[2023-03-17 10:35:02,805] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:35:02,805] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:35:02,805] [INFO] DQC Reference Directory: /var/lib/cwl/stgae3211c1-932e-4873-91cb-2d9f27f774ed/dqc_reference
[2023-03-17 10:35:04,551] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:35:04,551] [INFO] Task started: Prodigal
[2023-03-17 10:35:04,551] [INFO] Running command: cat /var/lib/cwl/stg493c8118-656c-4f96-994b-658381abe952/OceanDNA-a2473.fa | prodigal -d OceanDNA-a2473/cds.fna -a OceanDNA-a2473/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:35:14,166] [INFO] Task succeeded: Prodigal
[2023-03-17 10:35:14,167] [INFO] Task started: HMMsearch
[2023-03-17 10:35:14,167] [INFO] Running command: hmmsearch --tblout OceanDNA-a2473/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae3211c1-932e-4873-91cb-2d9f27f774ed/dqc_reference/reference_markers.hmm OceanDNA-a2473/protein.faa > /dev/null
[2023-03-17 10:35:14,334] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:35:14,334] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg493c8118-656c-4f96-994b-658381abe952/OceanDNA-a2473.fa]
[2023-03-17 10:35:14,346] [INFO] Query marker FASTA was written to OceanDNA-a2473/markers.fasta
[2023-03-17 10:35:14,347] [INFO] Task started: Blastn
[2023-03-17 10:35:14,347] [INFO] Running command: blastn -query OceanDNA-a2473/markers.fasta -db /var/lib/cwl/stgae3211c1-932e-4873-91cb-2d9f27f774ed/dqc_reference/reference_markers.fasta -out OceanDNA-a2473/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:14,804] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:14,805] [INFO] Selected 5 target genomes.
[2023-03-17 10:35:14,805] [INFO] Target genome list was writen to OceanDNA-a2473/target_genomes.txt
[2023-03-17 10:35:14,808] [INFO] Task started: fastANI
[2023-03-17 10:35:14,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg493c8118-656c-4f96-994b-658381abe952/OceanDNA-a2473.fa --refList OceanDNA-a2473/target_genomes.txt --output OceanDNA-a2473/fastani_result.tsv --threads 1
[2023-03-17 10:35:16,514] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:16,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae3211c1-932e-4873-91cb-2d9f27f774ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:35:16,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae3211c1-932e-4873-91cb-2d9f27f774ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:35:16,515] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:35:16,515] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:35:16,515] [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
--------------------------------------------------------------------------------
[2023-03-17 10:35:16,516] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2473/tc_result.tsv
[2023-03-17 10:35:16,516] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:35:16,516] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:35:16,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae3211c1-932e-4873-91cb-2d9f27f774ed/dqc_reference/checkm_data
[2023-03-17 10:35:16,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:35:16,699] [INFO] Task started: CheckM
[2023-03-17 10:35:16,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2473/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2473/checkm_input OceanDNA-a2473/checkm_result
[2023-03-17 10:35:47,412] [INFO] Task succeeded: CheckM
[2023-03-17 10:35:47,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:35:47,415] [INFO] ===== Completeness check finished =====
[2023-03-17 10:35:47,415] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:35:47,415] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2473/markers.fasta)
[2023-03-17 10:35:47,416] [INFO] Task started: Blastn
[2023-03-17 10:35:47,416] [INFO] Running command: blastn -query OceanDNA-a2473/markers.fasta -db /var/lib/cwl/stgae3211c1-932e-4873-91cb-2d9f27f774ed/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2473/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:47,969] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:47,970] [INFO] Selected 8 target genomes.
[2023-03-17 10:35:47,970] [INFO] Target genome list was writen to OceanDNA-a2473/target_genomes_gtdb.txt
[2023-03-17 10:35:48,211] [INFO] Task started: fastANI
[2023-03-17 10:35:48,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg493c8118-656c-4f96-994b-658381abe952/OceanDNA-a2473.fa --refList OceanDNA-a2473/target_genomes_gtdb.txt --output OceanDNA-a2473/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:35:50,737] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:50,742] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:35:50,742] [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_018691345.1	s__MGIIa-L1 sp018691345	99.8036	454	495	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002506275.1	s__MGIIa-L1 sp002506275	86.5979	267	495	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	98.77	0.87	0.72	5	-
GCA_018701175.1	s__MGIIa-L1 sp018701175	82.456	352	495	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.50	99.46	0.87	0.84	5	-
GCA_003602605.1	s__MGIIa-L1 sp003602605	81.0352	355	495	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520595.1	s__MGIIa-L1 sp902520595	77.5085	95	495	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937025.1	s__MGIIa-L1 sp009937025	77.3662	150	495	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602645.1	s__MGIIa-L1 sp003602645	76.7533	67	495	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:35:50,743] [INFO] GTDB search result was written to OceanDNA-a2473/result_gtdb.tsv
[2023-03-17 10:35:50,743] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:35:50,744] [INFO] DFAST_QC result json was written to OceanDNA-a2473/dqc_result.json
[2023-03-17 10:35:50,744] [INFO] DFAST_QC completed!
[2023-03-17 10:35:50,744] [INFO] Total running time: 0h0m48s