[2023-03-19 02:05:13,383] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:13,383] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:13,383] [INFO] DQC Reference Directory: /var/lib/cwl/stgc26540d2-9bfe-4ee8-9063-8cea834d9486/dqc_reference
[2023-03-19 02:05:14,578] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:14,578] [INFO] Task started: Prodigal
[2023-03-19 02:05:14,578] [INFO] Running command: cat /var/lib/cwl/stg695a7dc6-bf1e-4911-af90-6fa2094fe9c2/OceanDNA-b2505.fa | prodigal -d OceanDNA-b2505/cds.fna -a OceanDNA-b2505/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:24,708] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:24,708] [INFO] Task started: HMMsearch
[2023-03-19 02:05:24,709] [INFO] Running command: hmmsearch --tblout OceanDNA-b2505/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc26540d2-9bfe-4ee8-9063-8cea834d9486/dqc_reference/reference_markers.hmm OceanDNA-b2505/protein.faa > /dev/null
[2023-03-19 02:05:24,913] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:24,913] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg695a7dc6-bf1e-4911-af90-6fa2094fe9c2/OceanDNA-b2505.fa]
[2023-03-19 02:05:24,928] [INFO] Query marker FASTA was written to OceanDNA-b2505/markers.fasta
[2023-03-19 02:05:24,929] [INFO] Task started: Blastn
[2023-03-19 02:05:24,929] [INFO] Running command: blastn -query OceanDNA-b2505/markers.fasta -db /var/lib/cwl/stgc26540d2-9bfe-4ee8-9063-8cea834d9486/dqc_reference/reference_markers.fasta -out OceanDNA-b2505/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:25,508] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:25,509] [INFO] Selected 20 target genomes.
[2023-03-19 02:05:25,509] [INFO] Target genome list was writen to OceanDNA-b2505/target_genomes.txt
[2023-03-19 02:05:25,521] [INFO] Task started: fastANI
[2023-03-19 02:05:25,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg695a7dc6-bf1e-4911-af90-6fa2094fe9c2/OceanDNA-b2505.fa --refList OceanDNA-b2505/target_genomes.txt --output OceanDNA-b2505/fastani_result.tsv --threads 1
[2023-03-19 02:05:41,456] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:41,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc26540d2-9bfe-4ee8-9063-8cea834d9486/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:41,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc26540d2-9bfe-4ee8-9063-8cea834d9486/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:41,463] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:41,463] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:05:41,463] [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
Modestobacter marinus	strain=DSM 45201	GCA_023383595.1	477641	477641	type	True	75.3551	56	497	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	75.3402	75	497	95	below_threshold
Modestobacter marinus	strain=CGMCC 4.5581	GCA_014645755.1	477641	477641	type	True	75.3218	61	497	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	75.3079	62	497	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	75.2217	66	497	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	75.1146	61	497	95	below_threshold
Motilibacter rhizosphaerae	strain=DSM 45622	GCA_004216915.1	598652	598652	type	True	75.1115	64	497	95	below_threshold
Streptomyces albireticuli	strain=NRRL B-1670	GCA_002286695.1	1940	1940	type	True	75.0846	59	497	95	below_threshold
Pseudonocardia endophytica	strain=DSM 44969	GCA_004339565.1	401976	401976	type	True	75.0427	66	497	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	75.0284	61	497	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:05:41,463] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2505/tc_result.tsv
[2023-03-19 02:05:41,463] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:41,464] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:41,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc26540d2-9bfe-4ee8-9063-8cea834d9486/dqc_reference/checkm_data
[2023-03-19 02:05:41,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:41,468] [INFO] Task started: CheckM
[2023-03-19 02:05:41,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2505/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2505/checkm_input OceanDNA-b2505/checkm_result
[2023-03-19 02:06:17,983] [INFO] Task succeeded: CheckM
[2023-03-19 02:06:17,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:06:17,985] [INFO] ===== Completeness check finished =====
[2023-03-19 02:06:17,986] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:06:17,986] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2505/markers.fasta)
[2023-03-19 02:06:17,986] [INFO] Task started: Blastn
[2023-03-19 02:06:17,986] [INFO] Running command: blastn -query OceanDNA-b2505/markers.fasta -db /var/lib/cwl/stgc26540d2-9bfe-4ee8-9063-8cea834d9486/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2505/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:06:18,790] [INFO] Task succeeded: Blastn
[2023-03-19 02:06:18,791] [INFO] Selected 16 target genomes.
[2023-03-19 02:06:18,791] [INFO] Target genome list was writen to OceanDNA-b2505/target_genomes_gtdb.txt
[2023-03-19 02:06:19,253] [INFO] Task started: fastANI
[2023-03-19 02:06:19,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg695a7dc6-bf1e-4911-af90-6fa2094fe9c2/OceanDNA-b2505.fa --refList OceanDNA-b2505/target_genomes_gtdb.txt --output OceanDNA-b2505/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:06:27,522] [INFO] Task succeeded: fastANI
[2023-03-19 02:06:27,527] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:06:27,527] [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_017577575.1	s__ZC4RG17 sp017577575	76.485	105	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__ZC4RG35;g__ZC4RG17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488325.1	s__S012-128 sp015488325	76.4235	82	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__S012-128;g__S012-128	95.0	99.25	99.12	0.90	0.88	5	-
GCA_016215655.1	s__UBA11373 sp016215655	76.1914	52	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA11373;g__UBA11373	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450985.1	s__UBA6912 sp002450985	75.9705	84	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA5794;g__UBA6912	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870535.1	s__VGBK01 sp016870535	75.6509	50	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA11373;g__VGBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	75.2098	65	497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:06:27,527] [INFO] GTDB search result was written to OceanDNA-b2505/result_gtdb.tsv
[2023-03-19 02:06:27,527] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:06:27,528] [INFO] DFAST_QC result json was written to OceanDNA-b2505/dqc_result.json
[2023-03-19 02:06:27,528] [INFO] DFAST_QC completed!
[2023-03-19 02:06:27,528] [INFO] Total running time: 0h1m14s