[2023-03-18 10:16:34,830] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:16:34,831] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:16:34,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg73032360-5a7f-463f-a68f-ea947f0d4688/dqc_reference
[2023-03-18 10:16:35,968] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:16:35,968] [INFO] Task started: Prodigal
[2023-03-18 10:16:35,968] [INFO] Running command: cat /var/lib/cwl/stg8132f668-09a8-42ff-b77e-d8ef912c73ff/OceanDNA-b1251.fa | prodigal -d OceanDNA-b1251/cds.fna -a OceanDNA-b1251/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:16:50,297] [INFO] Task succeeded: Prodigal
[2023-03-18 10:16:50,297] [INFO] Task started: HMMsearch
[2023-03-18 10:16:50,297] [INFO] Running command: hmmsearch --tblout OceanDNA-b1251/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73032360-5a7f-463f-a68f-ea947f0d4688/dqc_reference/reference_markers.hmm OceanDNA-b1251/protein.faa > /dev/null
[2023-03-18 10:16:50,459] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:16:50,459] [INFO] Found 6/6 markers.
[2023-03-18 10:16:50,472] [INFO] Query marker FASTA was written to OceanDNA-b1251/markers.fasta
[2023-03-18 10:16:50,474] [INFO] Task started: Blastn
[2023-03-18 10:16:50,474] [INFO] Running command: blastn -query OceanDNA-b1251/markers.fasta -db /var/lib/cwl/stg73032360-5a7f-463f-a68f-ea947f0d4688/dqc_reference/reference_markers.fasta -out OceanDNA-b1251/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:16:51,221] [INFO] Task succeeded: Blastn
[2023-03-18 10:16:51,221] [INFO] Selected 24 target genomes.
[2023-03-18 10:16:51,222] [INFO] Target genome list was writen to OceanDNA-b1251/target_genomes.txt
[2023-03-18 10:16:51,236] [INFO] Task started: fastANI
[2023-03-18 10:16:51,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg8132f668-09a8-42ff-b77e-d8ef912c73ff/OceanDNA-b1251.fa --refList OceanDNA-b1251/target_genomes.txt --output OceanDNA-b1251/fastani_result.tsv --threads 1
[2023-03-18 10:17:07,429] [INFO] Task succeeded: fastANI
[2023-03-18 10:17:07,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73032360-5a7f-463f-a68f-ea947f0d4688/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:17:07,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73032360-5a7f-463f-a68f-ea947f0d4688/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:17:07,438] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:17:07,439] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:17:07,439] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.0951	170	747	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.8818	172	747	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.5731	149	747	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.4472	77	747	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.3437	120	747	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.1821	74	747	95	below_threshold
Stackebrandtia albiflava	strain=DSM 45044	GCA_007994225.1	406432	406432	type	True	75.5887	62	747	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	75.5302	57	747	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	75.3758	62	747	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	75.3419	98	747	95	below_threshold
Micromonospora matsumotoense	strain=DSM 44100	GCA_900091525.1	121616	121616	type	True	75.3281	92	747	95	below_threshold
Nocardia transvalensis	strain=DSM 43582	GCA_014203315.1	37333	37333	type	True	75.1997	63	747	95	below_threshold
Nocardia transvalensis	strain=NBRC 15921	GCA_000308875.1	37333	37333	type	True	75.028	63	747	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:17:07,439] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1251/tc_result.tsv
[2023-03-18 10:17:07,439] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:17:07,439] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:17:07,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73032360-5a7f-463f-a68f-ea947f0d4688/dqc_reference/checkm_data
[2023-03-18 10:17:07,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:17:07,444] [INFO] Task started: CheckM
[2023-03-18 10:17:07,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1251/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1251/checkm_input OceanDNA-b1251/checkm_result
[2023-03-18 10:17:46,273] [INFO] Task succeeded: CheckM
[2023-03-18 10:17:46,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:17:46,279] [INFO] ===== Completeness check finished =====
[2023-03-18 10:17:46,279] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:17:46,279] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1251/markers.fasta)
[2023-03-18 10:17:46,281] [INFO] Task started: Blastn
[2023-03-18 10:17:46,281] [INFO] Running command: blastn -query OceanDNA-b1251/markers.fasta -db /var/lib/cwl/stg73032360-5a7f-463f-a68f-ea947f0d4688/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1251/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:17:47,594] [INFO] Task succeeded: Blastn
[2023-03-18 10:17:47,597] [INFO] Selected 11 target genomes.
[2023-03-18 10:17:47,597] [INFO] Target genome list was writen to OceanDNA-b1251/target_genomes_gtdb.txt
[2023-03-18 10:17:47,644] [INFO] Task started: fastANI
[2023-03-18 10:17:47,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg8132f668-09a8-42ff-b77e-d8ef912c73ff/OceanDNA-b1251.fa --refList OceanDNA-b1251/target_genomes_gtdb.txt --output OceanDNA-b1251/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:17:52,606] [INFO] Task succeeded: fastANI
[2023-03-18 10:17:52,612] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:17:52,613] [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_012961035.1	s__UBA9410 sp012961035	97.8637	622	747	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	conclusive
GCA_014240365.1	s__UBA9410 sp014240365	88.9509	580	747	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	-
GCA_016845305.1	s__UBA9410 sp016845305	80.9462	517	747	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239855.1	s__UBA9410 sp014239855	80.6302	465	747	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727895.1	s__UBA9410 sp002727895	80.0587	348	747	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_014237715.1	s__UBA9410 sp014237715	79.831	433	747	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_002346745.1	s__S20-B6 sp002346745	79.436	371	747	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_002717365.1	s__UBA9410 sp002717365	79.0542	304	747	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381945.1	s__S20-B6 sp014381945	78.8917	337	747	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002365325.1	s__UBA3125 sp002365325	77.8447	202	747	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.82	97.98	0.79	0.76	7	-
--------------------------------------------------------------------------------
[2023-03-18 10:17:52,614] [INFO] GTDB search result was written to OceanDNA-b1251/result_gtdb.tsv
[2023-03-18 10:17:52,615] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:17:52,619] [INFO] DFAST_QC result json was written to OceanDNA-b1251/dqc_result.json
[2023-03-18 10:17:52,619] [INFO] DFAST_QC completed!
[2023-03-18 10:17:52,619] [INFO] Total running time: 0h1m18s