[2023-03-17 11:13:09,841] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:13:09,841] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:13:09,841] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0ddb10d-35ea-4ae4-9140-b0b5de73b2d2/dqc_reference
[2023-03-17 11:13:10,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:13:10,999] [INFO] Task started: Prodigal
[2023-03-17 11:13:11,000] [INFO] Running command: cat /var/lib/cwl/stg1ab48824-5abd-4c99-8b6d-6957dda12e83/OceanDNA-b26923.fa | prodigal -d OceanDNA-b26923/cds.fna -a OceanDNA-b26923/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:13:27,768] [INFO] Task succeeded: Prodigal
[2023-03-17 11:13:27,769] [INFO] Task started: HMMsearch
[2023-03-17 11:13:27,769] [INFO] Running command: hmmsearch --tblout OceanDNA-b26923/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0ddb10d-35ea-4ae4-9140-b0b5de73b2d2/dqc_reference/reference_markers.hmm OceanDNA-b26923/protein.faa > /dev/null
[2023-03-17 11:13:27,997] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:13:27,998] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1ab48824-5abd-4c99-8b6d-6957dda12e83/OceanDNA-b26923.fa]
[2023-03-17 11:13:28,105] [INFO] Query marker FASTA was written to OceanDNA-b26923/markers.fasta
[2023-03-17 11:13:28,106] [INFO] Task started: Blastn
[2023-03-17 11:13:28,106] [INFO] Running command: blastn -query OceanDNA-b26923/markers.fasta -db /var/lib/cwl/stgb0ddb10d-35ea-4ae4-9140-b0b5de73b2d2/dqc_reference/reference_markers.fasta -out OceanDNA-b26923/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:13:28,838] [INFO] Task succeeded: Blastn
[2023-03-17 11:13:28,867] [INFO] Selected 24 target genomes.
[2023-03-17 11:13:28,867] [INFO] Target genome list was writen to OceanDNA-b26923/target_genomes.txt
[2023-03-17 11:13:28,901] [INFO] Task started: fastANI
[2023-03-17 11:13:28,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ab48824-5abd-4c99-8b6d-6957dda12e83/OceanDNA-b26923.fa --refList OceanDNA-b26923/target_genomes.txt --output OceanDNA-b26923/fastani_result.tsv --threads 1
[2023-03-17 11:13:45,123] [INFO] Task succeeded: fastANI
[2023-03-17 11:13:45,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0ddb10d-35ea-4ae4-9140-b0b5de73b2d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:13:45,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0ddb10d-35ea-4ae4-9140-b0b5de73b2d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:13:45,133] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:13:45,133] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:13:45,133] [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
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	87.7368	515	599	95	below_threshold
Roseibium marinum	strain=DSM 17023	GCA_002906165.1	281252	281252	type	True	79.4678	299	599	95	below_threshold
Roseibium alexandrii	strain=DFL-11	GCA_000158095.2	388408	388408	type	True	78.4816	162	599	95	below_threshold
Roseibium album	strain=CECT 5095	GCA_001404515.1	311410	311410	type	True	78.4483	212	599	95	below_threshold
Roseibium suaedae	strain=DSM 22153	GCA_900142725.1	735517	735517	type	True	78.3231	167	599	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	78.2309	158	599	95	below_threshold
Roseibium denhamense	strain=JCM 10543	GCA_009711415.1	76305	76305	type	True	77.8662	154	599	95	below_threshold
Roseibium limicola	strain=CAU 1637	GCA_017313085.1	2816037	2816037	type	True	77.6735	123	599	95	below_threshold
Roseibium polysiphoniae	strain=KACC 19711	GCA_014842925.1	2571221	2571221	type	True	77.5978	113	599	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	77.506	129	599	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	77.506	129	599	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	77.4588	137	599	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	77.4127	140	599	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	76.7377	96	599	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:13:45,144] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26923/tc_result.tsv
[2023-03-17 11:13:45,154] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:13:45,154] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:13:45,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0ddb10d-35ea-4ae4-9140-b0b5de73b2d2/dqc_reference/checkm_data
[2023-03-17 11:13:45,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:13:45,164] [INFO] Task started: CheckM
[2023-03-17 11:13:45,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26923/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26923/checkm_input OceanDNA-b26923/checkm_result
[2023-03-17 11:14:30,328] [INFO] Task succeeded: CheckM
[2023-03-17 11:14:30,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.91%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:14:30,342] [INFO] ===== Completeness check finished =====
[2023-03-17 11:14:30,342] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:14:30,342] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26923/markers.fasta)
[2023-03-17 11:14:30,343] [INFO] Task started: Blastn
[2023-03-17 11:14:30,343] [INFO] Running command: blastn -query OceanDNA-b26923/markers.fasta -db /var/lib/cwl/stgb0ddb10d-35ea-4ae4-9140-b0b5de73b2d2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26923/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:14:31,631] [INFO] Task succeeded: Blastn
[2023-03-17 11:14:31,631] [INFO] Selected 12 target genomes.
[2023-03-17 11:14:31,632] [INFO] Target genome list was writen to OceanDNA-b26923/target_genomes_gtdb.txt
[2023-03-17 11:14:31,647] [INFO] Task started: fastANI
[2023-03-17 11:14:31,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ab48824-5abd-4c99-8b6d-6957dda12e83/OceanDNA-b26923.fa --refList OceanDNA-b26923/target_genomes_gtdb.txt --output OceanDNA-b26923/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:14:43,561] [INFO] Task succeeded: fastANI
[2023-03-17 11:14:43,569] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:14:43,569] [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_001999245.1	s__Roseibium aggregatum_A	98.2319	592	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.61	96.85	0.93	0.89	16	conclusive
GCF_000168975.1	s__Roseibium aggregatum	87.758	514	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008107695.1	s__Roseibium sp008107695	86.1729	486	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237595.1	s__Roseibium sp002237595	80.3206	335	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075075.1	s__Roseibium sp003075075	79.7625	275	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008107755.1	s__Roseibium sp008107755	79.6443	267	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002906165.1	s__Roseibium marinum	79.4678	299	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309185.1	s__Roseibium aggregatum_B	79.4001	276	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001624695.1	s__Roseibium sp001624695	79.2739	276	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643925.1	s__Roseibium sp017643925	78.9671	219	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000158095.2	s__Roseibium alexandrii	78.4816	162	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.43	97.43	0.93	0.93	2	-
GCF_000521215.1	s__Roseibium sp000521215	78.047	213	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:14:43,569] [INFO] GTDB search result was written to OceanDNA-b26923/result_gtdb.tsv
[2023-03-17 11:14:43,569] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:14:43,571] [INFO] DFAST_QC result json was written to OceanDNA-b26923/dqc_result.json
[2023-03-17 11:14:43,571] [INFO] DFAST_QC completed!
[2023-03-17 11:14:43,571] [INFO] Total running time: 0h1m34s