[2023-03-18 10:37:58,272] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:37:58,272] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:37:58,272] [INFO] DQC Reference Directory: /var/lib/cwl/stge05010e7-e143-44e2-9f38-305959d98d8a/dqc_reference
[2023-03-18 10:37:59,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:37:59,405] [INFO] Task started: Prodigal
[2023-03-18 10:37:59,405] [INFO] Running command: cat /var/lib/cwl/stg93a16b2b-90e0-4525-a031-efa8abfc63f4/OceanDNA-b24003.fa | prodigal -d OceanDNA-b24003/cds.fna -a OceanDNA-b24003/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:38:10,356] [INFO] Task succeeded: Prodigal
[2023-03-18 10:38:10,356] [INFO] Task started: HMMsearch
[2023-03-18 10:38:10,356] [INFO] Running command: hmmsearch --tblout OceanDNA-b24003/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge05010e7-e143-44e2-9f38-305959d98d8a/dqc_reference/reference_markers.hmm OceanDNA-b24003/protein.faa > /dev/null
[2023-03-18 10:38:10,532] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:38:10,532] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg93a16b2b-90e0-4525-a031-efa8abfc63f4/OceanDNA-b24003.fa]
[2023-03-18 10:38:10,551] [INFO] Query marker FASTA was written to OceanDNA-b24003/markers.fasta
[2023-03-18 10:38:10,552] [INFO] Task started: Blastn
[2023-03-18 10:38:10,552] [INFO] Running command: blastn -query OceanDNA-b24003/markers.fasta -db /var/lib/cwl/stge05010e7-e143-44e2-9f38-305959d98d8a/dqc_reference/reference_markers.fasta -out OceanDNA-b24003/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:38:11,205] [INFO] Task succeeded: Blastn
[2023-03-18 10:38:11,206] [INFO] Selected 22 target genomes.
[2023-03-18 10:38:11,206] [INFO] Target genome list was writen to OceanDNA-b24003/target_genomes.txt
[2023-03-18 10:38:11,244] [INFO] Task started: fastANI
[2023-03-18 10:38:11,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg93a16b2b-90e0-4525-a031-efa8abfc63f4/OceanDNA-b24003.fa --refList OceanDNA-b24003/target_genomes.txt --output OceanDNA-b24003/fastani_result.tsv --threads 1
[2023-03-18 10:38:25,961] [INFO] Task succeeded: fastANI
[2023-03-18 10:38:25,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge05010e7-e143-44e2-9f38-305959d98d8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:38:25,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge05010e7-e143-44e2-9f38-305959d98d8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:38:25,966] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:38:25,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:38:25,966] [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
Parvularcula mediterranea	strain=ZS-1/3	GCA_013085255.1	2732508	2732508	type	True	77.7922	150	534	95	below_threshold
Parvularcula lutaonensis	strain=KCTC 22245	GCA_014651915.1	491923	491923	type	True	77.646	129	534	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:38:25,966] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24003/tc_result.tsv
[2023-03-18 10:38:25,966] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:38:25,966] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:38:25,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge05010e7-e143-44e2-9f38-305959d98d8a/dqc_reference/checkm_data
[2023-03-18 10:38:25,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:38:25,971] [INFO] Task started: CheckM
[2023-03-18 10:38:25,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24003/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24003/checkm_input OceanDNA-b24003/checkm_result
[2023-03-18 10:38:57,727] [INFO] Task succeeded: CheckM
[2023-03-18 10:38:57,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.37%
Contamintation: 2.15%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 10:38:57,731] [INFO] ===== Completeness check finished =====
[2023-03-18 10:38:57,731] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:38:57,731] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24003/markers.fasta)
[2023-03-18 10:38:57,732] [INFO] Task started: Blastn
[2023-03-18 10:38:57,732] [INFO] Running command: blastn -query OceanDNA-b24003/markers.fasta -db /var/lib/cwl/stge05010e7-e143-44e2-9f38-305959d98d8a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24003/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:38:58,901] [INFO] Task succeeded: Blastn
[2023-03-18 10:38:58,901] [INFO] Selected 22 target genomes.
[2023-03-18 10:38:58,902] [INFO] Target genome list was writen to OceanDNA-b24003/target_genomes_gtdb.txt
[2023-03-18 10:38:58,979] [INFO] Task started: fastANI
[2023-03-18 10:38:58,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg93a16b2b-90e0-4525-a031-efa8abfc63f4/OceanDNA-b24003.fa --refList OceanDNA-b24003/target_genomes_gtdb.txt --output OceanDNA-b24003/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:39:13,726] [INFO] Task succeeded: fastANI
[2023-03-18 10:39:13,729] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:39:13,729] [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_013215175.1	s__Parvularcula sp013215175	99.2053	482	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013085255.1	s__Parvularcula mediterranea	77.7922	150	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651915.1	s__Parvularcula lutaonensis	77.646	129	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:39:13,731] [INFO] GTDB search result was written to OceanDNA-b24003/result_gtdb.tsv
[2023-03-18 10:39:13,734] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:39:13,737] [INFO] DFAST_QC result json was written to OceanDNA-b24003/dqc_result.json
[2023-03-18 10:39:13,738] [INFO] DFAST_QC completed!
[2023-03-18 10:39:13,738] [INFO] Total running time: 0h1m15s