[2023-03-15 12:44:24,474] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,474] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,474] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ce6cc4c-393e-467c-bfdb-fa83229bcbb5/dqc_reference
[2023-03-15 12:44:26,206] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,207] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,207] [INFO] Running command: cat /var/lib/cwl/stgc8fec6cd-8673-4741-af24-cfa99e3f3d6f/OceanDNA-b387.fa | prodigal -d OceanDNA-b387/cds.fna -a OceanDNA-b387/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:33,467] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:33,467] [INFO] Task started: HMMsearch
[2023-03-15 12:44:33,467] [INFO] Running command: hmmsearch --tblout OceanDNA-b387/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ce6cc4c-393e-467c-bfdb-fa83229bcbb5/dqc_reference/reference_markers.hmm OceanDNA-b387/protein.faa > /dev/null
[2023-03-15 12:44:33,612] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:33,612] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc8fec6cd-8673-4741-af24-cfa99e3f3d6f/OceanDNA-b387.fa]
[2023-03-15 12:44:33,623] [INFO] Query marker FASTA was written to OceanDNA-b387/markers.fasta
[2023-03-15 12:44:33,623] [INFO] Task started: Blastn
[2023-03-15 12:44:33,623] [INFO] Running command: blastn -query OceanDNA-b387/markers.fasta -db /var/lib/cwl/stg3ce6cc4c-393e-467c-bfdb-fa83229bcbb5/dqc_reference/reference_markers.fasta -out OceanDNA-b387/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:34,071] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:34,072] [INFO] Selected 10 target genomes.
[2023-03-15 12:44:34,072] [INFO] Target genome list was writen to OceanDNA-b387/target_genomes.txt
[2023-03-15 12:44:34,078] [INFO] Task started: fastANI
[2023-03-15 12:44:34,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8fec6cd-8673-4741-af24-cfa99e3f3d6f/OceanDNA-b387.fa --refList OceanDNA-b387/target_genomes.txt --output OceanDNA-b387/fastani_result.tsv --threads 1
[2023-03-15 12:44:43,280] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:43,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ce6cc4c-393e-467c-bfdb-fa83229bcbb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:43,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ce6cc4c-393e-467c-bfdb-fa83229bcbb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:43,283] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:43,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:44:43,284] [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
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.9341	91	376	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:44:43,284] [INFO] DFAST Taxonomy check result was written to OceanDNA-b387/tc_result.tsv
[2023-03-15 12:44:43,284] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:43,284] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:43,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ce6cc4c-393e-467c-bfdb-fa83229bcbb5/dqc_reference/checkm_data
[2023-03-15 12:44:43,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:43,288] [INFO] Task started: CheckM
[2023-03-15 12:44:43,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b387/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b387/checkm_input OceanDNA-b387/checkm_result
[2023-03-15 12:45:05,975] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:05,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:45:05,978] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:05,978] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:05,978] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b387/markers.fasta)
[2023-03-15 12:45:05,978] [INFO] Task started: Blastn
[2023-03-15 12:45:05,978] [INFO] Running command: blastn -query OceanDNA-b387/markers.fasta -db /var/lib/cwl/stg3ce6cc4c-393e-467c-bfdb-fa83229bcbb5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b387/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:06,518] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:06,518] [INFO] Selected 10 target genomes.
[2023-03-15 12:45:06,519] [INFO] Target genome list was writen to OceanDNA-b387/target_genomes_gtdb.txt
[2023-03-15 12:45:06,586] [INFO] Task started: fastANI
[2023-03-15 12:45:06,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8fec6cd-8673-4741-af24-cfa99e3f3d6f/OceanDNA-b387.fa --refList OceanDNA-b387/target_genomes_gtdb.txt --output OceanDNA-b387/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:45:13,169] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:13,174] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:45:13,175] [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_009924875.1	s__Casp-actino5 sp009924875	97.6545	178	376	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017859785.1	s__Casp-actino5 sp017859785	84.6041	322	376	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.23	98.27	0.91	0.86	15	-
GCA_010024485.1	s__Casp-actino5 sp010024485	80.799	186	376	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.53	98.53	0.77	0.77	2	-
GCA_009704985.1	s__VFMC01 sp009704985	77.2209	100	376	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698945.1	s__Ilumatobacter sp002698945	76.3796	91	376	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213745.1	s__JABSQH01 sp013213745	76.3136	67	376	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009726095.1	s__WLMZ01 sp009726095	75.5899	51	376	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__WLMZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:45:13,175] [INFO] GTDB search result was written to OceanDNA-b387/result_gtdb.tsv
[2023-03-15 12:45:13,175] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:45:13,176] [INFO] DFAST_QC result json was written to OceanDNA-b387/dqc_result.json
[2023-03-15 12:45:13,176] [INFO] DFAST_QC completed!
[2023-03-15 12:45:13,176] [INFO] Total running time: 0h0m49s