[2023-03-19 01:50:01,866] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,866] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,866] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e86c5eb-e04f-4b66-856a-2c6fcf15ce4d/dqc_reference
[2023-03-19 01:50:03,572] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:03,572] [INFO] Task started: Prodigal
[2023-03-19 01:50:03,572] [INFO] Running command: cat /var/lib/cwl/stg2c3ad161-235f-4077-a536-6ad399be5b3e/OceanDNA-b44444.fa | prodigal -d OceanDNA-b44444/cds.fna -a OceanDNA-b44444/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:21,427] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:21,428] [INFO] Task started: HMMsearch
[2023-03-19 01:50:21,428] [INFO] Running command: hmmsearch --tblout OceanDNA-b44444/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e86c5eb-e04f-4b66-856a-2c6fcf15ce4d/dqc_reference/reference_markers.hmm OceanDNA-b44444/protein.faa > /dev/null
[2023-03-19 01:50:21,625] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:21,626] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2c3ad161-235f-4077-a536-6ad399be5b3e/OceanDNA-b44444.fa]
[2023-03-19 01:50:21,648] [INFO] Query marker FASTA was written to OceanDNA-b44444/markers.fasta
[2023-03-19 01:50:21,650] [INFO] Task started: Blastn
[2023-03-19 01:50:21,650] [INFO] Running command: blastn -query OceanDNA-b44444/markers.fasta -db /var/lib/cwl/stg8e86c5eb-e04f-4b66-856a-2c6fcf15ce4d/dqc_reference/reference_markers.fasta -out OceanDNA-b44444/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:22,219] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:22,221] [INFO] Selected 25 target genomes.
[2023-03-19 01:50:22,221] [INFO] Target genome list was writen to OceanDNA-b44444/target_genomes.txt
[2023-03-19 01:50:22,234] [INFO] Task started: fastANI
[2023-03-19 01:50:22,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c3ad161-235f-4077-a536-6ad399be5b3e/OceanDNA-b44444.fa --refList OceanDNA-b44444/target_genomes.txt --output OceanDNA-b44444/fastani_result.tsv --threads 1
[2023-03-19 01:50:37,803] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:37,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e86c5eb-e04f-4b66-856a-2c6fcf15ce4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:37,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e86c5eb-e04f-4b66-856a-2c6fcf15ce4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:37,807] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:37,807] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:50:37,807] [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	76.295	71	1003	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:50:37,807] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44444/tc_result.tsv
[2023-03-19 01:50:37,807] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:37,807] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:37,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e86c5eb-e04f-4b66-856a-2c6fcf15ce4d/dqc_reference/checkm_data
[2023-03-19 01:50:37,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:37,883] [INFO] Task started: CheckM
[2023-03-19 01:50:37,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44444/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44444/checkm_input OceanDNA-b44444/checkm_result
[2023-03-19 01:51:23,848] [INFO] Task succeeded: CheckM
[2023-03-19 01:51:23,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.80%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:51:23,854] [INFO] ===== Completeness check finished =====
[2023-03-19 01:51:23,855] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:51:23,855] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44444/markers.fasta)
[2023-03-19 01:51:23,856] [INFO] Task started: Blastn
[2023-03-19 01:51:23,856] [INFO] Running command: blastn -query OceanDNA-b44444/markers.fasta -db /var/lib/cwl/stg8e86c5eb-e04f-4b66-856a-2c6fcf15ce4d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44444/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:51:24,718] [INFO] Task succeeded: Blastn
[2023-03-19 01:51:24,719] [INFO] Selected 23 target genomes.
[2023-03-19 01:51:24,719] [INFO] Target genome list was writen to OceanDNA-b44444/target_genomes_gtdb.txt
[2023-03-19 01:51:24,739] [INFO] Task started: fastANI
[2023-03-19 01:51:24,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c3ad161-235f-4077-a536-6ad399be5b3e/OceanDNA-b44444.fa --refList OceanDNA-b44444/target_genomes_gtdb.txt --output OceanDNA-b44444/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:51:37,619] [INFO] Task succeeded: fastANI
[2023-03-19 01:51:37,626] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:51:37,626] [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_013042375.1	s__UBA1847 sp013042375	76.4103	113	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.79	99.73	0.92	0.88	6	-
GCA_018677555.1	s__IDS-8 sp018677555	76.368	72	1003	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_013043165.1	s__UBA1847 sp013043165	76.2678	67	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.92	99.83	0.96	0.93	3	-
GCA_009937525.1	s__JAACFE01 sp009937525	76.2559	107	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001045.1	s__UBA1847 sp013001045	76.0391	52	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.51	99.51	0.75	0.75	2	-
GCA_009937505.1	s__JAACFE01 sp009937505	76.0188	87	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127715.1	s__PWYM01 sp007127715	76.0096	56	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PWYM01;f__PWYM01;g__PWYM01	95.0	99.45	99.43	0.90	0.89	3	-
GCA_016789885.1	s__SHZI01 sp016789885	75.9767	59	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__SHZI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151645.1	s__JAADHU01 sp013151645	75.9339	58	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAADHU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704655.1	s__RPQJ01 sp016704655	75.8278	53	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	98.97	98.97	0.93	0.93	2	-
GCA_003567855.1	s__PWYM01 sp003567855	75.7448	63	1003	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PWYM01;f__PWYM01;g__PWYM01	95.0	99.44	99.37	0.87	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-19 01:51:37,627] [INFO] GTDB search result was written to OceanDNA-b44444/result_gtdb.tsv
[2023-03-19 01:51:37,629] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:51:37,633] [INFO] DFAST_QC result json was written to OceanDNA-b44444/dqc_result.json
[2023-03-19 01:51:37,633] [INFO] DFAST_QC completed!
[2023-03-19 01:51:37,633] [INFO] Total running time: 0h1m36s