[2023-03-16 03:47:32,879] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,879] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,879] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6050109-5592-4cf6-92ec-3d77a5a07ff1/dqc_reference
[2023-03-16 03:47:34,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,534] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,534] [INFO] Running command: cat /var/lib/cwl/stgbd4fe51b-f212-4951-99dd-492b7cd3bffa/OceanDNA-b15189.fa | prodigal -d OceanDNA-b15189/cds.fna -a OceanDNA-b15189/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:46,330] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:46,330] [INFO] Task started: HMMsearch
[2023-03-16 03:47:46,330] [INFO] Running command: hmmsearch --tblout OceanDNA-b15189/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6050109-5592-4cf6-92ec-3d77a5a07ff1/dqc_reference/reference_markers.hmm OceanDNA-b15189/protein.faa > /dev/null
[2023-03-16 03:47:46,529] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:46,530] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbd4fe51b-f212-4951-99dd-492b7cd3bffa/OceanDNA-b15189.fa]
[2023-03-16 03:47:46,549] [INFO] Query marker FASTA was written to OceanDNA-b15189/markers.fasta
[2023-03-16 03:47:46,550] [INFO] Task started: Blastn
[2023-03-16 03:47:46,550] [INFO] Running command: blastn -query OceanDNA-b15189/markers.fasta -db /var/lib/cwl/stgd6050109-5592-4cf6-92ec-3d77a5a07ff1/dqc_reference/reference_markers.fasta -out OceanDNA-b15189/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:47,111] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:47,112] [INFO] Selected 15 target genomes.
[2023-03-16 03:47:47,112] [INFO] Target genome list was writen to OceanDNA-b15189/target_genomes.txt
[2023-03-16 03:47:47,122] [INFO] Task started: fastANI
[2023-03-16 03:47:47,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd4fe51b-f212-4951-99dd-492b7cd3bffa/OceanDNA-b15189.fa --refList OceanDNA-b15189/target_genomes.txt --output OceanDNA-b15189/fastani_result.tsv --threads 1
[2023-03-16 03:47:59,457] [INFO] Task succeeded: fastANI
[2023-03-16 03:47:59,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6050109-5592-4cf6-92ec-3d77a5a07ff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:47:59,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6050109-5592-4cf6-92ec-3d77a5a07ff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:47:59,464] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:47:59,464] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:47:59,464] [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
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	75.3124	55	608	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	75.0648	64	608	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	75.0358	88	608	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	75.0257	74	608	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.9781	75	608	95	below_threshold
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	74.864	57	608	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	74.7744	104	608	95	below_threshold
Modestobacter versicolor	strain=CP153-2	GCA_003226595.1	429133	429133	type	True	74.7612	50	608	95	below_threshold
Modestobacter versicolor	strain=DSM 16678	GCA_014195485.1	429133	429133	type	True	74.7251	57	608	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:47:59,464] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15189/tc_result.tsv
[2023-03-16 03:47:59,464] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:47:59,464] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:47:59,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6050109-5592-4cf6-92ec-3d77a5a07ff1/dqc_reference/checkm_data
[2023-03-16 03:47:59,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:47:59,470] [INFO] Task started: CheckM
[2023-03-16 03:47:59,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15189/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15189/checkm_input OceanDNA-b15189/checkm_result
[2023-03-16 03:48:32,017] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:32,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.10%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:32,021] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:32,021] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:32,021] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15189/markers.fasta)
[2023-03-16 03:48:32,021] [INFO] Task started: Blastn
[2023-03-16 03:48:32,021] [INFO] Running command: blastn -query OceanDNA-b15189/markers.fasta -db /var/lib/cwl/stgd6050109-5592-4cf6-92ec-3d77a5a07ff1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15189/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:32,501] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:32,502] [INFO] Selected 10 target genomes.
[2023-03-16 03:48:32,502] [INFO] Target genome list was writen to OceanDNA-b15189/target_genomes_gtdb.txt
[2023-03-16 03:48:32,564] [INFO] Task started: fastANI
[2023-03-16 03:48:32,564] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd4fe51b-f212-4951-99dd-492b7cd3bffa/OceanDNA-b15189.fa --refList OceanDNA-b15189/target_genomes_gtdb.txt --output OceanDNA-b15189/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:36,336] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:36,342] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:48:36,343] [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_002840675.1	s__W-Chloroflexi-9 sp002840675	78.9614	231	608	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__W-Chloroflexi-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917615.1	s__SHYQ01 sp903917615	78.001	123	608	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SHYQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875635.1	s__SURF-43 sp016875635	77.7365	143	608	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SURF-43	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297315.1	s__SURF-43 sp004297315	77.7179	152	608	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SURF-43	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599735.1	s__SURF-43 sp003599735	77.6977	100	608	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SURF-43	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379925.1	s__WHSU01 sp009379925	77.3838	162	608	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__WHSU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866055.1	s__VGNK01 sp016866055	77.0447	155	608	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VGNK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692685.1	s__RBC038 sp009692685	76.9918	95	608	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__RBC038	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875695.1	s__SHYP01 sp016875695	76.8513	65	608	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SHYP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:48:36,343] [INFO] GTDB search result was written to OceanDNA-b15189/result_gtdb.tsv
[2023-03-16 03:48:36,343] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:36,344] [INFO] DFAST_QC result json was written to OceanDNA-b15189/dqc_result.json
[2023-03-16 03:48:36,344] [INFO] DFAST_QC completed!
[2023-03-16 03:48:36,344] [INFO] Total running time: 0h1m3s