[2023-03-18 21:34:09,331] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:34:09,333] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:34:09,333] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ea04d00-b513-4625-a855-41ef6c414d95/dqc_reference
[2023-03-18 21:34:10,572] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:34:10,573] [INFO] Task started: Prodigal
[2023-03-18 21:34:10,573] [INFO] Running command: cat /var/lib/cwl/stg7b711349-2fea-4b31-ac50-b0e68fcb80da/OceanDNA-b510.fa | prodigal -d OceanDNA-b510/cds.fna -a OceanDNA-b510/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:34:28,667] [INFO] Task succeeded: Prodigal
[2023-03-18 21:34:28,667] [INFO] Task started: HMMsearch
[2023-03-18 21:34:28,667] [INFO] Running command: hmmsearch --tblout OceanDNA-b510/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ea04d00-b513-4625-a855-41ef6c414d95/dqc_reference/reference_markers.hmm OceanDNA-b510/protein.faa > /dev/null
[2023-03-18 21:34:28,861] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:34:28,861] [INFO] Found 6/6 markers.
[2023-03-18 21:34:28,892] [INFO] Query marker FASTA was written to OceanDNA-b510/markers.fasta
[2023-03-18 21:34:28,894] [INFO] Task started: Blastn
[2023-03-18 21:34:28,894] [INFO] Running command: blastn -query OceanDNA-b510/markers.fasta -db /var/lib/cwl/stg8ea04d00-b513-4625-a855-41ef6c414d95/dqc_reference/reference_markers.fasta -out OceanDNA-b510/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:34:29,589] [INFO] Task succeeded: Blastn
[2023-03-18 21:34:29,593] [INFO] Selected 20 target genomes.
[2023-03-18 21:34:29,594] [INFO] Target genome list was writen to OceanDNA-b510/target_genomes.txt
[2023-03-18 21:34:29,603] [INFO] Task started: fastANI
[2023-03-18 21:34:29,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b711349-2fea-4b31-ac50-b0e68fcb80da/OceanDNA-b510.fa --refList OceanDNA-b510/target_genomes.txt --output OceanDNA-b510/fastani_result.tsv --threads 1
[2023-03-18 21:34:44,317] [INFO] Task succeeded: fastANI
[2023-03-18 21:34:44,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ea04d00-b513-4625-a855-41ef6c414d95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:34:44,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ea04d00-b513-4625-a855-41ef6c414d95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:34:44,330] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:34:44,330] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:34:44,331] [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
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	78.2076	370	946	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	77.5185	358	946	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.7101	149	946	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.178	120	946	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.8996	51	946	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.6452	67	946	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:34:44,332] [INFO] DFAST Taxonomy check result was written to OceanDNA-b510/tc_result.tsv
[2023-03-18 21:34:44,335] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:34:44,335] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:34:44,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ea04d00-b513-4625-a855-41ef6c414d95/dqc_reference/checkm_data
[2023-03-18 21:34:44,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:34:44,568] [INFO] Task started: CheckM
[2023-03-18 21:34:44,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b510/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b510/checkm_input OceanDNA-b510/checkm_result
[2023-03-18 21:35:31,944] [INFO] Task succeeded: CheckM
[2023-03-18 21:35:31,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:35:31,962] [INFO] ===== Completeness check finished =====
[2023-03-18 21:35:31,963] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:35:31,963] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b510/markers.fasta)
[2023-03-18 21:35:31,964] [INFO] Task started: Blastn
[2023-03-18 21:35:31,964] [INFO] Running command: blastn -query OceanDNA-b510/markers.fasta -db /var/lib/cwl/stg8ea04d00-b513-4625-a855-41ef6c414d95/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b510/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:35:33,282] [INFO] Task succeeded: Blastn
[2023-03-18 21:35:33,288] [INFO] Selected 20 target genomes.
[2023-03-18 21:35:33,288] [INFO] Target genome list was writen to OceanDNA-b510/target_genomes_gtdb.txt
[2023-03-18 21:35:33,374] [INFO] Task started: fastANI
[2023-03-18 21:35:33,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b711349-2fea-4b31-ac50-b0e68fcb80da/OceanDNA-b510.fa --refList OceanDNA-b510/target_genomes_gtdb.txt --output OceanDNA-b510/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:35:45,830] [INFO] Task succeeded: fastANI
[2023-03-18 21:35:45,837] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:35:45,838] [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_905480335.1	s__Ilumatobacter_A sp905480335	99.8054	883	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	78.2174	370	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	77.5099	359	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	77.2383	214	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666235.1	s__Ilumatobacter_A sp018666235	76.9717	205	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.79	99.78	0.94	0.93	4	-
GCF_004364865.1	s__Ilumatobacter fluminis	76.7101	149	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693335.1	s__SKSP01 sp007693335	76.4602	138	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213745.1	s__JABSQH01 sp013213745	76.3656	163	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698945.1	s__Ilumatobacter sp002698945	76.2498	124	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024485.1	s__Casp-actino5 sp010024485	76.1248	52	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.53	98.53	0.77	0.77	2	-
GCA_009704985.1	s__VFMC01 sp009704985	76.0424	150	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017859395.1	s__Casp-actino5 sp017859395	75.9258	55	946	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.27	98.20	0.94	0.88	4	-
GCF_014203355.1	s__Kutzneria kofuensis	74.6359	54	946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:35:45,840] [INFO] GTDB search result was written to OceanDNA-b510/result_gtdb.tsv
[2023-03-18 21:35:45,843] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:35:45,847] [INFO] DFAST_QC result json was written to OceanDNA-b510/dqc_result.json
[2023-03-18 21:35:45,847] [INFO] DFAST_QC completed!
[2023-03-18 21:35:45,847] [INFO] Total running time: 0h1m37s