[2023-03-19 01:12:13,940] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:12:13,940] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:12:13,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e67f347-a350-4ba4-b7d7-8560dbf472f6/dqc_reference
[2023-03-19 01:12:15,732] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:12:15,733] [INFO] Task started: Prodigal
[2023-03-19 01:12:15,733] [INFO] Running command: cat /var/lib/cwl/stgc311a971-9aff-4ca4-bd71-370eb8317a96/OceanDNA-b2739.fa | prodigal -d OceanDNA-b2739/cds.fna -a OceanDNA-b2739/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:12:22,544] [INFO] Task succeeded: Prodigal
[2023-03-19 01:12:22,544] [INFO] Task started: HMMsearch
[2023-03-19 01:12:22,544] [INFO] Running command: hmmsearch --tblout OceanDNA-b2739/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e67f347-a350-4ba4-b7d7-8560dbf472f6/dqc_reference/reference_markers.hmm OceanDNA-b2739/protein.faa > /dev/null
[2023-03-19 01:12:22,720] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:12:22,721] [INFO] Found 6/6 markers.
[2023-03-19 01:12:22,731] [INFO] Query marker FASTA was written to OceanDNA-b2739/markers.fasta
[2023-03-19 01:12:22,732] [INFO] Task started: Blastn
[2023-03-19 01:12:22,732] [INFO] Running command: blastn -query OceanDNA-b2739/markers.fasta -db /var/lib/cwl/stg9e67f347-a350-4ba4-b7d7-8560dbf472f6/dqc_reference/reference_markers.fasta -out OceanDNA-b2739/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:12:23,405] [INFO] Task succeeded: Blastn
[2023-03-19 01:12:23,406] [INFO] Selected 28 target genomes.
[2023-03-19 01:12:23,406] [INFO] Target genome list was writen to OceanDNA-b2739/target_genomes.txt
[2023-03-19 01:12:23,422] [INFO] Task started: fastANI
[2023-03-19 01:12:23,422] [INFO] Running command: fastANI --query /var/lib/cwl/stgc311a971-9aff-4ca4-bd71-370eb8317a96/OceanDNA-b2739.fa --refList OceanDNA-b2739/target_genomes.txt --output OceanDNA-b2739/fastani_result.tsv --threads 1
[2023-03-19 01:12:37,094] [INFO] Task succeeded: fastANI
[2023-03-19 01:12:37,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e67f347-a350-4ba4-b7d7-8560dbf472f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:12:37,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e67f347-a350-4ba4-b7d7-8560dbf472f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:12:37,095] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:12:37,095] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:12:37,095] [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
--------------------------------------------------------------------------------
[2023-03-19 01:12:37,095] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2739/tc_result.tsv
[2023-03-19 01:12:37,095] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:12:37,096] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:12:37,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e67f347-a350-4ba4-b7d7-8560dbf472f6/dqc_reference/checkm_data
[2023-03-19 01:12:37,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:12:37,101] [INFO] Task started: CheckM
[2023-03-19 01:12:37,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2739/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2739/checkm_input OceanDNA-b2739/checkm_result
[2023-03-19 01:12:59,738] [INFO] Task succeeded: CheckM
[2023-03-19 01:12:59,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 01:12:59,740] [INFO] ===== Completeness check finished =====
[2023-03-19 01:12:59,740] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:12:59,740] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2739/markers.fasta)
[2023-03-19 01:12:59,741] [INFO] Task started: Blastn
[2023-03-19 01:12:59,741] [INFO] Running command: blastn -query OceanDNA-b2739/markers.fasta -db /var/lib/cwl/stg9e67f347-a350-4ba4-b7d7-8560dbf472f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2739/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:00,618] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:00,619] [INFO] Selected 21 target genomes.
[2023-03-19 01:13:00,619] [INFO] Target genome list was writen to OceanDNA-b2739/target_genomes_gtdb.txt
[2023-03-19 01:13:00,634] [INFO] Task started: fastANI
[2023-03-19 01:13:00,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgc311a971-9aff-4ca4-bd71-370eb8317a96/OceanDNA-b2739.fa --refList OceanDNA-b2739/target_genomes_gtdb.txt --output OceanDNA-b2739/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:13:08,339] [INFO] Task succeeded: fastANI
[2023-03-19 01:13:08,344] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:13:08,344] [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_018666065.1	s__Pontimonas sp018666065	99.5637	316	360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018402295.1	s__Pontimonas sp018402295	79.4986	127	360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000754445.1	s__Pontimonas sp000754445	78.3422	66	360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	99.88	99.88	0.89	0.89	2	-
GCA_009704535.1	s__Pontimonas sp009704535	78.3382	69	360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	99.38	99.38	0.88	0.88	2	-
GCA_001438965.1	s__Pontimonas sp001438965	77.9056	68	360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	99.36	99.36	0.84	0.84	2	-
GCA_017857245.1	s__Pontimonas sp017857245	77.4948	70	360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	98.06	96.78	0.86	0.79	3	-
GCA_017852615.1	s__Pontimonas sp017852615	77.0846	83	360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	97.57	97.21	0.82	0.78	7	-
--------------------------------------------------------------------------------
[2023-03-19 01:13:08,345] [INFO] GTDB search result was written to OceanDNA-b2739/result_gtdb.tsv
[2023-03-19 01:13:08,345] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:13:08,346] [INFO] DFAST_QC result json was written to OceanDNA-b2739/dqc_result.json
[2023-03-19 01:13:08,346] [INFO] DFAST_QC completed!
[2023-03-19 01:13:08,346] [INFO] Total running time: 0h0m54s