[2023-03-18 00:25:17,730] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:25:17,730] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:25:17,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg22eeb3fe-502c-45d8-b4f7-b3805474bf32/dqc_reference
[2023-03-18 00:25:18,823] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:25:18,824] [INFO] Task started: Prodigal
[2023-03-18 00:25:18,824] [INFO] Running command: cat /var/lib/cwl/stg458fed27-8732-4b86-b078-5b53a2265624/OceanDNA-b32852.fa | prodigal -d OceanDNA-b32852/cds.fna -a OceanDNA-b32852/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:25:32,211] [INFO] Task succeeded: Prodigal
[2023-03-18 00:25:32,211] [INFO] Task started: HMMsearch
[2023-03-18 00:25:32,211] [INFO] Running command: hmmsearch --tblout OceanDNA-b32852/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22eeb3fe-502c-45d8-b4f7-b3805474bf32/dqc_reference/reference_markers.hmm OceanDNA-b32852/protein.faa > /dev/null
[2023-03-18 00:25:32,385] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:25:32,386] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg458fed27-8732-4b86-b078-5b53a2265624/OceanDNA-b32852.fa]
[2023-03-18 00:25:32,402] [INFO] Query marker FASTA was written to OceanDNA-b32852/markers.fasta
[2023-03-18 00:25:32,404] [INFO] Task started: Blastn
[2023-03-18 00:25:32,404] [INFO] Running command: blastn -query OceanDNA-b32852/markers.fasta -db /var/lib/cwl/stg22eeb3fe-502c-45d8-b4f7-b3805474bf32/dqc_reference/reference_markers.fasta -out OceanDNA-b32852/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:25:33,102] [INFO] Task succeeded: Blastn
[2023-03-18 00:25:33,102] [INFO] Selected 27 target genomes.
[2023-03-18 00:25:33,103] [INFO] Target genome list was writen to OceanDNA-b32852/target_genomes.txt
[2023-03-18 00:25:33,145] [INFO] Task started: fastANI
[2023-03-18 00:25:33,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg458fed27-8732-4b86-b078-5b53a2265624/OceanDNA-b32852.fa --refList OceanDNA-b32852/target_genomes.txt --output OceanDNA-b32852/fastani_result.tsv --threads 1
[2023-03-18 00:25:51,127] [INFO] Task succeeded: fastANI
[2023-03-18 00:25:51,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22eeb3fe-502c-45d8-b4f7-b3805474bf32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:25:51,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22eeb3fe-502c-45d8-b4f7-b3805474bf32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:25:51,183] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:25:51,183] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:25:51,183] [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
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.9015	60	711	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.8354	64	711	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	75.8223	59	711	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.8039	58	711	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	75.7918	59	711	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.7853	72	711	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	75.7134	76	711	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.6306	69	711	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.5989	94	711	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.5591	95	711	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.4499	72	711	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.4499	72	711	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	75.4436	53	711	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.305	56	711	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	75.2451	60	711	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:25:51,188] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32852/tc_result.tsv
[2023-03-18 00:25:51,250] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:25:51,251] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:25:51,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22eeb3fe-502c-45d8-b4f7-b3805474bf32/dqc_reference/checkm_data
[2023-03-18 00:25:51,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:25:51,255] [INFO] Task started: CheckM
[2023-03-18 00:25:51,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32852/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32852/checkm_input OceanDNA-b32852/checkm_result
[2023-03-18 00:26:27,342] [INFO] Task succeeded: CheckM
[2023-03-18 00:26:27,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:26:27,346] [INFO] ===== Completeness check finished =====
[2023-03-18 00:26:27,346] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:26:27,346] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32852/markers.fasta)
[2023-03-18 00:26:27,347] [INFO] Task started: Blastn
[2023-03-18 00:26:27,347] [INFO] Running command: blastn -query OceanDNA-b32852/markers.fasta -db /var/lib/cwl/stg22eeb3fe-502c-45d8-b4f7-b3805474bf32/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32852/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:26:28,485] [INFO] Task succeeded: Blastn
[2023-03-18 00:26:28,486] [INFO] Selected 22 target genomes.
[2023-03-18 00:26:28,486] [INFO] Target genome list was writen to OceanDNA-b32852/target_genomes_gtdb.txt
[2023-03-18 00:26:28,692] [INFO] Task started: fastANI
[2023-03-18 00:26:28,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg458fed27-8732-4b86-b078-5b53a2265624/OceanDNA-b32852.fa --refList OceanDNA-b32852/target_genomes_gtdb.txt --output OceanDNA-b32852/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:26:43,270] [INFO] Task succeeded: fastANI
[2023-03-18 00:26:43,277] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:26:43,278] [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_002501105.1	s__UBA7887 sp002501105	99.0268	551	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7887;f__UBA7887;g__UBA7887	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003576705.1	s__SYSU-D60015 sp003576705	75.9608	98	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	75.8622	76	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172325.1	s__Oceanibacterium hippocampi	75.8354	64	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Oceanibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721365.1	s__GCA-2721365 sp002721365	75.8224	67	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2721365;f__GCA-2721365;g__GCA-2721365	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258835.1	s__Rhodobium orientis	75.8039	58	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCF_008728835.1	s__Hypericibacter adhaerens	75.7853	72	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	75.7297	80	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869915.1	s__CAIOSQ01 sp016869915	75.7061	54	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	97.96	97.96	0.75	0.75	2	-
GCA_009377445.1	s__WHUA01 sp009377445	75.7029	52	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264455.2	s__Tistrella mobilis	75.6852	60	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Tistrellales;f__Tistrellaceae;g__Tistrella	95.0	96.38	95.97	0.88	0.84	5	-
GCA_001657395.1	s__Pelagibius sp001657395	75.5651	63	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:26:43,278] [INFO] GTDB search result was written to OceanDNA-b32852/result_gtdb.tsv
[2023-03-18 00:26:43,278] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:26:43,280] [INFO] DFAST_QC result json was written to OceanDNA-b32852/dqc_result.json
[2023-03-18 00:26:43,280] [INFO] DFAST_QC completed!
[2023-03-18 00:26:43,280] [INFO] Total running time: 0h1m26s