[2023-03-18 22:05:52,742] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:05:52,742] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:05:52,742] [INFO] DQC Reference Directory: /var/lib/cwl/stga771dd6e-33b9-4929-9955-f760c1929322/dqc_reference
[2023-03-18 22:05:55,257] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:05:55,258] [INFO] Task started: Prodigal
[2023-03-18 22:05:55,258] [INFO] Running command: cat /var/lib/cwl/stgdbecccf0-6647-4c90-8482-0754f9834753/OceanDNA-b21361.fa | prodigal -d OceanDNA-b21361/cds.fna -a OceanDNA-b21361/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:06:05,695] [INFO] Task succeeded: Prodigal
[2023-03-18 22:06:05,696] [INFO] Task started: HMMsearch
[2023-03-18 22:06:05,696] [INFO] Running command: hmmsearch --tblout OceanDNA-b21361/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga771dd6e-33b9-4929-9955-f760c1929322/dqc_reference/reference_markers.hmm OceanDNA-b21361/protein.faa > /dev/null
[2023-03-18 22:06:05,846] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:06:05,847] [INFO] Found 6/6 markers.
[2023-03-18 22:06:05,858] [INFO] Query marker FASTA was written to OceanDNA-b21361/markers.fasta
[2023-03-18 22:06:05,860] [INFO] Task started: Blastn
[2023-03-18 22:06:05,860] [INFO] Running command: blastn -query OceanDNA-b21361/markers.fasta -db /var/lib/cwl/stga771dd6e-33b9-4929-9955-f760c1929322/dqc_reference/reference_markers.fasta -out OceanDNA-b21361/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:06:06,366] [INFO] Task succeeded: Blastn
[2023-03-18 22:06:06,367] [INFO] Selected 8 target genomes.
[2023-03-18 22:06:06,367] [INFO] Target genome list was writen to OceanDNA-b21361/target_genomes.txt
[2023-03-18 22:06:06,374] [INFO] Task started: fastANI
[2023-03-18 22:06:06,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbecccf0-6647-4c90-8482-0754f9834753/OceanDNA-b21361.fa --refList OceanDNA-b21361/target_genomes.txt --output OceanDNA-b21361/fastani_result.tsv --threads 1
[2023-03-18 22:06:10,026] [INFO] Task succeeded: fastANI
[2023-03-18 22:06:10,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga771dd6e-33b9-4929-9955-f760c1929322/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:06:10,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga771dd6e-33b9-4929-9955-f760c1929322/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:06:10,027] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:06:10,027] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:06:10,027] [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 22:06:10,027] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21361/tc_result.tsv
[2023-03-18 22:06:10,027] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:06:10,027] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:06:10,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga771dd6e-33b9-4929-9955-f760c1929322/dqc_reference/checkm_data
[2023-03-18 22:06:10,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:06:10,079] [INFO] Task started: CheckM
[2023-03-18 22:06:10,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21361/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21361/checkm_input OceanDNA-b21361/checkm_result
[2023-03-18 22:06:41,741] [INFO] Task succeeded: CheckM
[2023-03-18 22:06:41,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:06:41,744] [INFO] ===== Completeness check finished =====
[2023-03-18 22:06:41,744] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:06:41,744] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21361/markers.fasta)
[2023-03-18 22:06:41,745] [INFO] Task started: Blastn
[2023-03-18 22:06:41,746] [INFO] Running command: blastn -query OceanDNA-b21361/markers.fasta -db /var/lib/cwl/stga771dd6e-33b9-4929-9955-f760c1929322/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21361/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:06:42,485] [INFO] Task succeeded: Blastn
[2023-03-18 22:06:42,486] [INFO] Selected 15 target genomes.
[2023-03-18 22:06:42,486] [INFO] Target genome list was writen to OceanDNA-b21361/target_genomes_gtdb.txt
[2023-03-18 22:06:42,652] [INFO] Task started: fastANI
[2023-03-18 22:06:42,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbecccf0-6647-4c90-8482-0754f9834753/OceanDNA-b21361.fa --refList OceanDNA-b21361/target_genomes_gtdb.txt --output OceanDNA-b21361/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:06:48,463] [INFO] Task succeeded: fastANI
[2023-03-18 22:06:48,466] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:06:48,466] [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_002328825.1	s__UBA2166 sp002328825	99.8411	506	566	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA2166;g__UBA2166	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002726235.1	s__UBA2166 sp002726235	82.8727	410	566	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA2166;g__UBA2166	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012965905.1	s__UBA2166 sp012965905	77.7023	199	566	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA2166;g__UBA2166	95.0	99.36	99.15	0.85	0.82	4	-
--------------------------------------------------------------------------------
[2023-03-18 22:06:48,466] [INFO] GTDB search result was written to OceanDNA-b21361/result_gtdb.tsv
[2023-03-18 22:06:48,466] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:06:48,467] [INFO] DFAST_QC result json was written to OceanDNA-b21361/dqc_result.json
[2023-03-18 22:06:48,467] [INFO] DFAST_QC completed!
[2023-03-18 22:06:48,467] [INFO] Total running time: 0h0m56s