[2023-03-14 11:36:02,654] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:36:02,654] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:36:02,654] [INFO] DQC Reference Directory: /var/lib/cwl/stga56ff9f5-9d59-47e1-a8ed-274038a7bc40/dqc_reference
[2023-03-14 11:36:04,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:36:04,406] [INFO] Task started: Prodigal
[2023-03-14 11:36:04,407] [INFO] Running command: cat /var/lib/cwl/stg60f7b455-e961-4173-aa13-62c4cfbe0f4e/OceanDNA-a2978.fa | prodigal -d OceanDNA-a2978/cds.fna -a OceanDNA-a2978/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:36:13,866] [INFO] Task succeeded: Prodigal
[2023-03-14 11:36:13,867] [INFO] Task started: HMMsearch
[2023-03-14 11:36:13,867] [INFO] Running command: hmmsearch --tblout OceanDNA-a2978/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga56ff9f5-9d59-47e1-a8ed-274038a7bc40/dqc_reference/reference_markers.hmm OceanDNA-a2978/protein.faa > /dev/null
[2023-03-14 11:36:14,027] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:36:14,027] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg60f7b455-e961-4173-aa13-62c4cfbe0f4e/OceanDNA-a2978.fa]
[2023-03-14 11:36:14,039] [INFO] Query marker FASTA was written to OceanDNA-a2978/markers.fasta
[2023-03-14 11:36:14,041] [INFO] Task started: Blastn
[2023-03-14 11:36:14,041] [INFO] Running command: blastn -query OceanDNA-a2978/markers.fasta -db /var/lib/cwl/stga56ff9f5-9d59-47e1-a8ed-274038a7bc40/dqc_reference/reference_markers.fasta -out OceanDNA-a2978/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:14,472] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:14,477] [INFO] Selected 2 target genomes.
[2023-03-14 11:36:14,477] [INFO] Target genome list was writen to OceanDNA-a2978/target_genomes.txt
[2023-03-14 11:36:14,479] [INFO] Task started: fastANI
[2023-03-14 11:36:14,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg60f7b455-e961-4173-aa13-62c4cfbe0f4e/OceanDNA-a2978.fa --refList OceanDNA-a2978/target_genomes.txt --output OceanDNA-a2978/fastani_result.tsv --threads 1
[2023-03-14 11:36:15,803] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:15,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga56ff9f5-9d59-47e1-a8ed-274038a7bc40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:36:15,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga56ff9f5-9d59-47e1-a8ed-274038a7bc40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:36:15,804] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:36:15,804] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:36:15,804] [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
--------------------------------------------------------------------------------
[2023-03-14 11:36:15,804] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2978/tc_result.tsv
[2023-03-14 11:36:15,804] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:36:15,804] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:36:15,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga56ff9f5-9d59-47e1-a8ed-274038a7bc40/dqc_reference/checkm_data
[2023-03-14 11:36:15,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:36:15,813] [INFO] Task started: CheckM
[2023-03-14 11:36:15,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2978/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2978/checkm_input OceanDNA-a2978/checkm_result
[2023-03-14 11:36:45,616] [INFO] Task succeeded: CheckM
[2023-03-14 11:36:45,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.11%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 11:36:45,619] [INFO] ===== Completeness check finished =====
[2023-03-14 11:36:45,619] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:36:45,619] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2978/markers.fasta)
[2023-03-14 11:36:45,620] [INFO] Task started: Blastn
[2023-03-14 11:36:45,620] [INFO] Running command: blastn -query OceanDNA-a2978/markers.fasta -db /var/lib/cwl/stga56ff9f5-9d59-47e1-a8ed-274038a7bc40/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2978/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:46,026] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:46,027] [INFO] Selected 11 target genomes.
[2023-03-14 11:36:46,027] [INFO] Target genome list was writen to OceanDNA-a2978/target_genomes_gtdb.txt
[2023-03-14 11:36:46,065] [INFO] Task started: fastANI
[2023-03-14 11:36:46,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg60f7b455-e961-4173-aa13-62c4cfbe0f4e/OceanDNA-a2978.fa --refList OceanDNA-a2978/target_genomes_gtdb.txt --output OceanDNA-a2978/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:36:49,771] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:49,779] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:36:49,780] [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_002689105.1	s__Poseidonia sp002689105	99.1213	389	453	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.72	96.72	0.80	0.80	2	conclusive
GCA_002495645.1	s__Poseidonia sp002495645	81.4855	320	453	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_002725275.1	s__Poseidonia sp002725275	78.9211	183	453	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.76	96.60	0.76	0.75	3	-
GCA_002714305.1	s__Poseidonia sp002714305	78.9032	183	453	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.69	98.28	0.79	0.76	8	-
GCA_013330155.1	s__Poseidonia sp8339u	78.5164	166	453	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.08	98.16	0.89	0.82	3	-
GCA_002704515.1	s__Poseidonia sp002704515	78.325	182	453	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722695.1	s__Poseidonia sp002722695	78.0749	136	453	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.22	99.22	0.79	0.79	3	-
GCA_002694525.1	s__Poseidonia sp002694525	77.9245	147	453	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779705.1	s__Poseidonia sp016779705	77.7088	135	453	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778305.1	s__Poseidonia sp016778305	77.0156	93	453	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.89	99.85	0.97	0.96	5	-
--------------------------------------------------------------------------------
[2023-03-14 11:36:49,780] [INFO] GTDB search result was written to OceanDNA-a2978/result_gtdb.tsv
[2023-03-14 11:36:49,780] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:36:49,781] [INFO] DFAST_QC result json was written to OceanDNA-a2978/dqc_result.json
[2023-03-14 11:36:49,781] [INFO] DFAST_QC completed!
[2023-03-14 11:36:49,782] [INFO] Total running time: 0h0m47s