[2023-03-17 04:35:35,492] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:35:35,492] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:35:35,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgd585382a-4be6-40d8-a949-b7fd7e2197f1/dqc_reference
[2023-03-17 04:35:36,687] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:35:36,688] [INFO] Task started: Prodigal
[2023-03-17 04:35:36,688] [INFO] Running command: cat /var/lib/cwl/stgfe8697a5-98bc-4fc0-9131-389380a1e648/OceanDNA-a3213.fa | prodigal -d OceanDNA-a3213/cds.fna -a OceanDNA-a3213/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:35:43,623] [INFO] Task succeeded: Prodigal
[2023-03-17 04:35:43,624] [INFO] Task started: HMMsearch
[2023-03-17 04:35:43,624] [INFO] Running command: hmmsearch --tblout OceanDNA-a3213/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd585382a-4be6-40d8-a949-b7fd7e2197f1/dqc_reference/reference_markers.hmm OceanDNA-a3213/protein.faa > /dev/null
[2023-03-17 04:35:43,776] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:35:43,776] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfe8697a5-98bc-4fc0-9131-389380a1e648/OceanDNA-a3213.fa]
[2023-03-17 04:35:43,787] [INFO] Query marker FASTA was written to OceanDNA-a3213/markers.fasta
[2023-03-17 04:35:43,788] [INFO] Task started: Blastn
[2023-03-17 04:35:43,788] [INFO] Running command: blastn -query OceanDNA-a3213/markers.fasta -db /var/lib/cwl/stgd585382a-4be6-40d8-a949-b7fd7e2197f1/dqc_reference/reference_markers.fasta -out OceanDNA-a3213/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:35:44,211] [INFO] Task succeeded: Blastn
[2023-03-17 04:35:44,211] [INFO] Selected 4 target genomes.
[2023-03-17 04:35:44,212] [INFO] Target genome list was writen to OceanDNA-a3213/target_genomes.txt
[2023-03-17 04:35:44,214] [INFO] Task started: fastANI
[2023-03-17 04:35:44,214] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe8697a5-98bc-4fc0-9131-389380a1e648/OceanDNA-a3213.fa --refList OceanDNA-a3213/target_genomes.txt --output OceanDNA-a3213/fastani_result.tsv --threads 1
[2023-03-17 04:35:46,049] [INFO] Task succeeded: fastANI
[2023-03-17 04:35:46,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd585382a-4be6-40d8-a949-b7fd7e2197f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:35:46,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd585382a-4be6-40d8-a949-b7fd7e2197f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:35:46,050] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:35:46,050] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:35:46,050] [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 04:35:46,050] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3213/tc_result.tsv
[2023-03-17 04:35:46,050] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:35:46,050] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:35:46,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd585382a-4be6-40d8-a949-b7fd7e2197f1/dqc_reference/checkm_data
[2023-03-17 04:35:46,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:35:46,183] [INFO] Task started: CheckM
[2023-03-17 04:35:46,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3213/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3213/checkm_input OceanDNA-a3213/checkm_result
[2023-03-17 04:36:09,207] [INFO] Task succeeded: CheckM
[2023-03-17 04:36:09,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.90%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 04:36:09,209] [INFO] ===== Completeness check finished =====
[2023-03-17 04:36:09,209] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:36:09,209] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3213/markers.fasta)
[2023-03-17 04:36:09,210] [INFO] Task started: Blastn
[2023-03-17 04:36:09,210] [INFO] Running command: blastn -query OceanDNA-a3213/markers.fasta -db /var/lib/cwl/stgd585382a-4be6-40d8-a949-b7fd7e2197f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3213/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:36:09,628] [INFO] Task succeeded: Blastn
[2023-03-17 04:36:09,629] [INFO] Selected 8 target genomes.
[2023-03-17 04:36:09,629] [INFO] Target genome list was writen to OceanDNA-a3213/target_genomes_gtdb.txt
[2023-03-17 04:36:10,141] [INFO] Task started: fastANI
[2023-03-17 04:36:10,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe8697a5-98bc-4fc0-9131-389380a1e648/OceanDNA-a3213.fa --refList OceanDNA-a3213/target_genomes_gtdb.txt --output OceanDNA-a3213/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:36:13,055] [INFO] Task succeeded: fastANI
[2023-03-17 04:36:13,059] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:36:13,059] [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_012964335.1	s__MGIIb-Q1 sp012964335	93.6564	378	400	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	99.77	99.71	0.95	0.94	8	-
GCA_012959435.1	s__MGIIb-Q1 sp012959435	87.4868	352	400	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384685.1	s__MGIIb-Q1 sp014384685	84.5656	226	400	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845345.1	s__MGIIb-Q1 sp016845345	83.2602	340	400	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650285.1	s__MGIIb-Q1 sp018650285	78.2393	181	400	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:36:13,059] [INFO] GTDB search result was written to OceanDNA-a3213/result_gtdb.tsv
[2023-03-17 04:36:13,059] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:36:13,060] [INFO] DFAST_QC result json was written to OceanDNA-a3213/dqc_result.json
[2023-03-17 04:36:13,060] [INFO] DFAST_QC completed!
[2023-03-17 04:36:13,060] [INFO] Total running time: 0h0m38s