[2023-03-16 10:46:24,309] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:46:24,309] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:46:24,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg507ebd2f-bea5-490f-b516-6b50e5917da9/dqc_reference
[2023-03-16 10:46:25,486] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:46:25,486] [INFO] Task started: Prodigal
[2023-03-16 10:46:25,486] [INFO] Running command: cat /var/lib/cwl/stgc77a92a1-c1e4-4794-9194-30ec2914d0ae/OceanDNA-b2817.fa | prodigal -d OceanDNA-b2817/cds.fna -a OceanDNA-b2817/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:46:48,799] [INFO] Task succeeded: Prodigal
[2023-03-16 10:46:48,799] [INFO] Task started: HMMsearch
[2023-03-16 10:46:48,799] [INFO] Running command: hmmsearch --tblout OceanDNA-b2817/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg507ebd2f-bea5-490f-b516-6b50e5917da9/dqc_reference/reference_markers.hmm OceanDNA-b2817/protein.faa > /dev/null
[2023-03-16 10:46:49,109] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:46:49,110] [INFO] Found 6/6 markers.
[2023-03-16 10:46:49,127] [INFO] Query marker FASTA was written to OceanDNA-b2817/markers.fasta
[2023-03-16 10:46:49,128] [INFO] Task started: Blastn
[2023-03-16 10:46:49,128] [INFO] Running command: blastn -query OceanDNA-b2817/markers.fasta -db /var/lib/cwl/stg507ebd2f-bea5-490f-b516-6b50e5917da9/dqc_reference/reference_markers.fasta -out OceanDNA-b2817/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:46:50,174] [INFO] Task succeeded: Blastn
[2023-03-16 10:46:50,174] [INFO] Selected 15 target genomes.
[2023-03-16 10:46:50,175] [INFO] Target genome list was writen to OceanDNA-b2817/target_genomes.txt
[2023-03-16 10:46:50,220] [INFO] Task started: fastANI
[2023-03-16 10:46:50,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgc77a92a1-c1e4-4794-9194-30ec2914d0ae/OceanDNA-b2817.fa --refList OceanDNA-b2817/target_genomes.txt --output OceanDNA-b2817/fastani_result.tsv --threads 1
[2023-03-16 10:46:59,117] [INFO] Task succeeded: fastANI
[2023-03-16 10:46:59,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg507ebd2f-bea5-490f-b516-6b50e5917da9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:46:59,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg507ebd2f-bea5-490f-b516-6b50e5917da9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:46:59,127] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:46:59,127] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:46:59,127] [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
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	82.7783	550	830	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	82.7717	554	830	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	80.258	425	830	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	80.192	441	830	95	below_threshold
Microcella alkaliphila	strain=AC4r	GCA_004216855.1	279828	279828	type	True	80.0559	418	830	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	78.6306	331	830	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	78.5375	287	830	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.423	304	830	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.2302	305	830	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	78.2163	327	830	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.216	333	830	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.0793	266	830	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.0755	308	830	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	78.0541	268	830	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	77.9497	327	830	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:46:59,127] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2817/tc_result.tsv
[2023-03-16 10:46:59,127] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:46:59,127] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:46:59,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg507ebd2f-bea5-490f-b516-6b50e5917da9/dqc_reference/checkm_data
[2023-03-16 10:46:59,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:46:59,132] [INFO] Task started: CheckM
[2023-03-16 10:46:59,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2817/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2817/checkm_input OceanDNA-b2817/checkm_result
[2023-03-16 10:47:40,873] [INFO] Task succeeded: CheckM
[2023-03-16 10:47:40,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.15%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:47:40,876] [INFO] ===== Completeness check finished =====
[2023-03-16 10:47:40,876] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:47:40,876] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2817/markers.fasta)
[2023-03-16 10:47:40,877] [INFO] Task started: Blastn
[2023-03-16 10:47:40,877] [INFO] Running command: blastn -query OceanDNA-b2817/markers.fasta -db /var/lib/cwl/stg507ebd2f-bea5-490f-b516-6b50e5917da9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2817/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:47:42,520] [INFO] Task succeeded: Blastn
[2023-03-16 10:47:42,521] [INFO] Selected 13 target genomes.
[2023-03-16 10:47:42,521] [INFO] Target genome list was writen to OceanDNA-b2817/target_genomes_gtdb.txt
[2023-03-16 10:47:42,529] [INFO] Task started: fastANI
[2023-03-16 10:47:42,529] [INFO] Running command: fastANI --query /var/lib/cwl/stgc77a92a1-c1e4-4794-9194-30ec2914d0ae/OceanDNA-b2817.fa --refList OceanDNA-b2817/target_genomes_gtdb.txt --output OceanDNA-b2817/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:47:49,290] [INFO] Task succeeded: fastANI
[2023-03-16 10:47:49,298] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:47:49,298] [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_005778835.1	s__Chryseoglobus sp005778835	88.7088	585	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423075.1	s__Chryseoglobus sp002423075	87.2577	448	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464255.1	s__Chryseoglobus sp001464255	84.6037	419	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280615.1	s__Chryseoglobus sp002280615	84.4843	349	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200395.1	s__Chryseoglobus frigidaquae	82.7865	553	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013823625.1	s__Chryseoglobus sp013823625	82.4171	546	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013297625.1	s__Chryseoglobus sp013297625	82.2741	480	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009371975.2	s__Marinisubtilis pacificus	81.9762	521	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	97.81	97.81	0.83	0.83	2	-
GCF_013414345.1	s__Marinisubtilis indicus	81.6043	515	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	96.33	95.90	0.85	0.83	6	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	81.5258	504	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012530535.1	s__Yonghaparkia sp012530535	81.117	492	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813345.1	s__Marinisubtilis sp002813345	81.0044	451	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137945.1	s__Yonghaparkia alkaliphila	80.8222	456	830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:47:49,299] [INFO] GTDB search result was written to OceanDNA-b2817/result_gtdb.tsv
[2023-03-16 10:47:49,299] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:47:49,300] [INFO] DFAST_QC result json was written to OceanDNA-b2817/dqc_result.json
[2023-03-16 10:47:49,301] [INFO] DFAST_QC completed!
[2023-03-16 10:47:49,301] [INFO] Total running time: 0h1m25s