[2023-03-18 02:13:13,421] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:13:13,422] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:13:13,422] [INFO] DQC Reference Directory: /var/lib/cwl/stg4706dd91-6a66-47b1-83f1-a04cb372676f/dqc_reference
[2023-03-18 02:13:14,493] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:13:14,494] [INFO] Task started: Prodigal
[2023-03-18 02:13:14,495] [INFO] Running command: cat /var/lib/cwl/stga372a3ce-9205-4859-a111-db57c53625c5/OceanDNA-b18024.fa | prodigal -d OceanDNA-b18024/cds.fna -a OceanDNA-b18024/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:13:18,110] [INFO] Task succeeded: Prodigal
[2023-03-18 02:13:18,110] [INFO] Task started: HMMsearch
[2023-03-18 02:13:18,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b18024/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4706dd91-6a66-47b1-83f1-a04cb372676f/dqc_reference/reference_markers.hmm OceanDNA-b18024/protein.faa > /dev/null
[2023-03-18 02:13:18,262] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:13:18,263] [INFO] Found 6/6 markers.
[2023-03-18 02:13:18,269] [INFO] Query marker FASTA was written to OceanDNA-b18024/markers.fasta
[2023-03-18 02:13:18,271] [INFO] Task started: Blastn
[2023-03-18 02:13:18,271] [INFO] Running command: blastn -query OceanDNA-b18024/markers.fasta -db /var/lib/cwl/stg4706dd91-6a66-47b1-83f1-a04cb372676f/dqc_reference/reference_markers.fasta -out OceanDNA-b18024/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:13:18,833] [INFO] Task succeeded: Blastn
[2023-03-18 02:13:18,837] [INFO] Selected 16 target genomes.
[2023-03-18 02:13:18,838] [INFO] Target genome list was writen to OceanDNA-b18024/target_genomes.txt
[2023-03-18 02:13:18,867] [INFO] Task started: fastANI
[2023-03-18 02:13:18,867] [INFO] Running command: fastANI --query /var/lib/cwl/stga372a3ce-9205-4859-a111-db57c53625c5/OceanDNA-b18024.fa --refList OceanDNA-b18024/target_genomes.txt --output OceanDNA-b18024/fastani_result.tsv --threads 1
[2023-03-18 02:13:25,086] [INFO] Task succeeded: fastANI
[2023-03-18 02:13:25,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4706dd91-6a66-47b1-83f1-a04cb372676f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:13:25,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4706dd91-6a66-47b1-83f1-a04cb372676f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:13:25,087] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:13:25,087] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:13:25,087] [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
--------------------------------------------------------------------------------
[2023-03-18 02:13:25,090] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18024/tc_result.tsv
[2023-03-18 02:13:25,091] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:13:25,091] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:13:25,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4706dd91-6a66-47b1-83f1-a04cb372676f/dqc_reference/checkm_data
[2023-03-18 02:13:25,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:13:25,099] [INFO] Task started: CheckM
[2023-03-18 02:13:25,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18024/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18024/checkm_input OceanDNA-b18024/checkm_result
[2023-03-18 02:13:40,916] [INFO] Task succeeded: CheckM
[2023-03-18 02:13:40,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.59%
Contamintation: 9.47%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 02:13:40,921] [INFO] ===== Completeness check finished =====
[2023-03-18 02:13:40,922] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:13:40,922] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18024/markers.fasta)
[2023-03-18 02:13:40,923] [INFO] Task started: Blastn
[2023-03-18 02:13:40,923] [INFO] Running command: blastn -query OceanDNA-b18024/markers.fasta -db /var/lib/cwl/stg4706dd91-6a66-47b1-83f1-a04cb372676f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18024/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:13:41,793] [INFO] Task succeeded: Blastn
[2023-03-18 02:13:41,794] [INFO] Selected 20 target genomes.
[2023-03-18 02:13:41,794] [INFO] Target genome list was writen to OceanDNA-b18024/target_genomes_gtdb.txt
[2023-03-18 02:13:41,812] [INFO] Task started: fastANI
[2023-03-18 02:13:41,812] [INFO] Running command: fastANI --query /var/lib/cwl/stga372a3ce-9205-4859-a111-db57c53625c5/OceanDNA-b18024.fa --refList OceanDNA-b18024/target_genomes_gtdb.txt --output OceanDNA-b18024/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:13:47,465] [INFO] Task succeeded: fastANI
[2023-03-18 02:13:47,470] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:13:47,470] [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_902575395.1	s__Marinisoma sp902575395	98.7537	164	222	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002348725.1	s__Marinisoma sp002348725	91.2367	160	222	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.66	99.62	0.84	0.83	4	-
GCA_012963075.1	s__Marinisoma sp012963075	79.6908	103	222	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182795.1	s__Marinisoma sp905182795	77.3393	93	222	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402815.1	s__Marinisoma atlanticum	77.2577	89	222	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_902578385.1	s__Marinisoma sp002710515	77.0035	68	222	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.88	96.56	0.86	0.83	7	-
GCA_902629855.1	s__Marinisoma sp902629855	76.4583	53	222	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	98.59	98.03	0.85	0.83	5	-
--------------------------------------------------------------------------------
[2023-03-18 02:13:47,476] [INFO] GTDB search result was written to OceanDNA-b18024/result_gtdb.tsv
[2023-03-18 02:13:47,476] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:13:47,477] [INFO] DFAST_QC result json was written to OceanDNA-b18024/dqc_result.json
[2023-03-18 02:13:47,477] [INFO] DFAST_QC completed!
[2023-03-18 02:13:47,477] [INFO] Total running time: 0h0m34s