[2023-03-17 09:11:23,901] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:11:23,901] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:11:23,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg6cd43093-38d8-4828-893a-049fc684560a/dqc_reference
[2023-03-17 09:11:24,998] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:11:24,999] [INFO] Task started: Prodigal
[2023-03-17 09:11:24,999] [INFO] Running command: cat /var/lib/cwl/stg8086c2bd-d7d3-4140-b3af-c567082b9d60/OceanDNA-b30215.fa | prodigal -d OceanDNA-b30215/cds.fna -a OceanDNA-b30215/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:11:42,050] [INFO] Task succeeded: Prodigal
[2023-03-17 09:11:42,050] [INFO] Task started: HMMsearch
[2023-03-17 09:11:42,050] [INFO] Running command: hmmsearch --tblout OceanDNA-b30215/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6cd43093-38d8-4828-893a-049fc684560a/dqc_reference/reference_markers.hmm OceanDNA-b30215/protein.faa > /dev/null
[2023-03-17 09:11:42,253] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:11:42,253] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8086c2bd-d7d3-4140-b3af-c567082b9d60/OceanDNA-b30215.fa]
[2023-03-17 09:11:42,276] [INFO] Query marker FASTA was written to OceanDNA-b30215/markers.fasta
[2023-03-17 09:11:42,278] [INFO] Task started: Blastn
[2023-03-17 09:11:42,278] [INFO] Running command: blastn -query OceanDNA-b30215/markers.fasta -db /var/lib/cwl/stg6cd43093-38d8-4828-893a-049fc684560a/dqc_reference/reference_markers.fasta -out OceanDNA-b30215/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:11:43,090] [INFO] Task succeeded: Blastn
[2023-03-17 09:11:43,095] [INFO] Selected 16 target genomes.
[2023-03-17 09:11:43,096] [INFO] Target genome list was writen to OceanDNA-b30215/target_genomes.txt
[2023-03-17 09:11:43,227] [INFO] Task started: fastANI
[2023-03-17 09:11:43,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg8086c2bd-d7d3-4140-b3af-c567082b9d60/OceanDNA-b30215.fa --refList OceanDNA-b30215/target_genomes.txt --output OceanDNA-b30215/fastani_result.tsv --threads 1
[2023-03-17 09:11:54,684] [INFO] Task succeeded: fastANI
[2023-03-17 09:11:54,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6cd43093-38d8-4828-893a-049fc684560a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:11:54,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6cd43093-38d8-4828-893a-049fc684560a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:11:54,693] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:11:54,693] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:11:54,693] [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
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	94.7354	801	890	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	86.6517	748	890	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	79.3184	448	890	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.1624	342	890	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.1586	334	890	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.0563	333	890	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.049	331	890	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.7851	308	890	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	76.9376	164	890	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.6561	224	890	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	76.6094	88	890	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	76.6019	129	890	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	76.2462	103	890	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:11:54,696] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30215/tc_result.tsv
[2023-03-17 09:11:54,698] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:11:54,698] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:11:54,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6cd43093-38d8-4828-893a-049fc684560a/dqc_reference/checkm_data
[2023-03-17 09:11:54,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:11:54,868] [INFO] Task started: CheckM
[2023-03-17 09:11:54,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30215/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30215/checkm_input OceanDNA-b30215/checkm_result
[2023-03-17 09:12:39,393] [INFO] Task succeeded: CheckM
[2023-03-17 09:12:39,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:12:39,451] [INFO] ===== Completeness check finished =====
[2023-03-17 09:12:39,451] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:12:39,451] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30215/markers.fasta)
[2023-03-17 09:12:39,452] [INFO] Task started: Blastn
[2023-03-17 09:12:39,453] [INFO] Running command: blastn -query OceanDNA-b30215/markers.fasta -db /var/lib/cwl/stg6cd43093-38d8-4828-893a-049fc684560a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30215/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:12:40,828] [INFO] Task succeeded: Blastn
[2023-03-17 09:12:40,831] [INFO] Selected 12 target genomes.
[2023-03-17 09:12:40,831] [INFO] Target genome list was writen to OceanDNA-b30215/target_genomes_gtdb.txt
[2023-03-17 09:12:40,896] [INFO] Task started: fastANI
[2023-03-17 09:12:40,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg8086c2bd-d7d3-4140-b3af-c567082b9d60/OceanDNA-b30215.fa --refList OceanDNA-b30215/target_genomes_gtdb.txt --output OceanDNA-b30215/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:12:49,345] [INFO] Task succeeded: fastANI
[2023-03-17 09:12:49,353] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:12:49,353] [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_006064855.1	s__Sulfitobacter sp006064855	98.8982	759	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900103185.1	s__Sulfitobacter litoralis	94.7354	801	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_900106935.1	s__Sulfitobacter pontiacus	86.665	747	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_013282155.1	s__Sulfitobacter sp013282155	80.1998	506	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000156335.1	s__Sulfitobacter sp000156335	79.9056	493	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	79.5898	412	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	79.3184	448	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.7851	308	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	77.6967	337	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	77.053	230	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	76.9376	164	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478745.1	s__Ascidiaceihabitans sp002478745	76.1846	77	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.75	99.75	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-17 09:12:49,354] [INFO] GTDB search result was written to OceanDNA-b30215/result_gtdb.tsv
[2023-03-17 09:12:49,355] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:12:49,359] [INFO] DFAST_QC result json was written to OceanDNA-b30215/dqc_result.json
[2023-03-17 09:12:49,359] [INFO] DFAST_QC completed!
[2023-03-17 09:12:49,359] [INFO] Total running time: 0h1m25s