[2023-03-15 10:56:33,014] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:56:33,015] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:56:33,015] [INFO] DQC Reference Directory: /var/lib/cwl/stga5501213-be12-4fa6-aebf-750daedd41cd/dqc_reference
[2023-03-15 10:56:34,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:56:34,123] [INFO] Task started: Prodigal
[2023-03-15 10:56:34,123] [INFO] Running command: cat /var/lib/cwl/stga0dc8b6c-a365-43b2-9b1d-75908ed2ff39/OceanDNA-b22203.fa | prodigal -d OceanDNA-b22203/cds.fna -a OceanDNA-b22203/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:56:47,979] [INFO] Task succeeded: Prodigal
[2023-03-15 10:56:47,980] [INFO] Task started: HMMsearch
[2023-03-15 10:56:47,980] [INFO] Running command: hmmsearch --tblout OceanDNA-b22203/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5501213-be12-4fa6-aebf-750daedd41cd/dqc_reference/reference_markers.hmm OceanDNA-b22203/protein.faa > /dev/null
[2023-03-15 10:56:48,154] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:56:48,155] [INFO] Found 6/6 markers.
[2023-03-15 10:56:48,173] [INFO] Query marker FASTA was written to OceanDNA-b22203/markers.fasta
[2023-03-15 10:56:48,173] [INFO] Task started: Blastn
[2023-03-15 10:56:48,173] [INFO] Running command: blastn -query OceanDNA-b22203/markers.fasta -db /var/lib/cwl/stga5501213-be12-4fa6-aebf-750daedd41cd/dqc_reference/reference_markers.fasta -out OceanDNA-b22203/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:56:48,718] [INFO] Task succeeded: Blastn
[2023-03-15 10:56:48,719] [INFO] Selected 25 target genomes.
[2023-03-15 10:56:48,719] [INFO] Target genome list was writen to OceanDNA-b22203/target_genomes.txt
[2023-03-15 10:56:48,731] [INFO] Task started: fastANI
[2023-03-15 10:56:48,731] [INFO] Running command: fastANI --query /var/lib/cwl/stga0dc8b6c-a365-43b2-9b1d-75908ed2ff39/OceanDNA-b22203.fa --refList OceanDNA-b22203/target_genomes.txt --output OceanDNA-b22203/fastani_result.tsv --threads 1
[2023-03-15 10:57:08,516] [INFO] Task succeeded: fastANI
[2023-03-15 10:57:08,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5501213-be12-4fa6-aebf-750daedd41cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:57:08,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5501213-be12-4fa6-aebf-750daedd41cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:57:08,517] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:57:08,517] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:57:08,517] [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 10:57:08,517] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22203/tc_result.tsv
[2023-03-15 10:57:08,517] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:57:08,517] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:57:08,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5501213-be12-4fa6-aebf-750daedd41cd/dqc_reference/checkm_data
[2023-03-15 10:57:08,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:57:08,525] [INFO] Task started: CheckM
[2023-03-15 10:57:08,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22203/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22203/checkm_input OceanDNA-b22203/checkm_result
[2023-03-15 10:57:57,431] [INFO] Task succeeded: CheckM
[2023-03-15 10:57:57,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:57:57,434] [INFO] ===== Completeness check finished =====
[2023-03-15 10:57:57,434] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:57:57,434] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22203/markers.fasta)
[2023-03-15 10:57:57,434] [INFO] Task started: Blastn
[2023-03-15 10:57:57,434] [INFO] Running command: blastn -query OceanDNA-b22203/markers.fasta -db /var/lib/cwl/stga5501213-be12-4fa6-aebf-750daedd41cd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22203/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:57:58,251] [INFO] Task succeeded: Blastn
[2023-03-15 10:57:58,252] [INFO] Selected 10 target genomes.
[2023-03-15 10:57:58,252] [INFO] Target genome list was writen to OceanDNA-b22203/target_genomes_gtdb.txt
[2023-03-15 10:57:58,263] [INFO] Task started: fastANI
[2023-03-15 10:57:58,263] [INFO] Running command: fastANI --query /var/lib/cwl/stga0dc8b6c-a365-43b2-9b1d-75908ed2ff39/OceanDNA-b22203.fa --refList OceanDNA-b22203/target_genomes_gtdb.txt --output OceanDNA-b22203/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:58:04,126] [INFO] Task succeeded: fastANI
[2023-03-15 10:58:04,132] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:58:04,132] [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_002167845.2	s__UBA12014 sp002167845	99.5336	656	711	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	99.48	99.48	0.92	0.92	2	conclusive
GCA_014237965.1	s__UBA12014 sp014237965	89.8018	558	711	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480395.1	s__UBA12014 sp905480395	80.6729	485	711	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690755.1	s__UBA12014 sp002690755	80.5489	350	711	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	99.96	99.96	0.92	0.92	2	-
GCA_002683215.1	s__UBA12014 sp002683215	79.8924	276	711	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936695.1	s__UBA12014 sp009936695	79.7243	271	711	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684755.1	s__UBA12014 sp002684755	79.5534	307	711	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684855.1	s__UBA12014 sp002684855	78.6717	254	711	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903891095.1	s__QWPT01 sp903891095	76.261	68	711	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	99.40	98.92	0.94	0.91	5	-
--------------------------------------------------------------------------------
[2023-03-15 10:58:04,133] [INFO] GTDB search result was written to OceanDNA-b22203/result_gtdb.tsv
[2023-03-15 10:58:04,133] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:58:04,133] [INFO] DFAST_QC result json was written to OceanDNA-b22203/dqc_result.json
[2023-03-15 10:58:04,134] [INFO] DFAST_QC completed!
[2023-03-15 10:58:04,134] [INFO] Total running time: 0h1m31s