[2023-03-17 00:26:56,231] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:26:56,231] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:26:56,231] [INFO] DQC Reference Directory: /var/lib/cwl/stg92379ffb-06af-45d2-8595-1fa54b9569f6/dqc_reference
[2023-03-17 00:26:57,316] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:26:57,316] [INFO] Task started: Prodigal
[2023-03-17 00:26:57,316] [INFO] Running command: cat /var/lib/cwl/stgc4b67880-68b1-4c65-8eb1-c7c1ed565203/OceanDNA-b13008.fa | prodigal -d OceanDNA-b13008/cds.fna -a OceanDNA-b13008/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:27:06,677] [INFO] Task succeeded: Prodigal
[2023-03-17 00:27:06,677] [INFO] Task started: HMMsearch
[2023-03-17 00:27:06,677] [INFO] Running command: hmmsearch --tblout OceanDNA-b13008/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92379ffb-06af-45d2-8595-1fa54b9569f6/dqc_reference/reference_markers.hmm OceanDNA-b13008/protein.faa > /dev/null
[2023-03-17 00:27:06,836] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:27:06,837] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc4b67880-68b1-4c65-8eb1-c7c1ed565203/OceanDNA-b13008.fa]
[2023-03-17 00:27:06,849] [INFO] Query marker FASTA was written to OceanDNA-b13008/markers.fasta
[2023-03-17 00:27:06,850] [INFO] Task started: Blastn
[2023-03-17 00:27:06,850] [INFO] Running command: blastn -query OceanDNA-b13008/markers.fasta -db /var/lib/cwl/stg92379ffb-06af-45d2-8595-1fa54b9569f6/dqc_reference/reference_markers.fasta -out OceanDNA-b13008/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:27:07,335] [INFO] Task succeeded: Blastn
[2023-03-17 00:27:07,336] [INFO] Selected 13 target genomes.
[2023-03-17 00:27:07,336] [INFO] Target genome list was writen to OceanDNA-b13008/target_genomes.txt
[2023-03-17 00:27:07,340] [INFO] Task started: fastANI
[2023-03-17 00:27:07,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4b67880-68b1-4c65-8eb1-c7c1ed565203/OceanDNA-b13008.fa --refList OceanDNA-b13008/target_genomes.txt --output OceanDNA-b13008/fastani_result.tsv --threads 1
[2023-03-17 00:30:19,890] [INFO] Task succeeded: fastANI
[2023-03-17 00:30:19,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92379ffb-06af-45d2-8595-1fa54b9569f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:30:19,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92379ffb-06af-45d2-8595-1fa54b9569f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:30:19,891] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:30:19,891] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:30:19,891] [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 00:30:19,891] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13008/tc_result.tsv
[2023-03-17 00:30:19,891] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:30:19,891] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:30:19,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92379ffb-06af-45d2-8595-1fa54b9569f6/dqc_reference/checkm_data
[2023-03-17 00:30:19,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:30:19,900] [INFO] Task started: CheckM
[2023-03-17 00:30:19,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13008/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13008/checkm_input OceanDNA-b13008/checkm_result
[2023-03-17 00:30:48,165] [INFO] Task succeeded: CheckM
[2023-03-17 00:30:48,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 00:30:48,168] [INFO] ===== Completeness check finished =====
[2023-03-17 00:30:48,168] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:30:48,168] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13008/markers.fasta)
[2023-03-17 00:30:48,168] [INFO] Task started: Blastn
[2023-03-17 00:30:48,168] [INFO] Running command: blastn -query OceanDNA-b13008/markers.fasta -db /var/lib/cwl/stg92379ffb-06af-45d2-8595-1fa54b9569f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13008/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:30:48,817] [INFO] Task succeeded: Blastn
[2023-03-17 00:30:48,818] [INFO] Selected 8 target genomes.
[2023-03-17 00:30:48,818] [INFO] Target genome list was writen to OceanDNA-b13008/target_genomes_gtdb.txt
[2023-03-17 00:30:48,831] [INFO] Task started: fastANI
[2023-03-17 00:30:48,831] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4b67880-68b1-4c65-8eb1-c7c1ed565203/OceanDNA-b13008.fa --refList OceanDNA-b13008/target_genomes_gtdb.txt --output OceanDNA-b13008/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:30:51,528] [INFO] Task succeeded: fastANI
[2023-03-17 00:30:51,533] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:30:51,533] [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_002730655.1	s__UBA1275 sp002730655	99.0659	240	458	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA1275	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902529115.1	s__UBA1275 sp902529115	93.8779	357	458	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA1275	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002348545.1	s__UBA1275 sp002348545	90.8728	342	458	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA1275	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720745.1	s__UBA1275 sp002720745	90.7822	413	458	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA1275	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529365.1	s__UBA1275 sp902529365	81.5792	291	458	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA1275	95.0	98.73	98.57	0.77	0.75	3	-
GCA_002457365.1	s__UBA1275 sp002457365	81.1429	253	458	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA1275	95.0	98.49	97.81	0.75	0.70	7	-
GCA_018401935.1	s__UBA1275 sp018401935	80.8412	317	458	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA1275	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:30:51,533] [INFO] GTDB search result was written to OceanDNA-b13008/result_gtdb.tsv
[2023-03-17 00:30:51,533] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:30:51,534] [INFO] DFAST_QC result json was written to OceanDNA-b13008/dqc_result.json
[2023-03-17 00:30:51,534] [INFO] DFAST_QC completed!
[2023-03-17 00:30:51,534] [INFO] Total running time: 0h3m55s