[2023-03-15 13:03:53,437] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,437] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,437] [INFO] DQC Reference Directory: /var/lib/cwl/stgab3f8ff1-2c67-4732-9003-8c7ef39c7469/dqc_reference
[2023-03-15 13:03:54,591] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,592] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,592] [INFO] Running command: cat /var/lib/cwl/stg9139542a-f99d-41cf-91a8-bde5c367e152/OceanDNA-b22134.fa | prodigal -d OceanDNA-b22134/cds.fna -a OceanDNA-b22134/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:03,709] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:03,709] [INFO] Task started: HMMsearch
[2023-03-15 13:04:03,709] [INFO] Running command: hmmsearch --tblout OceanDNA-b22134/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab3f8ff1-2c67-4732-9003-8c7ef39c7469/dqc_reference/reference_markers.hmm OceanDNA-b22134/protein.faa > /dev/null
[2023-03-15 13:04:03,949] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:03,949] [INFO] Found 6/6 markers.
[2023-03-15 13:04:03,961] [INFO] Query marker FASTA was written to OceanDNA-b22134/markers.fasta
[2023-03-15 13:04:03,962] [INFO] Task started: Blastn
[2023-03-15 13:04:03,962] [INFO] Running command: blastn -query OceanDNA-b22134/markers.fasta -db /var/lib/cwl/stgab3f8ff1-2c67-4732-9003-8c7ef39c7469/dqc_reference/reference_markers.fasta -out OceanDNA-b22134/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:04,486] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:04,487] [INFO] Selected 13 target genomes.
[2023-03-15 13:04:04,487] [INFO] Target genome list was writen to OceanDNA-b22134/target_genomes.txt
[2023-03-15 13:04:04,524] [INFO] Task started: fastANI
[2023-03-15 13:04:04,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg9139542a-f99d-41cf-91a8-bde5c367e152/OceanDNA-b22134.fa --refList OceanDNA-b22134/target_genomes.txt --output OceanDNA-b22134/fastani_result.tsv --threads 1
[2023-03-15 13:04:09,711] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:09,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab3f8ff1-2c67-4732-9003-8c7ef39c7469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:09,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab3f8ff1-2c67-4732-9003-8c7ef39c7469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:09,711] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:09,711] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:04:09,711] [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
--------------------------------------------------------------------------------
[2023-03-15 13:04:09,712] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22134/tc_result.tsv
[2023-03-15 13:04:09,712] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:09,712] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:09,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab3f8ff1-2c67-4732-9003-8c7ef39c7469/dqc_reference/checkm_data
[2023-03-15 13:04:09,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:09,723] [INFO] Task started: CheckM
[2023-03-15 13:04:09,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22134/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22134/checkm_input OceanDNA-b22134/checkm_result
[2023-03-15 13:04:38,004] [INFO] Task succeeded: CheckM
[2023-03-15 13:04:38,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:04:38,007] [INFO] ===== Completeness check finished =====
[2023-03-15 13:04:38,007] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:04:38,007] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22134/markers.fasta)
[2023-03-15 13:04:38,007] [INFO] Task started: Blastn
[2023-03-15 13:04:38,007] [INFO] Running command: blastn -query OceanDNA-b22134/markers.fasta -db /var/lib/cwl/stgab3f8ff1-2c67-4732-9003-8c7ef39c7469/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22134/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:38,722] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:38,723] [INFO] Selected 21 target genomes.
[2023-03-15 13:04:38,723] [INFO] Target genome list was writen to OceanDNA-b22134/target_genomes_gtdb.txt
[2023-03-15 13:04:38,939] [INFO] Task started: fastANI
[2023-03-15 13:04:38,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg9139542a-f99d-41cf-91a8-bde5c367e152/OceanDNA-b22134.fa --refList OceanDNA-b22134/target_genomes_gtdb.txt --output OceanDNA-b22134/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:04:45,640] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:45,645] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:04:45,645] [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_018701395.1	s__GCA-002718515 sp018701395	77.007	86	484	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.63	99.41	0.94	0.92	4	-
GCA_014381555.1	s__GCA-002718515 sp014381555	76.9125	103	484	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.84	99.84	0.86	0.86	2	-
GCA_018657585.1	s__GCA-002718515 sp018657585	76.5917	75	484	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018665385.1	s__GCA-002718515 sp018665385	76.5323	71	484	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.09	99.03	0.85	0.83	4	-
GCA_016845245.1	s__GCA-002718515 sp016845245	76.4353	57	484	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238785.1	s__GCA-002718515 sp014238785	76.404	76	484	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238125.1	s__GCA-002718515 sp014238125	76.3133	53	484	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:04:45,645] [INFO] GTDB search result was written to OceanDNA-b22134/result_gtdb.tsv
[2023-03-15 13:04:45,646] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:04:45,646] [INFO] DFAST_QC result json was written to OceanDNA-b22134/dqc_result.json
[2023-03-15 13:04:45,646] [INFO] DFAST_QC completed!
[2023-03-15 13:04:45,647] [INFO] Total running time: 0h0m52s