[2023-03-18 10:46:22,150] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:46:22,150] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:46:22,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fb47652-f037-406b-8b8b-b1bd246d5e16/dqc_reference
[2023-03-18 10:46:23,266] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:46:23,266] [INFO] Task started: Prodigal
[2023-03-18 10:46:23,267] [INFO] Running command: cat /var/lib/cwl/stg7d81044a-56af-42d4-a83e-4a47409a7476/OceanDNA-b22833.fa | prodigal -d OceanDNA-b22833/cds.fna -a OceanDNA-b22833/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:47:09,932] [INFO] Task succeeded: Prodigal
[2023-03-18 10:47:09,932] [INFO] Task started: HMMsearch
[2023-03-18 10:47:09,932] [INFO] Running command: hmmsearch --tblout OceanDNA-b22833/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fb47652-f037-406b-8b8b-b1bd246d5e16/dqc_reference/reference_markers.hmm OceanDNA-b22833/protein.faa > /dev/null
[2023-03-18 10:47:10,210] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:47:10,210] [INFO] Found 6/6 markers.
[2023-03-18 10:47:10,250] [INFO] Query marker FASTA was written to OceanDNA-b22833/markers.fasta
[2023-03-18 10:47:10,252] [INFO] Task started: Blastn
[2023-03-18 10:47:10,252] [INFO] Running command: blastn -query OceanDNA-b22833/markers.fasta -db /var/lib/cwl/stg9fb47652-f037-406b-8b8b-b1bd246d5e16/dqc_reference/reference_markers.fasta -out OceanDNA-b22833/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:47:10,780] [INFO] Task succeeded: Blastn
[2023-03-18 10:47:10,785] [INFO] Selected 26 target genomes.
[2023-03-18 10:47:10,785] [INFO] Target genome list was writen to OceanDNA-b22833/target_genomes.txt
[2023-03-18 10:47:10,802] [INFO] Task started: fastANI
[2023-03-18 10:47:10,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d81044a-56af-42d4-a83e-4a47409a7476/OceanDNA-b22833.fa --refList OceanDNA-b22833/target_genomes.txt --output OceanDNA-b22833/fastani_result.tsv --threads 1
[2023-03-18 10:47:33,958] [INFO] Task succeeded: fastANI
[2023-03-18 10:47:33,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fb47652-f037-406b-8b8b-b1bd246d5e16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:47:33,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fb47652-f037-406b-8b8b-b1bd246d5e16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:47:33,963] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:47:33,964] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:47:33,964] [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	75.5546	81	2412	95	below_threshold
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	75.3273	76	2412	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.2945	115	2412	95	below_threshold
Rubinisphaera brasiliensis	strain=DSM 5305	GCA_000165715.3	119	119	type	True	74.9799	50	2412	95	below_threshold
Schlesneria paludicola	strain=DSM 18645	GCA_000255655.1	360056	360056	type	True	74.9556	50	2412	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	74.884	81	2412	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:47:33,966] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22833/tc_result.tsv
[2023-03-18 10:47:33,971] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:47:33,971] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:47:33,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fb47652-f037-406b-8b8b-b1bd246d5e16/dqc_reference/checkm_data
[2023-03-18 10:47:33,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:47:34,024] [INFO] Task started: CheckM
[2023-03-18 10:47:34,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22833/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22833/checkm_input OceanDNA-b22833/checkm_result
[2023-03-18 10:49:33,190] [INFO] Task succeeded: CheckM
[2023-03-18 10:49:33,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:49:33,214] [INFO] ===== Completeness check finished =====
[2023-03-18 10:49:33,214] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:49:33,214] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22833/markers.fasta)
[2023-03-18 10:49:33,216] [INFO] Task started: Blastn
[2023-03-18 10:49:33,216] [INFO] Running command: blastn -query OceanDNA-b22833/markers.fasta -db /var/lib/cwl/stg9fb47652-f037-406b-8b8b-b1bd246d5e16/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22833/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:49:34,140] [INFO] Task succeeded: Blastn
[2023-03-18 10:49:34,141] [INFO] Selected 21 target genomes.
[2023-03-18 10:49:34,141] [INFO] Target genome list was writen to OceanDNA-b22833/target_genomes_gtdb.txt
[2023-03-18 10:49:34,189] [INFO] Task started: fastANI
[2023-03-18 10:49:34,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d81044a-56af-42d4-a83e-4a47409a7476/OceanDNA-b22833.fa --refList OceanDNA-b22833/target_genomes_gtdb.txt --output OceanDNA-b22833/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:49:52,479] [INFO] Task succeeded: fastANI
[2023-03-18 10:49:52,485] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:49:52,486] [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_016779365.1	s__JABMPE01 sp016779365	86.4255	805	2412	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203845.1	s__JABMPE01 sp013203845	79.3468	1109	2412	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	76.279	326	2412	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872645.1	s__SXKJ01 sp016872645	75.3504	60	2412	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242525.1	s__Schlesneria sp018242525	75.3094	66	2412	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113665.1	s__Planctomicrobium piriforme	75.304	54	2412	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299185.1	s__AM-0621 sp900299185	75.1847	72	2412	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__AM-0621	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007744515.1	s__Calycomorphotria sp007744515	75.1689	50	2412	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Calycomorphotria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007745175.1	s__Caulifigura coniformis	74.891	79	2412	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Caulifigura	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:49:52,489] [INFO] GTDB search result was written to OceanDNA-b22833/result_gtdb.tsv
[2023-03-18 10:49:52,492] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:49:52,499] [INFO] DFAST_QC result json was written to OceanDNA-b22833/dqc_result.json
[2023-03-18 10:49:52,499] [INFO] DFAST_QC completed!
[2023-03-18 10:49:52,499] [INFO] Total running time: 0h3m30s