[2023-03-15 16:42:46,507] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:42:46,508] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:42:46,508] [INFO] DQC Reference Directory: /var/lib/cwl/stgf28e7be7-f338-4ae2-9f0b-c1e707513b6c/dqc_reference
[2023-03-15 16:42:48,309] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:42:48,310] [INFO] Task started: Prodigal
[2023-03-15 16:42:48,310] [INFO] Running command: cat /var/lib/cwl/stgf60702bd-be4f-4022-b2cf-67d094aa1cc5/OceanDNA-b22871.fa | prodigal -d OceanDNA-b22871/cds.fna -a OceanDNA-b22871/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:43:19,393] [INFO] Task succeeded: Prodigal
[2023-03-15 16:43:19,393] [INFO] Task started: HMMsearch
[2023-03-15 16:43:19,393] [INFO] Running command: hmmsearch --tblout OceanDNA-b22871/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf28e7be7-f338-4ae2-9f0b-c1e707513b6c/dqc_reference/reference_markers.hmm OceanDNA-b22871/protein.faa > /dev/null
[2023-03-15 16:43:19,673] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:43:19,673] [INFO] Found 6/6 markers.
[2023-03-15 16:43:19,717] [INFO] Query marker FASTA was written to OceanDNA-b22871/markers.fasta
[2023-03-15 16:43:19,718] [INFO] Task started: Blastn
[2023-03-15 16:43:19,718] [INFO] Running command: blastn -query OceanDNA-b22871/markers.fasta -db /var/lib/cwl/stgf28e7be7-f338-4ae2-9f0b-c1e707513b6c/dqc_reference/reference_markers.fasta -out OceanDNA-b22871/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:43:20,238] [INFO] Task succeeded: Blastn
[2023-03-15 16:43:20,240] [INFO] Selected 26 target genomes.
[2023-03-15 16:43:20,240] [INFO] Target genome list was writen to OceanDNA-b22871/target_genomes.txt
[2023-03-15 16:43:20,262] [INFO] Task started: fastANI
[2023-03-15 16:43:20,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgf60702bd-be4f-4022-b2cf-67d094aa1cc5/OceanDNA-b22871.fa --refList OceanDNA-b22871/target_genomes.txt --output OceanDNA-b22871/fastani_result.tsv --threads 1
[2023-03-15 16:43:43,781] [INFO] Task succeeded: fastANI
[2023-03-15 16:43:43,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf28e7be7-f338-4ae2-9f0b-c1e707513b6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:43:43,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf28e7be7-f338-4ae2-9f0b-c1e707513b6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:43:43,785] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:43:43,785] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:43:43,785] [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
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	76.3414	154	1549	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:43:43,786] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22871/tc_result.tsv
[2023-03-15 16:43:43,786] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:43:43,786] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:43:43,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf28e7be7-f338-4ae2-9f0b-c1e707513b6c/dqc_reference/checkm_data
[2023-03-15 16:43:43,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:43:43,881] [INFO] Task started: CheckM
[2023-03-15 16:43:43,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22871/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22871/checkm_input OceanDNA-b22871/checkm_result
[2023-03-15 16:45:01,160] [INFO] Task succeeded: CheckM
[2023-03-15 16:45:01,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:45:01,175] [INFO] ===== Completeness check finished =====
[2023-03-15 16:45:01,175] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:45:01,176] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22871/markers.fasta)
[2023-03-15 16:45:01,177] [INFO] Task started: Blastn
[2023-03-15 16:45:01,177] [INFO] Running command: blastn -query OceanDNA-b22871/markers.fasta -db /var/lib/cwl/stgf28e7be7-f338-4ae2-9f0b-c1e707513b6c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22871/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:45:02,281] [INFO] Task succeeded: Blastn
[2023-03-15 16:45:02,284] [INFO] Selected 26 target genomes.
[2023-03-15 16:45:02,284] [INFO] Target genome list was writen to OceanDNA-b22871/target_genomes_gtdb.txt
[2023-03-15 16:45:02,417] [INFO] Task started: fastANI
[2023-03-15 16:45:02,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgf60702bd-be4f-4022-b2cf-67d094aa1cc5/OceanDNA-b22871.fa --refList OceanDNA-b22871/target_genomes_gtdb.txt --output OceanDNA-b22871/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:45:28,714] [INFO] Task succeeded: fastANI
[2023-03-15 16:45:28,719] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:45:28,719] [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_014238335.1	s__Fuerstia sp014238335	80.7983	972	1549	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983935.1	s__Fuerstia marisgermanicae	76.3414	154	1549	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485495.1	s__S139-18 sp015485495	75.3451	51	1549	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__S139-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203845.1	s__JABMPE01 sp013203845	75.2496	58	1549	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124895.1	s__JABMPE01 sp016124895	75.0524	57	1549	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:45:28,720] [INFO] GTDB search result was written to OceanDNA-b22871/result_gtdb.tsv
[2023-03-15 16:45:28,721] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:45:28,723] [INFO] DFAST_QC result json was written to OceanDNA-b22871/dqc_result.json
[2023-03-15 16:45:28,723] [INFO] DFAST_QC completed!
[2023-03-15 16:45:28,723] [INFO] Total running time: 0h2m42s