[2023-03-18 01:53:08,441] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:53:08,441] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:53:08,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg38a7e3a8-5b88-4550-82c2-a62573a8b9bf/dqc_reference
[2023-03-18 01:53:09,595] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:53:09,595] [INFO] Task started: Prodigal
[2023-03-18 01:53:09,595] [INFO] Running command: cat /var/lib/cwl/stgd8d69e3d-dbe6-4281-9088-a504f54fafef/OceanDNA-b8955.fa | prodigal -d OceanDNA-b8955/cds.fna -a OceanDNA-b8955/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:53:16,696] [INFO] Task succeeded: Prodigal
[2023-03-18 01:53:16,697] [INFO] Task started: HMMsearch
[2023-03-18 01:53:16,697] [INFO] Running command: hmmsearch --tblout OceanDNA-b8955/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38a7e3a8-5b88-4550-82c2-a62573a8b9bf/dqc_reference/reference_markers.hmm OceanDNA-b8955/protein.faa > /dev/null
[2023-03-18 01:53:16,889] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:53:16,890] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd8d69e3d-dbe6-4281-9088-a504f54fafef/OceanDNA-b8955.fa]
[2023-03-18 01:53:16,899] [INFO] Query marker FASTA was written to OceanDNA-b8955/markers.fasta
[2023-03-18 01:53:16,900] [INFO] Task started: Blastn
[2023-03-18 01:53:16,900] [INFO] Running command: blastn -query OceanDNA-b8955/markers.fasta -db /var/lib/cwl/stg38a7e3a8-5b88-4550-82c2-a62573a8b9bf/dqc_reference/reference_markers.fasta -out OceanDNA-b8955/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:53:17,501] [INFO] Task succeeded: Blastn
[2023-03-18 01:53:17,502] [INFO] Selected 25 target genomes.
[2023-03-18 01:53:17,502] [INFO] Target genome list was writen to OceanDNA-b8955/target_genomes.txt
[2023-03-18 01:53:17,521] [INFO] Task started: fastANI
[2023-03-18 01:53:17,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8d69e3d-dbe6-4281-9088-a504f54fafef/OceanDNA-b8955.fa --refList OceanDNA-b8955/target_genomes.txt --output OceanDNA-b8955/fastani_result.tsv --threads 1
[2023-03-18 01:53:30,754] [INFO] Task succeeded: fastANI
[2023-03-18 01:53:30,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38a7e3a8-5b88-4550-82c2-a62573a8b9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:53:30,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38a7e3a8-5b88-4550-82c2-a62573a8b9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:53:30,754] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:53:30,754] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:53:30,754] [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
--------------------------------------------------------------------------------
[2023-03-18 01:53:30,755] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8955/tc_result.tsv
[2023-03-18 01:53:30,755] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:53:30,755] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:53:30,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38a7e3a8-5b88-4550-82c2-a62573a8b9bf/dqc_reference/checkm_data
[2023-03-18 01:53:30,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:53:30,760] [INFO] Task started: CheckM
[2023-03-18 01:53:30,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8955/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8955/checkm_input OceanDNA-b8955/checkm_result
[2023-03-18 01:53:54,607] [INFO] Task succeeded: CheckM
[2023-03-18 01:53:54,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 2.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:53:54,609] [INFO] ===== Completeness check finished =====
[2023-03-18 01:53:54,609] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:53:54,609] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8955/markers.fasta)
[2023-03-18 01:53:54,611] [INFO] Task started: Blastn
[2023-03-18 01:53:54,611] [INFO] Running command: blastn -query OceanDNA-b8955/markers.fasta -db /var/lib/cwl/stg38a7e3a8-5b88-4550-82c2-a62573a8b9bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8955/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:53:55,916] [INFO] Task succeeded: Blastn
[2023-03-18 01:53:55,917] [INFO] Selected 10 target genomes.
[2023-03-18 01:53:55,917] [INFO] Target genome list was writen to OceanDNA-b8955/target_genomes_gtdb.txt
[2023-03-18 01:53:55,926] [INFO] Task started: fastANI
[2023-03-18 01:53:55,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8d69e3d-dbe6-4281-9088-a504f54fafef/OceanDNA-b8955.fa --refList OceanDNA-b8955/target_genomes_gtdb.txt --output OceanDNA-b8955/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:53:58,326] [INFO] Task succeeded: fastANI
[2023-03-18 01:53:58,332] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:53:58,332] [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_902550325.1	s__MED-G14 sp902550325	95.6889	233	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	95.73	95.39	0.65	0.57	4	conclusive
GCA_902609185.1	s__MED-G14 sp902609185	94.8731	208	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526165.1	s__MED-G14 sp902526165	94.7952	284	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	95.12	95.12	0.75	0.75	2	-
GCA_003331875.1	s__MED-G14 sp003331875	90.3863	278	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902614065.1	s__MED-G14 sp002697465	83.0947	303	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	97.49	95.51	0.88	0.84	14	-
GCA_902586095.1	s__MED-G14 sp902586095	82.7779	245	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902544085.1	s__MED-G14 sp902544085	82.7339	305	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	99.92	99.92	0.94	0.94	2	-
GCA_902598295.1	s__MED-G14 sp902598295	82.2113	259	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546095.1	s__MED-G14 sp902546095	76.8183	75	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004321735.1	s__MED-G14 sp004321735	76.3673	71	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.77	95.40	0.78	0.75	4	-
--------------------------------------------------------------------------------
[2023-03-18 01:53:58,332] [INFO] GTDB search result was written to OceanDNA-b8955/result_gtdb.tsv
[2023-03-18 01:53:58,332] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:53:58,333] [INFO] DFAST_QC result json was written to OceanDNA-b8955/dqc_result.json
[2023-03-18 01:53:58,333] [INFO] DFAST_QC completed!
[2023-03-18 01:53:58,333] [INFO] Total running time: 0h0m50s