[2023-03-15 06:35:36,165] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:35:36,166] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:35:36,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg14ac06bd-eefc-492c-a7a3-469c0f00c55b/dqc_reference
[2023-03-15 06:35:37,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:35:37,284] [INFO] Task started: Prodigal
[2023-03-15 06:35:37,284] [INFO] Running command: cat /var/lib/cwl/stg69cb5a4f-57fa-4128-8d87-d9c1d71b4b2b/OceanDNA-b30206.fa | prodigal -d OceanDNA-b30206/cds.fna -a OceanDNA-b30206/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:36:00,551] [INFO] Task succeeded: Prodigal
[2023-03-15 06:36:00,551] [INFO] Task started: HMMsearch
[2023-03-15 06:36:00,551] [INFO] Running command: hmmsearch --tblout OceanDNA-b30206/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14ac06bd-eefc-492c-a7a3-469c0f00c55b/dqc_reference/reference_markers.hmm OceanDNA-b30206/protein.faa > /dev/null
[2023-03-15 06:36:00,750] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:36:00,751] [INFO] Found 6/6 markers.
[2023-03-15 06:36:00,788] [INFO] Query marker FASTA was written to OceanDNA-b30206/markers.fasta
[2023-03-15 06:36:00,789] [INFO] Task started: Blastn
[2023-03-15 06:36:00,789] [INFO] Running command: blastn -query OceanDNA-b30206/markers.fasta -db /var/lib/cwl/stg14ac06bd-eefc-492c-a7a3-469c0f00c55b/dqc_reference/reference_markers.fasta -out OceanDNA-b30206/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:36:01,599] [INFO] Task succeeded: Blastn
[2023-03-15 06:36:01,601] [INFO] Selected 22 target genomes.
[2023-03-15 06:36:01,602] [INFO] Target genome list was writen to OceanDNA-b30206/target_genomes.txt
[2023-03-15 06:36:01,614] [INFO] Task started: fastANI
[2023-03-15 06:36:01,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg69cb5a4f-57fa-4128-8d87-d9c1d71b4b2b/OceanDNA-b30206.fa --refList OceanDNA-b30206/target_genomes.txt --output OceanDNA-b30206/fastani_result.tsv --threads 1
[2023-03-15 06:36:17,485] [INFO] Task succeeded: fastANI
[2023-03-15 06:36:17,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14ac06bd-eefc-492c-a7a3-469c0f00c55b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:36:17,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14ac06bd-eefc-492c-a7a3-469c0f00c55b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:36:17,497] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:36:17,497] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:36:17,498] [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 undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	79.0071	514	1180	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	78.4179	435	1180	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	78.3638	438	1180	95	below_threshold
Sulfitobacter guttiformis	strain=DSM 11458	GCA_003610455.1	74349	74349	type	True	78.2713	491	1180	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	78.211	422	1180	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.103	468	1180	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.0871	469	1180	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.9711	370	1180	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.9679	437	1180	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.8602	388	1180	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.8577	387	1180	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.7777	415	1180	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.5315	347	1180	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.3084	274	1180	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.2172	320	1180	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.2003	316	1180	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.9996	302	1180	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.8949	221	1180	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.8666	221	1180	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8296	203	1180	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.7714	172	1180	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.6565	235	1180	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:36:17,500] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30206/tc_result.tsv
[2023-03-15 06:36:17,505] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:36:17,506] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:36:17,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14ac06bd-eefc-492c-a7a3-469c0f00c55b/dqc_reference/checkm_data
[2023-03-15 06:36:17,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:36:17,518] [INFO] Task started: CheckM
[2023-03-15 06:36:17,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30206/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30206/checkm_input OceanDNA-b30206/checkm_result
[2023-03-15 06:37:14,348] [INFO] Task succeeded: CheckM
[2023-03-15 06:37:14,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:37:14,352] [INFO] ===== Completeness check finished =====
[2023-03-15 06:37:14,352] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:37:14,352] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30206/markers.fasta)
[2023-03-15 06:37:14,353] [INFO] Task started: Blastn
[2023-03-15 06:37:14,353] [INFO] Running command: blastn -query OceanDNA-b30206/markers.fasta -db /var/lib/cwl/stg14ac06bd-eefc-492c-a7a3-469c0f00c55b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30206/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:37:15,845] [INFO] Task succeeded: Blastn
[2023-03-15 06:37:15,846] [INFO] Selected 21 target genomes.
[2023-03-15 06:37:15,846] [INFO] Target genome list was writen to OceanDNA-b30206/target_genomes_gtdb.txt
[2023-03-15 06:37:15,891] [INFO] Task started: fastANI
[2023-03-15 06:37:15,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg69cb5a4f-57fa-4128-8d87-d9c1d71b4b2b/OceanDNA-b30206.fa --refList OceanDNA-b30206/target_genomes_gtdb.txt --output OceanDNA-b30206/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:37:33,061] [INFO] Task succeeded: fastANI
[2023-03-15 06:37:33,073] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:37:33,073] [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_018200035.1	s__Sulfitobacter sp018200035	79.1122	597	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196805.1	s__Sulfitobacter undariae	79.0071	514	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	78.4269	434	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003610455.1	s__Sulfitobacter guttiformis	78.2713	491	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.2548	479	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	78.211	422	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_009363555.1	s__Sulfitobacter sp009363555	78.1636	442	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.0859	469	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCA_017854855.1	s__Sulfitobacter sp017854855	78.0179	418	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113435.1	s__Sulfitobacter dubius	77.8691	387	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_900102535.1	s__Sulfitobacter delicatus	77.8577	387	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	77.8208	367	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	77.7962	408	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.7936	413	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.7245	401	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_001886735.1	s__Sulfitobacter alexandrii	77.6634	460	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013317235.1	s__Leisingera sp013317235	77.3924	314	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.2172	320	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002405.1	s__Sulfitobacter sp013002405	77.1645	328	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001518015.1	s__Epibacterium horizontis	77.0705	254	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000158135.1	s__Ruegeria sp000158135	77.0028	225	1180	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:37:33,075] [INFO] GTDB search result was written to OceanDNA-b30206/result_gtdb.tsv
[2023-03-15 06:37:33,077] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:37:33,082] [INFO] DFAST_QC result json was written to OceanDNA-b30206/dqc_result.json
[2023-03-15 06:37:33,082] [INFO] DFAST_QC completed!
[2023-03-15 06:37:33,082] [INFO] Total running time: 0h1m57s