[2023-03-18 09:11:00,892] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:11:00,893] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:11:00,893] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a7c4062-20b2-4f06-9be3-bfd884783e43/dqc_reference
[2023-03-18 09:11:01,986] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:11:01,986] [INFO] Task started: Prodigal
[2023-03-18 09:11:01,986] [INFO] Running command: cat /var/lib/cwl/stg68584b3b-20d8-4bfa-91eb-8bf48825d847/OceanDNA-b17506.fa | prodigal -d OceanDNA-b17506/cds.fna -a OceanDNA-b17506/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:11:15,503] [INFO] Task succeeded: Prodigal
[2023-03-18 09:11:15,503] [INFO] Task started: HMMsearch
[2023-03-18 09:11:15,504] [INFO] Running command: hmmsearch --tblout OceanDNA-b17506/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a7c4062-20b2-4f06-9be3-bfd884783e43/dqc_reference/reference_markers.hmm OceanDNA-b17506/protein.faa > /dev/null
[2023-03-18 09:11:15,667] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:11:15,668] [INFO] Found 6/6 markers.
[2023-03-18 09:11:15,683] [INFO] Query marker FASTA was written to OceanDNA-b17506/markers.fasta
[2023-03-18 09:11:15,684] [INFO] Task started: Blastn
[2023-03-18 09:11:15,684] [INFO] Running command: blastn -query OceanDNA-b17506/markers.fasta -db /var/lib/cwl/stg4a7c4062-20b2-4f06-9be3-bfd884783e43/dqc_reference/reference_markers.fasta -out OceanDNA-b17506/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:11:16,187] [INFO] Task succeeded: Blastn
[2023-03-18 09:11:16,188] [INFO] Selected 15 target genomes.
[2023-03-18 09:11:16,188] [INFO] Target genome list was writen to OceanDNA-b17506/target_genomes.txt
[2023-03-18 09:11:16,196] [INFO] Task started: fastANI
[2023-03-18 09:11:16,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg68584b3b-20d8-4bfa-91eb-8bf48825d847/OceanDNA-b17506.fa --refList OceanDNA-b17506/target_genomes.txt --output OceanDNA-b17506/fastani_result.tsv --threads 1
[2023-03-18 09:11:23,691] [INFO] Task succeeded: fastANI
[2023-03-18 09:11:23,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a7c4062-20b2-4f06-9be3-bfd884783e43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:11:23,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a7c4062-20b2-4f06-9be3-bfd884783e43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:11:23,692] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:11:23,692] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:11:23,692] [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 09:11:23,692] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17506/tc_result.tsv
[2023-03-18 09:11:23,692] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:11:23,692] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:11:23,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a7c4062-20b2-4f06-9be3-bfd884783e43/dqc_reference/checkm_data
[2023-03-18 09:11:23,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:11:23,702] [INFO] Task started: CheckM
[2023-03-18 09:11:23,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17506/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17506/checkm_input OceanDNA-b17506/checkm_result
[2023-03-18 09:12:01,447] [INFO] Task succeeded: CheckM
[2023-03-18 09:12:01,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:12:01,454] [INFO] ===== Completeness check finished =====
[2023-03-18 09:12:01,454] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:12:01,454] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17506/markers.fasta)
[2023-03-18 09:12:01,455] [INFO] Task started: Blastn
[2023-03-18 09:12:01,455] [INFO] Running command: blastn -query OceanDNA-b17506/markers.fasta -db /var/lib/cwl/stg4a7c4062-20b2-4f06-9be3-bfd884783e43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17506/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:12:02,174] [INFO] Task succeeded: Blastn
[2023-03-18 09:12:02,178] [INFO] Selected 8 target genomes.
[2023-03-18 09:12:02,178] [INFO] Target genome list was writen to OceanDNA-b17506/target_genomes_gtdb.txt
[2023-03-18 09:12:02,192] [INFO] Task started: fastANI
[2023-03-18 09:12:02,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg68584b3b-20d8-4bfa-91eb-8bf48825d847/OceanDNA-b17506.fa --refList OceanDNA-b17506/target_genomes_gtdb.txt --output OceanDNA-b17506/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:12:07,120] [INFO] Task succeeded: fastANI
[2023-03-18 09:12:07,124] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:12:07,124] [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_002501085.1	s__UBA1138 sp002501085	99.6851	668	764	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	98.27	98.27	0.83	0.83	2	conclusive
GCA_002313925.1	s__UBA1138 sp002313925	94.0563	614	764	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	96.15	95.66	0.87	0.85	5	-
GCA_012960225.1	s__UBA1138 sp012960225	92.9942	692	764	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.89	99.89	0.95	0.95	2	-
GCA_002724575.1	s__UBA1138 sp002724575	87.585	589	764	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	96.61	95.09	0.77	0.73	4	-
GCA_002311875.1	s__UBA1138 sp002311875	81.4266	597	764	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.17	99.17	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:12:07,126] [INFO] GTDB search result was written to OceanDNA-b17506/result_gtdb.tsv
[2023-03-18 09:12:07,127] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:12:07,127] [INFO] DFAST_QC result json was written to OceanDNA-b17506/dqc_result.json
[2023-03-18 09:12:07,127] [INFO] DFAST_QC completed!
[2023-03-18 09:12:07,127] [INFO] Total running time: 0h1m6s