[2023-03-14 11:40:05,645] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,645] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg5838607d-dff5-4892-bb96-804e6d8c880f/dqc_reference
[2023-03-14 11:40:06,756] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,756] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,756] [INFO] Running command: cat /var/lib/cwl/stg7f4de601-f70f-48f8-af6b-eaa7d7e2d65b/OceanDNA-b2828.fa | prodigal -d OceanDNA-b2828/cds.fna -a OceanDNA-b2828/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:31,062] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:31,062] [INFO] Task started: HMMsearch
[2023-03-14 11:40:31,062] [INFO] Running command: hmmsearch --tblout OceanDNA-b2828/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5838607d-dff5-4892-bb96-804e6d8c880f/dqc_reference/reference_markers.hmm OceanDNA-b2828/protein.faa > /dev/null
[2023-03-14 11:40:31,282] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:31,282] [INFO] Found 6/6 markers.
[2023-03-14 11:40:31,313] [INFO] Query marker FASTA was written to OceanDNA-b2828/markers.fasta
[2023-03-14 11:40:31,314] [INFO] Task started: Blastn
[2023-03-14 11:40:31,314] [INFO] Running command: blastn -query OceanDNA-b2828/markers.fasta -db /var/lib/cwl/stg5838607d-dff5-4892-bb96-804e6d8c880f/dqc_reference/reference_markers.fasta -out OceanDNA-b2828/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:32,397] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:32,402] [INFO] Selected 21 target genomes.
[2023-03-14 11:40:32,402] [INFO] Target genome list was writen to OceanDNA-b2828/target_genomes.txt
[2023-03-14 11:40:32,414] [INFO] Task started: fastANI
[2023-03-14 11:40:32,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f4de601-f70f-48f8-af6b-eaa7d7e2d65b/OceanDNA-b2828.fa --refList OceanDNA-b2828/target_genomes.txt --output OceanDNA-b2828/fastani_result.tsv --threads 1
[2023-03-14 11:40:50,014] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:50,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5838607d-dff5-4892-bb96-804e6d8c880f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:40:50,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5838607d-dff5-4892-bb96-804e6d8c880f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:40:50,027] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:40:50,027] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:40:50,027] [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
Arthrobacter pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	81.0701	652	1311	95	below_threshold
Pseudarthrobacter psychrotolerans	strain=YJ56	GCA_009911795.1	2697569	2697569	type	True	81.0029	662	1311	95	below_threshold
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	80.9998	636	1311	95	below_threshold
Pseudarthrobacter sulfonivorans	strain=ALL	GCA_014712225.1	121292	121292	type	True	80.9734	643	1311	95	below_threshold
Arthrobacter ipis	strain=IA7	GCA_014694315.1	2716202	2716202	type	True	80.8931	631	1311	95	below_threshold
Pseudarthrobacter scleromae	strain=CGMCC 1.3601	GCA_014644515.1	158897	158897	type	True	80.6469	605	1311	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	80.6185	603	1311	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	80.5058	621	1311	95	below_threshold
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	80.5052	624	1311	95	below_threshold
Pseudarthrobacter equi	strain=IMMIB L-1606	GCA_900105535.1	728066	728066	type	True	80.4589	598	1311	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_000022025.1	85085	85085	type	True	80.4109	615	1311	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	80.3774	611	1311	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	80.3541	579	1311	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	80.3467	575	1311	95	below_threshold
Arthrobacter cupressi	strain=CGMCC 1.10783	GCA_900099975.1	1045773	1045773	type	True	80.3397	571	1311	95	below_threshold
Pseudarthrobacter phenanthrenivorans	strain=Sphe3	GCA_000189535.1	361575	361575	type	True	80.2104	632	1311	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	79.6989	469	1311	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	79.0541	486	1311	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.5836	383	1311	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.5345	315	1311	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.5245	323	1311	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:40:50,029] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2828/tc_result.tsv
[2023-03-14 11:40:50,031] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:40:50,031] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:50,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5838607d-dff5-4892-bb96-804e6d8c880f/dqc_reference/checkm_data
[2023-03-14 11:40:50,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:50,040] [INFO] Task started: CheckM
[2023-03-14 11:40:50,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2828/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2828/checkm_input OceanDNA-b2828/checkm_result
[2023-03-14 11:41:49,189] [INFO] Task succeeded: CheckM
[2023-03-14 11:41:49,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:41:49,207] [INFO] ===== Completeness check finished =====
[2023-03-14 11:41:49,207] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:41:49,207] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2828/markers.fasta)
[2023-03-14 11:41:49,208] [INFO] Task started: Blastn
[2023-03-14 11:41:49,208] [INFO] Running command: blastn -query OceanDNA-b2828/markers.fasta -db /var/lib/cwl/stg5838607d-dff5-4892-bb96-804e6d8c880f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2828/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:41:51,020] [INFO] Task succeeded: Blastn
[2023-03-14 11:41:51,023] [INFO] Selected 8 target genomes.
[2023-03-14 11:41:51,024] [INFO] Target genome list was writen to OceanDNA-b2828/target_genomes_gtdb.txt
[2023-03-14 11:41:51,030] [INFO] Task started: fastANI
[2023-03-14 11:41:51,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f4de601-f70f-48f8-af6b-eaa7d7e2d65b/OceanDNA-b2828.fa --refList OceanDNA-b2828/target_genomes_gtdb.txt --output OceanDNA-b2828/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:41:58,691] [INFO] Task succeeded: fastANI
[2023-03-14 11:41:58,697] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:41:58,697] [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
GCF_000427315.1	s__Arthrobacter_I sp000427315	89.078	791	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009928425.1	s__Arthrobacter_I sp009928425	88.9172	945	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750145.1	s__Arthrobacter_I sp001750145	88.5576	990	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422645.1	s__Arthrobacter_I sp001422645	88.0622	932	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679325.1	s__Arthrobacter_I sp007679325	87.8787	936	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001512305.1	s__Arthrobacter_I sp001512305	86.5195	971	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858535.1	s__Arthrobacter_I sp007858535	84.0681	779	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102895.1	s__Arthrobacter_I sp900102895	83.5092	771	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:41:58,700] [INFO] GTDB search result was written to OceanDNA-b2828/result_gtdb.tsv
[2023-03-14 11:41:58,703] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:41:58,706] [INFO] DFAST_QC result json was written to OceanDNA-b2828/dqc_result.json
[2023-03-14 11:41:58,707] [INFO] DFAST_QC completed!
[2023-03-14 11:41:58,707] [INFO] Total running time: 0h1m53s