[2023-03-16 03:47:32,865] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,865] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,865] [INFO] DQC Reference Directory: /var/lib/cwl/stg481f5663-962d-45da-818b-4894a034889a/dqc_reference
[2023-03-16 03:47:34,481] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,481] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,481] [INFO] Running command: cat /var/lib/cwl/stg848668a6-8c48-4cb2-85c8-5da54f454142/OceanDNA-b7133.fa | prodigal -d OceanDNA-b7133/cds.fna -a OceanDNA-b7133/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:40,766] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:40,766] [INFO] Task started: HMMsearch
[2023-03-16 03:47:40,766] [INFO] Running command: hmmsearch --tblout OceanDNA-b7133/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg481f5663-962d-45da-818b-4894a034889a/dqc_reference/reference_markers.hmm OceanDNA-b7133/protein.faa > /dev/null
[2023-03-16 03:47:40,896] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:40,897] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg848668a6-8c48-4cb2-85c8-5da54f454142/OceanDNA-b7133.fa]
[2023-03-16 03:47:40,907] [INFO] Query marker FASTA was written to OceanDNA-b7133/markers.fasta
[2023-03-16 03:47:40,907] [INFO] Task started: Blastn
[2023-03-16 03:47:40,908] [INFO] Running command: blastn -query OceanDNA-b7133/markers.fasta -db /var/lib/cwl/stg481f5663-962d-45da-818b-4894a034889a/dqc_reference/reference_markers.fasta -out OceanDNA-b7133/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:41,369] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:41,370] [INFO] Selected 25 target genomes.
[2023-03-16 03:47:41,370] [INFO] Target genome list was writen to OceanDNA-b7133/target_genomes.txt
[2023-03-16 03:47:41,382] [INFO] Task started: fastANI
[2023-03-16 03:47:41,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg848668a6-8c48-4cb2-85c8-5da54f454142/OceanDNA-b7133.fa --refList OceanDNA-b7133/target_genomes.txt --output OceanDNA-b7133/fastani_result.tsv --threads 1
[2023-03-16 03:47:54,435] [INFO] Task succeeded: fastANI
[2023-03-16 03:47:54,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg481f5663-962d-45da-818b-4894a034889a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:47:54,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg481f5663-962d-45da-818b-4894a034889a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:47:54,439] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:47:54,439] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:47:54,439] [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
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.3253	54	274	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.0505	50	274	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:47:54,439] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7133/tc_result.tsv
[2023-03-16 03:47:54,439] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:47:54,439] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:47:54,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg481f5663-962d-45da-818b-4894a034889a/dqc_reference/checkm_data
[2023-03-16 03:47:54,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:47:54,443] [INFO] Task started: CheckM
[2023-03-16 03:47:54,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7133/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7133/checkm_input OceanDNA-b7133/checkm_result
[2023-03-16 03:48:15,698] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:15,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:15,700] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:15,700] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:15,701] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7133/markers.fasta)
[2023-03-16 03:48:15,701] [INFO] Task started: Blastn
[2023-03-16 03:48:15,701] [INFO] Running command: blastn -query OceanDNA-b7133/markers.fasta -db /var/lib/cwl/stg481f5663-962d-45da-818b-4894a034889a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7133/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:16,157] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:16,158] [INFO] Selected 21 target genomes.
[2023-03-16 03:48:16,158] [INFO] Target genome list was writen to OceanDNA-b7133/target_genomes_gtdb.txt
[2023-03-16 03:48:16,195] [INFO] Task started: fastANI
[2023-03-16 03:48:16,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg848668a6-8c48-4cb2-85c8-5da54f454142/OceanDNA-b7133.fa --refList OceanDNA-b7133/target_genomes_gtdb.txt --output OceanDNA-b7133/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:27,839] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:27,843] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:48:27,843] [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_002733415.1	s__GCA-2733415 sp002733415	78.7841	142	274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2733415	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214625.1	s__GCA-2733415 sp013214625	78.4548	148	274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2733415	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	76.1891	61	274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	75.864	53	274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:48:27,843] [INFO] GTDB search result was written to OceanDNA-b7133/result_gtdb.tsv
[2023-03-16 03:48:27,843] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:27,844] [INFO] DFAST_QC result json was written to OceanDNA-b7133/dqc_result.json
[2023-03-16 03:48:27,844] [INFO] DFAST_QC completed!
[2023-03-16 03:48:27,844] [INFO] Total running time: 0h0m55s