[2023-03-14 11:33:35,016] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:35,016] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:35,016] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfba5a21-0def-4072-b5ee-02898f636fdd/dqc_reference
[2023-03-14 11:33:36,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,157] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,158] [INFO] Running command: cat /var/lib/cwl/stg6ca205e1-af5f-4827-aaeb-6763df535951/OceanDNA-b22518.fa | prodigal -d OceanDNA-b22518/cds.fna -a OceanDNA-b22518/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:34:35,000] [INFO] Task succeeded: Prodigal
[2023-03-14 11:34:35,001] [INFO] Task started: HMMsearch
[2023-03-14 11:34:35,001] [INFO] Running command: hmmsearch --tblout OceanDNA-b22518/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfba5a21-0def-4072-b5ee-02898f636fdd/dqc_reference/reference_markers.hmm OceanDNA-b22518/protein.faa > /dev/null
[2023-03-14 11:34:35,360] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:34:35,360] [INFO] Found 6/6 markers.
[2023-03-14 11:34:35,408] [INFO] Query marker FASTA was written to OceanDNA-b22518/markers.fasta
[2023-03-14 11:34:35,408] [INFO] Task started: Blastn
[2023-03-14 11:34:35,408] [INFO] Running command: blastn -query OceanDNA-b22518/markers.fasta -db /var/lib/cwl/stgdfba5a21-0def-4072-b5ee-02898f636fdd/dqc_reference/reference_markers.fasta -out OceanDNA-b22518/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:38,772] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:38,772] [INFO] Selected 24 target genomes.
[2023-03-14 11:34:38,773] [INFO] Target genome list was writen to OceanDNA-b22518/target_genomes.txt
[2023-03-14 11:34:38,787] [INFO] Task started: fastANI
[2023-03-14 11:34:38,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca205e1-af5f-4827-aaeb-6763df535951/OceanDNA-b22518.fa --refList OceanDNA-b22518/target_genomes.txt --output OceanDNA-b22518/fastani_result.tsv --threads 1
[2023-03-14 11:35:03,190] [INFO] Task succeeded: fastANI
[2023-03-14 11:35:03,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfba5a21-0def-4072-b5ee-02898f636fdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:35:03,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfba5a21-0def-4072-b5ee-02898f636fdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:35:03,196] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:35:03,197] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:35:03,197] [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
Aureliella helgolandensis	strain=Q31a	GCA_007752135.1	2527968	2527968	type	True	76.4058	76	2860	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	76.3731	50	2860	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	76.0256	54	2860	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	75.8761	51	2860	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	75.7274	59	2860	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	75.6606	61	2860	95	below_threshold
Rosistilla oblonga	strain=CA51	GCA_007751715.1	2527990	2527990	type	True	75.5083	51	2860	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:35:03,197] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22518/tc_result.tsv
[2023-03-14 11:35:03,197] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:35:03,197] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:35:03,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfba5a21-0def-4072-b5ee-02898f636fdd/dqc_reference/checkm_data
[2023-03-14 11:35:03,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:35:03,206] [INFO] Task started: CheckM
[2023-03-14 11:35:03,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22518/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22518/checkm_input OceanDNA-b22518/checkm_result
[2023-03-14 11:37:21,298] [INFO] Task succeeded: CheckM
[2023-03-14 11:37:21,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:37:21,312] [INFO] ===== Completeness check finished =====
[2023-03-14 11:37:21,312] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:37:21,313] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22518/markers.fasta)
[2023-03-14 11:37:21,314] [INFO] Task started: Blastn
[2023-03-14 11:37:21,314] [INFO] Running command: blastn -query OceanDNA-b22518/markers.fasta -db /var/lib/cwl/stgdfba5a21-0def-4072-b5ee-02898f636fdd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22518/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:37:22,167] [INFO] Task succeeded: Blastn
[2023-03-14 11:37:22,169] [INFO] Selected 28 target genomes.
[2023-03-14 11:37:22,169] [INFO] Target genome list was writen to OceanDNA-b22518/target_genomes_gtdb.txt
[2023-03-14 11:37:22,304] [INFO] Task started: fastANI
[2023-03-14 11:37:22,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca205e1-af5f-4827-aaeb-6763df535951/OceanDNA-b22518.fa --refList OceanDNA-b22518/target_genomes_gtdb.txt --output OceanDNA-b22518/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:37:48,710] [INFO] Task succeeded: fastANI
[2023-03-14 11:37:48,714] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:37:48,714] [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_002862265.1	s__Aureliella sp002862265	86.9042	1035	2860	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Aureliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752135.1	s__Aureliella helgolandensis	76.3792	77	2860	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Aureliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859915.1	s__Rhodopirellula pilleata	76.0166	54	2860	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741555.1	s__K23-9 sp007741555	75.9653	52	2860	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__K23-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741535.1	s__Rubripirellula sp007741535	75.8761	51	2860	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:37:48,716] [INFO] GTDB search result was written to OceanDNA-b22518/result_gtdb.tsv
[2023-03-14 11:37:48,718] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:37:48,720] [INFO] DFAST_QC result json was written to OceanDNA-b22518/dqc_result.json
[2023-03-14 11:37:48,721] [INFO] DFAST_QC completed!
[2023-03-14 11:37:48,721] [INFO] Total running time: 0h4m14s