[2023-03-15 07:52:40,268] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,268] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bcfbb7c-cc23-464b-b4a9-87e8a0ba1ebc/dqc_reference
[2023-03-15 07:52:41,449] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,449] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,449] [INFO] Running command: cat /var/lib/cwl/stga1190fb7-e04b-4f90-98ca-7f014789ca80/OceanDNA-b3034.fa | prodigal -d OceanDNA-b3034/cds.fna -a OceanDNA-b3034/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:45,410] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:45,410] [INFO] Task started: HMMsearch
[2023-03-15 07:52:45,410] [INFO] Running command: hmmsearch --tblout OceanDNA-b3034/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bcfbb7c-cc23-464b-b4a9-87e8a0ba1ebc/dqc_reference/reference_markers.hmm OceanDNA-b3034/protein.faa > /dev/null
[2023-03-15 07:52:45,575] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:45,576] [INFO] Found 6/6 markers.
[2023-03-15 07:52:45,583] [INFO] Query marker FASTA was written to OceanDNA-b3034/markers.fasta
[2023-03-15 07:52:45,583] [INFO] Task started: Blastn
[2023-03-15 07:52:45,583] [INFO] Running command: blastn -query OceanDNA-b3034/markers.fasta -db /var/lib/cwl/stg5bcfbb7c-cc23-464b-b4a9-87e8a0ba1ebc/dqc_reference/reference_markers.fasta -out OceanDNA-b3034/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:46,171] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:46,172] [INFO] Selected 23 target genomes.
[2023-03-15 07:52:46,172] [INFO] Target genome list was writen to OceanDNA-b3034/target_genomes.txt
[2023-03-15 07:52:46,186] [INFO] Task started: fastANI
[2023-03-15 07:52:46,186] [INFO] Running command: fastANI --query /var/lib/cwl/stga1190fb7-e04b-4f90-98ca-7f014789ca80/OceanDNA-b3034.fa --refList OceanDNA-b3034/target_genomes.txt --output OceanDNA-b3034/fastani_result.tsv --threads 1
[2023-03-15 07:52:57,027] [INFO] Task succeeded: fastANI
[2023-03-15 07:52:57,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bcfbb7c-cc23-464b-b4a9-87e8a0ba1ebc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:52:57,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bcfbb7c-cc23-464b-b4a9-87e8a0ba1ebc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:52:57,028] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:52:57,028] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:52:57,028] [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
--------------------------------------------------------------------------------
[2023-03-15 07:52:57,028] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3034/tc_result.tsv
[2023-03-15 07:52:57,028] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:52:57,028] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:52:57,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bcfbb7c-cc23-464b-b4a9-87e8a0ba1ebc/dqc_reference/checkm_data
[2023-03-15 07:52:57,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:52:57,033] [INFO] Task started: CheckM
[2023-03-15 07:52:57,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3034/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3034/checkm_input OceanDNA-b3034/checkm_result
[2023-03-15 07:53:13,528] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:13,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.15%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:13,530] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:13,530] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:13,531] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3034/markers.fasta)
[2023-03-15 07:53:13,531] [INFO] Task started: Blastn
[2023-03-15 07:53:13,531] [INFO] Running command: blastn -query OceanDNA-b3034/markers.fasta -db /var/lib/cwl/stg5bcfbb7c-cc23-464b-b4a9-87e8a0ba1ebc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3034/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:14,368] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:14,369] [INFO] Selected 15 target genomes.
[2023-03-15 07:53:14,369] [INFO] Target genome list was writen to OceanDNA-b3034/target_genomes_gtdb.txt
[2023-03-15 07:53:14,383] [INFO] Task started: fastANI
[2023-03-15 07:53:14,383] [INFO] Running command: fastANI --query /var/lib/cwl/stga1190fb7-e04b-4f90-98ca-7f014789ca80/OceanDNA-b3034.fa --refList OceanDNA-b3034/target_genomes_gtdb.txt --output OceanDNA-b3034/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:53:17,479] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:17,487] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:53:17,487] [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_000383815.1	s__Nanopelagicus sp000383815	95.0654	164	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009704285.1	s__Nanopelagicus sp009704285	94.0287	140	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569185.1	s__Nanopelagicus sp003569185	83.4352	142	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870455.1	s__Nanopelagicus sp016870455	83.1738	166	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287885.2	s__Nanopelagicus limnes	82.9184	169	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000294575.1	s__Nanopelagicus sp000294575	81.2508	137	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.86	98.86	0.86	0.86	2	-
GCF_002288005.1	s__Nanopelagicus hibericus	81.0737	141	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000378865.1	s__Nanopelagicus sp000378865	80.7874	94	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691185.1	s__Nanopelagicus sp009691185	80.4068	122	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001437855.1	s__Nanopelagicus sp001437855	79.6453	92	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	96.40	95.11	0.72	0.67	12	-
GCA_010030895.1	s__Nanopelagicus sp010030895	79.0991	103	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.34	97.93	0.89	0.87	8	-
GCA_903897475.1	s__Nanopelagicus sp903897475	78.7676	83	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.94	98.64	0.81	0.80	6	-
GCA_009698515.1	s__Nanopelagicus sp009698515	78.5378	73	237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.56	98.42	0.79	0.72	6	-
--------------------------------------------------------------------------------
[2023-03-15 07:53:17,488] [INFO] GTDB search result was written to OceanDNA-b3034/result_gtdb.tsv
[2023-03-15 07:53:17,488] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:53:17,489] [INFO] DFAST_QC result json was written to OceanDNA-b3034/dqc_result.json
[2023-03-15 07:53:17,489] [INFO] DFAST_QC completed!
[2023-03-15 07:53:17,489] [INFO] Total running time: 0h0m37s