [INFO] Target genome list was writen to OceanDNA-b23918/target_genomes_gtdb.txt
[2023-03-14 11:34:46,848] [INFO] Task started: fastANI
[2023-03-14 11:34:46,848] [INFO] Running command: fastANI --query /var/lib/cwl/stgfba88ea2-43e8-48f8-8331-63e1912797ce/OceanDNA-b23918.fa --refList OceanDNA-b23918/target_genomes_gtdb.txt --output OceanDNA-b23918/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:34:51,739] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:51,745] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:34:51,745] [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	86.536	707	868	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	78.6411	389	868	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	78.4427	384	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCA_015665295.1	s__Maricaulis sp015665295	78.3419	384	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480005.1	s__Maricaulis sp905480005	78.2653	337	868	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	78.1874	403	868	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	78.1867	299	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCF_016817355.1	s__Maricaulis parjimensis	78.1004	368	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:34:51,745] [INFO] GTDB search result was written to OceanDNA-b23918/result_gtdb.tsv
[2023-03-14 11:34:51,745] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:34:51,747] [INFO] DFAST_QC result json was written to OceanDNA-b23918/dqc_result.json
[2023-03-14 11:34:51,747] [INFO] DFAST_QC completed!
[2023-03-14 11:34:51,747] [INFO] Total running time: 0h1m17s