[2023-03-17 06:04:36,756] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:04:36,756] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:04:36,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg924d6509-69c7-4801-ac0b-5d5bf445d4ab/dqc_reference
[2023-03-17 06:04:37,965] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:04:37,966] [INFO] Task started: Prodigal
[2023-03-17 06:04:37,966] [INFO] Running command: cat /var/lib/cwl/stg6510c77b-3c5b-4059-9898-d16bef724ee1/OceanDNA-b44593.fa | prodigal -d OceanDNA-b44593/cds.fna -a OceanDNA-b44593/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:04:54,954] [INFO] Task succeeded: Prodigal
[2023-03-17 06:04:54,954] [INFO] Task started: HMMsearch
[2023-03-17 06:04:54,954] [INFO] Running command: hmmsearch --tblout OceanDNA-b44593/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg924d6509-69c7-4801-ac0b-5d5bf445d4ab/dqc_reference/reference_markers.hmm OceanDNA-b44593/protein.faa > /dev/null
[2023-03-17 06:04:55,144] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:04:55,145] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6510c77b-3c5b-4059-9898-d16bef724ee1/OceanDNA-b44593.fa]
[2023-03-17 06:04:55,163] [INFO] Query marker FASTA was written to OceanDNA-b44593/markers.fasta
[2023-03-17 06:04:55,163] [INFO] Task started: Blastn
[2023-03-17 06:04:55,163] [INFO] Running command: blastn -query OceanDNA-b44593/markers.fasta -db /var/lib/cwl/stg924d6509-69c7-4801-ac0b-5d5bf445d4ab/dqc_reference/reference_markers.fasta -out OceanDNA-b44593/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:04:55,778] [INFO] Task succeeded: Blastn
[2023-03-17 06:04:55,779] [INFO] Selected 29 target genomes.
[2023-03-17 06:04:55,779] [INFO] Target genome list was writen to OceanDNA-b44593/target_genomes.txt
[2023-03-17 06:04:55,793] [INFO] Task started: fastANI
[2023-03-17 06:04:55,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg6510c77b-3c5b-4059-9898-d16bef724ee1/OceanDNA-b44593.fa --refList OceanDNA-b44593/target_genomes.txt --output OceanDNA-b44593/fastani_result.tsv --threads 1
[2023-03-17 06:05:15,037] [INFO] Task succeeded: fastANI
[2023-03-17 06:05:15,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg924d6509-69c7-4801-ac0b-5d5bf445d4ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:05:15,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg924d6509-69c7-4801-ac0b-5d5bf445d4ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:05:15,041] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:05:15,041] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:05:15,041] [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
Woeseia oceani	strain=XK5	GCA_001677435.1	1548547	1548547	type	True	76.676	66	910	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:05:15,041] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44593/tc_result.tsv
[2023-03-17 06:05:15,041] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:05:15,041] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:05:15,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg924d6509-69c7-4801-ac0b-5d5bf445d4ab/dqc_reference/checkm_data
[2023-03-17 06:05:15,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:05:15,047] [INFO] Task started: CheckM
[2023-03-17 06:05:15,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44593/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44593/checkm_input OceanDNA-b44593/checkm_result
[2023-03-17 06:05:59,050] [INFO] Task succeeded: CheckM
[2023-03-17 06:05:59,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:05:59,053] [INFO] ===== Completeness check finished =====
[2023-03-17 06:05:59,053] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:05:59,053] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44593/markers.fasta)
[2023-03-17 06:05:59,055] [INFO] Task started: Blastn
[2023-03-17 06:05:59,055] [INFO] Running command: blastn -query OceanDNA-b44593/markers.fasta -db /var/lib/cwl/stg924d6509-69c7-4801-ac0b-5d5bf445d4ab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44593/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:06:00,061] [INFO] Task succeeded: Blastn
[2023-03-17 06:06:00,062] [INFO] Selected 23 target genomes.
[2023-03-17 06:06:00,062] [INFO] Target genome list was writen to OceanDNA-b44593/target_genomes_gtdb.txt
[2023-03-17 06:06:00,711] [INFO] Task started: fastANI
[2023-03-17 06:06:00,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg6510c77b-3c5b-4059-9898-d16bef724ee1/OceanDNA-b44593.fa --refList OceanDNA-b44593/target_genomes_gtdb.txt --output OceanDNA-b44593/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:06:12,311] [INFO] Task succeeded: fastANI
[2023-03-17 06:06:12,318] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:06:12,318] [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
GCF_001677435.1	s__Woeseia oceani	76.676	66	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__Woeseia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480255.1	s__SZUA-117 sp905480255	76.49	120	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SZUA-117	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004357475.1	s__SZUA-117 sp004357475	76.4675	59	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SZUA-117	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018677555.1	s__IDS-8 sp018677555	76.4277	73	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__IDS-8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042375.1	s__UBA1847 sp013042375	76.1892	88	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.79	99.73	0.92	0.88	6	-
GCA_009937505.1	s__JAACFE01 sp009937505	76.1439	77	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151645.1	s__JAADHU01 sp013151645	75.9963	62	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAADHU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004282875.1	s__UBA1847 sp004282875	75.9569	75	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937615.1	s__JAACFB01 sp009937615	75.9504	64	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338615.1	s__UBA1844 sp002338615	75.7658	59	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1844	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937605.1	s__UBA1847 sp009937605	75.6911	61	910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:06:12,319] [INFO] GTDB search result was written to OceanDNA-b44593/result_gtdb.tsv
[2023-03-17 06:06:12,319] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:06:12,320] [INFO] DFAST_QC result json was written to OceanDNA-b44593/dqc_result.json
[2023-03-17 06:06:12,320] [INFO] DFAST_QC completed!
[2023-03-17 06:06:12,320] [INFO] Total running time: 0h1m36s