[2023-03-15 11:09:10,895] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,895] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,895] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9b0fb73-86cb-4cfe-b825-420c4b4e4033/dqc_reference
[2023-03-15 11:09:12,314] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,314] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,314] [INFO] Running command: cat /var/lib/cwl/stg96333379-a10e-4e71-be7a-af939ed86970/OceanDNA-b1154.fa | prodigal -d OceanDNA-b1154/cds.fna -a OceanDNA-b1154/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:27,043] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:27,044] [INFO] Task started: HMMsearch
[2023-03-15 11:09:27,044] [INFO] Running command: hmmsearch --tblout OceanDNA-b1154/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9b0fb73-86cb-4cfe-b825-420c4b4e4033/dqc_reference/reference_markers.hmm OceanDNA-b1154/protein.faa > /dev/null
[2023-03-15 11:09:27,303] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:27,303] [INFO] Found 6/6 markers.
[2023-03-15 11:09:27,455] [INFO] Query marker FASTA was written to OceanDNA-b1154/markers.fasta
[2023-03-15 11:09:27,455] [INFO] Task started: Blastn
[2023-03-15 11:09:27,455] [INFO] Running command: blastn -query OceanDNA-b1154/markers.fasta -db /var/lib/cwl/stgd9b0fb73-86cb-4cfe-b825-420c4b4e4033/dqc_reference/reference_markers.fasta -out OceanDNA-b1154/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:28,162] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:28,163] [INFO] Selected 30 target genomes.
[2023-03-15 11:09:28,163] [INFO] Target genome list was writen to OceanDNA-b1154/target_genomes.txt
[2023-03-15 11:09:28,182] [INFO] Task started: fastANI
[2023-03-15 11:09:28,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg96333379-a10e-4e71-be7a-af939ed86970/OceanDNA-b1154.fa --refList OceanDNA-b1154/target_genomes.txt --output OceanDNA-b1154/fastani_result.tsv --threads 1
[2023-03-15 11:09:54,593] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:54,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9b0fb73-86cb-4cfe-b825-420c4b4e4033/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:54,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9b0fb73-86cb-4cfe-b825-420c4b4e4033/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:54,600] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:54,600] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:54,600] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.7932	87	512	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.5326	88	512	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.3954	76	512	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.8778	52	512	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	75.4294	53	512	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	75.0442	61	512	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	74.8187	65	512	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:54,626] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1154/tc_result.tsv
[2023-03-15 11:09:54,626] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:54,627] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:54,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9b0fb73-86cb-4cfe-b825-420c4b4e4033/dqc_reference/checkm_data
[2023-03-15 11:09:54,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:54,634] [INFO] Task started: CheckM
[2023-03-15 11:09:54,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1154/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1154/checkm_input OceanDNA-b1154/checkm_result
[2023-03-15 11:10:28,056] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:28,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.98%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:28,059] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:28,059] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:28,059] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1154/markers.fasta)
[2023-03-15 11:10:28,059] [INFO] Task started: Blastn
[2023-03-15 11:10:28,059] [INFO] Running command: blastn -query OceanDNA-b1154/markers.fasta -db /var/lib/cwl/stgd9b0fb73-86cb-4cfe-b825-420c4b4e4033/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1154/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:29,208] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:29,209] [INFO] Selected 16 target genomes.
[2023-03-15 11:10:29,209] [INFO] Target genome list was writen to OceanDNA-b1154/target_genomes_gtdb.txt
[2023-03-15 11:10:29,222] [INFO] Task started: fastANI
[2023-03-15 11:10:29,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg96333379-a10e-4e71-be7a-af939ed86970/OceanDNA-b1154.fa --refList OceanDNA-b1154/target_genomes_gtdb.txt --output OceanDNA-b1154/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:36,747] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:36,755] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:10:36,755] [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_002717365.1	s__UBA9410 sp002717365	89.5121	359	512	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_016845305.1	s__UBA9410 sp016845305	80.6693	354	512	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	80.2221	254	512	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_014239855.1	s__UBA9410 sp014239855	80.1032	312	512	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_014237715.1	s__UBA9410 sp014237715	79.5803	308	512	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_012961035.1	s__UBA9410 sp012961035	79.5404	311	512	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_014240365.1	s__UBA9410 sp014240365	79.1019	260	512	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_002346745.1	s__S20-B6 sp002346745	78.8493	213	512	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_003541675.1	s__UBA9410 sp003541675	78.6699	186	512	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_002699725.1	s__S20-B6 sp002699725	78.6267	190	512	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.58	98.41	0.87	0.86	3	-
GCA_002348705.1	s__UBA9410 sp002348705	77.8393	144	512	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.53	98.86	0.93	0.89	6	-
GCA_003697065.1	s__J010 sp003697065	76.5444	87	512	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:36,755] [INFO] GTDB search result was written to OceanDNA-b1154/result_gtdb.tsv
[2023-03-15 11:10:36,755] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:36,757] [INFO] DFAST_QC result json was written to OceanDNA-b1154/dqc_result.json
[2023-03-15 11:10:36,757] [INFO] DFAST_QC completed!
[2023-03-15 11:10:36,757] [INFO] Total running time: 0h1m26s