[2023-03-18 03:27:00,919] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,920] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,920] [INFO] DQC Reference Directory: /var/lib/cwl/stgc89686b7-84ac-4fae-a6df-6719a3b23773/dqc_reference
[2023-03-18 03:27:02,640] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,640] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,640] [INFO] Running command: cat /var/lib/cwl/stg865155cc-d116-4435-86ba-4cf61e8844fb/OceanDNA-b30221.fa | prodigal -d OceanDNA-b30221/cds.fna -a OceanDNA-b30221/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:26,493] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:26,493] [INFO] Task started: HMMsearch
[2023-03-18 03:27:26,493] [INFO] Running command: hmmsearch --tblout OceanDNA-b30221/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc89686b7-84ac-4fae-a6df-6719a3b23773/dqc_reference/reference_markers.hmm OceanDNA-b30221/protein.faa > /dev/null
[2023-03-18 03:27:26,698] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:26,698] [INFO] Found 6/6 markers.
[2023-03-18 03:27:26,721] [INFO] Query marker FASTA was written to OceanDNA-b30221/markers.fasta
[2023-03-18 03:27:26,721] [INFO] Task started: Blastn
[2023-03-18 03:27:26,721] [INFO] Running command: blastn -query OceanDNA-b30221/markers.fasta -db /var/lib/cwl/stgc89686b7-84ac-4fae-a6df-6719a3b23773/dqc_reference/reference_markers.fasta -out OceanDNA-b30221/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:27,448] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:27,449] [INFO] Selected 19 target genomes.
[2023-03-18 03:27:27,449] [INFO] Target genome list was writen to OceanDNA-b30221/target_genomes.txt
[2023-03-18 03:27:27,461] [INFO] Task started: fastANI
[2023-03-18 03:27:27,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg865155cc-d116-4435-86ba-4cf61e8844fb/OceanDNA-b30221.fa --refList OceanDNA-b30221/target_genomes.txt --output OceanDNA-b30221/fastani_result.tsv --threads 1
[2023-03-18 03:27:41,170] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:41,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc89686b7-84ac-4fae-a6df-6719a3b23773/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:41,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc89686b7-84ac-4fae-a6df-6719a3b23773/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:41,182] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:41,182] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:27:41,182] [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 marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	87.3037	958	1217	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	80.3981	616	1217	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	80.0785	586	1217	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	78.1754	428	1217	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.1704	423	1217	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.9529	412	1217	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.9393	422	1217	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	77.7452	326	1217	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.7348	370	1217	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.6909	368	1217	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.5477	385	1217	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	76.847	286	1217	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	76.5225	201	1217	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.4553	194	1217	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.3021	150	1217	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.2938	189	1217	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.1508	150	1217	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.0778	157	1217	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.0718	158	1217	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:27:41,182] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30221/tc_result.tsv
[2023-03-18 03:27:41,182] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:41,182] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:41,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc89686b7-84ac-4fae-a6df-6719a3b23773/dqc_reference/checkm_data
[2023-03-18 03:27:41,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:41,188] [INFO] Task started: CheckM
[2023-03-18 03:27:41,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30221/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30221/checkm_input OceanDNA-b30221/checkm_result
[2023-03-18 03:28:40,295] [INFO] Task succeeded: CheckM
[2023-03-18 03:28:40,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:28:40,299] [INFO] ===== Completeness check finished =====
[2023-03-18 03:28:40,299] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:28:40,299] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30221/markers.fasta)
[2023-03-18 03:28:40,299] [INFO] Task started: Blastn
[2023-03-18 03:28:40,299] [INFO] Running command: blastn -query OceanDNA-b30221/markers.fasta -db /var/lib/cwl/stgc89686b7-84ac-4fae-a6df-6719a3b23773/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30221/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:41,600] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:41,601] [INFO] Selected 9 target genomes.
[2023-03-18 03:28:41,601] [INFO] Target genome list was writen to OceanDNA-b30221/target_genomes_gtdb.txt
[2023-03-18 03:28:41,608] [INFO] Task started: fastANI
[2023-03-18 03:28:41,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg865155cc-d116-4435-86ba-4cf61e8844fb/OceanDNA-b30221.fa --refList OceanDNA-b30221/target_genomes_gtdb.txt --output OceanDNA-b30221/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:28:48,648] [INFO] Task succeeded: fastANI
[2023-03-18 03:28:48,654] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:28:48,654] [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_013139555.1	s__Sulfitobacter sp013139555	95.7383	863	1217	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_900116285.1	s__Sulfitobacter marinus	87.3037	958	1217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	85.6366	864	1217	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	81.7584	760	1217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	80.3981	616	1217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_006064855.1	s__Sulfitobacter sp006064855	80.0476	576	1217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622325.1	s__Sulfitobacter geojensis	78.1941	420	1217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_900113435.1	s__Sulfitobacter dubius	77.5475	385	1217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCA_002366775.1	s__Roseovarius sp002366775	76.7146	125	1217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:28:48,654] [INFO] GTDB search result was written to OceanDNA-b30221/result_gtdb.tsv
[2023-03-18 03:28:48,654] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:28:48,656] [INFO] DFAST_QC result json was written to OceanDNA-b30221/dqc_result.json
[2023-03-18 03:28:48,656] [INFO] DFAST_QC completed!
[2023-03-18 03:28:48,656] [INFO] Total running time: 0h1m48s