[2023-03-18 02:27:37,199] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:37,200] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:37,200] [INFO] DQC Reference Directory: /var/lib/cwl/stga1f106c5-c073-4466-ba0e-ddc1edc2dae1/dqc_reference
[2023-03-18 02:27:38,462] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:38,463] [INFO] Task started: Prodigal
[2023-03-18 02:27:38,463] [INFO] Running command: cat /var/lib/cwl/stg0bcbf664-ec53-40dd-9d4d-fa8397de25db/OceanDNA-b4104.fa | prodigal -d OceanDNA-b4104/cds.fna -a OceanDNA-b4104/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:04,000] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:04,001] [INFO] Task started: HMMsearch
[2023-03-18 02:28:04,001] [INFO] Running command: hmmsearch --tblout OceanDNA-b4104/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1f106c5-c073-4466-ba0e-ddc1edc2dae1/dqc_reference/reference_markers.hmm OceanDNA-b4104/protein.faa > /dev/null
[2023-03-18 02:28:04,358] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:04,359] [INFO] Found 6/6 markers.
[2023-03-18 02:28:04,390] [INFO] Query marker FASTA was written to OceanDNA-b4104/markers.fasta
[2023-03-18 02:28:04,390] [INFO] Task started: Blastn
[2023-03-18 02:28:04,390] [INFO] Running command: blastn -query OceanDNA-b4104/markers.fasta -db /var/lib/cwl/stga1f106c5-c073-4466-ba0e-ddc1edc2dae1/dqc_reference/reference_markers.fasta -out OceanDNA-b4104/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:04,927] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:04,928] [INFO] Selected 27 target genomes.
[2023-03-18 02:28:04,928] [INFO] Target genome list was writen to OceanDNA-b4104/target_genomes.txt
[2023-03-18 02:28:04,939] [INFO] Task started: fastANI
[2023-03-18 02:28:04,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bcbf664-ec53-40dd-9d4d-fa8397de25db/OceanDNA-b4104.fa --refList OceanDNA-b4104/target_genomes.txt --output OceanDNA-b4104/fastani_result.tsv --threads 1
[2023-03-18 02:28:28,067] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:28,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1f106c5-c073-4466-ba0e-ddc1edc2dae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:28,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1f106c5-c073-4466-ba0e-ddc1edc2dae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:28,071] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:28,071] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:28:28,071] [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
Marinoscillum pacificum	strain=MRN461	GCA_024714495.1	392723	392723	type	True	88.6352	789	904	95	below_threshold
Marinoscillum furvescens	strain=DSM 4134	GCA_003386095.1	1026	1026	type	True	76.6818	66	904	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:28:28,071] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4104/tc_result.tsv
[2023-03-18 02:28:28,072] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:28,072] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:28,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1f106c5-c073-4466-ba0e-ddc1edc2dae1/dqc_reference/checkm_data
[2023-03-18 02:28:28,073] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:28,134] [INFO] Task started: CheckM
[2023-03-18 02:28:28,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4104/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4104/checkm_input OceanDNA-b4104/checkm_result
[2023-03-18 02:29:34,901] [INFO] Task succeeded: CheckM
[2023-03-18 02:29:34,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.28%
Contamintation: 1.04%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 02:29:34,905] [INFO] ===== Completeness check finished =====
[2023-03-18 02:29:34,905] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:29:34,905] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4104/markers.fasta)
[2023-03-18 02:29:34,905] [INFO] Task started: Blastn
[2023-03-18 02:29:34,905] [INFO] Running command: blastn -query OceanDNA-b4104/markers.fasta -db /var/lib/cwl/stga1f106c5-c073-4466-ba0e-ddc1edc2dae1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4104/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:29:35,657] [INFO] Task succeeded: Blastn
[2023-03-18 02:29:35,658] [INFO] Selected 31 target genomes.
[2023-03-18 02:29:35,658] [INFO] Target genome list was writen to OceanDNA-b4104/target_genomes_gtdb.txt
[2023-03-18 02:29:35,685] [INFO] Task started: fastANI
[2023-03-18 02:29:35,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bcbf664-ec53-40dd-9d4d-fa8397de25db/OceanDNA-b4104.fa --refList OceanDNA-b4104/target_genomes_gtdb.txt --output OceanDNA-b4104/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:29:59,864] [INFO] Task succeeded: fastANI
[2023-03-18 02:29:59,867] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:29:59,867] [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_002729235.1	s__Marinoscillum sp002729235	83.4797	479	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marinoscillum	95.0	98.41	98.38	0.86	0.84	4	-
GCF_003386095.1	s__Marinoscillum furvescens	76.6818	66	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marinoscillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506655.1	s__Marinoscillum sp902506655	76.1473	64	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marinoscillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:29:59,868] [INFO] GTDB search result was written to OceanDNA-b4104/result_gtdb.tsv
[2023-03-18 02:29:59,868] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:29:59,868] [INFO] DFAST_QC result json was written to OceanDNA-b4104/dqc_result.json
[2023-03-18 02:29:59,868] [INFO] DFAST_QC completed!
[2023-03-18 02:29:59,868] [INFO] Total running time: 0h2m23s