[2023-03-15 10:34:47,894] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:34:47,908] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:34:47,908] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1d4bc1a-4bed-40be-9437-bd4c9d892c6e/dqc_reference
[2023-03-15 10:34:49,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:34:49,423] [INFO] Task started: Prodigal
[2023-03-15 10:34:49,423] [INFO] Running command: cat /var/lib/cwl/stg77600633-e5ca-4c0a-afbd-e15ef86f8f52/OceanDNA-b14563.fa | prodigal -d OceanDNA-b14563/cds.fna -a OceanDNA-b14563/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:34:58,743] [INFO] Task succeeded: Prodigal
[2023-03-15 10:34:58,743] [INFO] Task started: HMMsearch
[2023-03-15 10:34:58,743] [INFO] Running command: hmmsearch --tblout OceanDNA-b14563/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1d4bc1a-4bed-40be-9437-bd4c9d892c6e/dqc_reference/reference_markers.hmm OceanDNA-b14563/protein.faa > /dev/null
[2023-03-15 10:34:58,896] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:34:58,896] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg77600633-e5ca-4c0a-afbd-e15ef86f8f52/OceanDNA-b14563.fa]
[2023-03-15 10:34:58,915] [INFO] Query marker FASTA was written to OceanDNA-b14563/markers.fasta
[2023-03-15 10:34:58,915] [INFO] Task started: Blastn
[2023-03-15 10:34:58,915] [INFO] Running command: blastn -query OceanDNA-b14563/markers.fasta -db /var/lib/cwl/stgc1d4bc1a-4bed-40be-9437-bd4c9d892c6e/dqc_reference/reference_markers.fasta -out OceanDNA-b14563/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:34:59,419] [INFO] Task succeeded: Blastn
[2023-03-15 10:34:59,422] [INFO] Selected 5 target genomes.
[2023-03-15 10:34:59,422] [INFO] Target genome list was writen to OceanDNA-b14563/target_genomes.txt
[2023-03-15 10:34:59,425] [INFO] Task started: fastANI
[2023-03-15 10:34:59,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg77600633-e5ca-4c0a-afbd-e15ef86f8f52/OceanDNA-b14563.fa --refList OceanDNA-b14563/target_genomes.txt --output OceanDNA-b14563/fastani_result.tsv --threads 1
[2023-03-15 10:35:02,410] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:02,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1d4bc1a-4bed-40be-9437-bd4c9d892c6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:35:02,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1d4bc1a-4bed-40be-9437-bd4c9d892c6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:35:02,411] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:35:02,411] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:35:02,411] [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
--------------------------------------------------------------------------------
[2023-03-15 10:35:02,417] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14563/tc_result.tsv
[2023-03-15 10:35:02,417] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:35:02,418] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:35:02,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1d4bc1a-4bed-40be-9437-bd4c9d892c6e/dqc_reference/checkm_data
[2023-03-15 10:35:02,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:35:02,460] [INFO] Task started: CheckM
[2023-03-15 10:35:02,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14563/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14563/checkm_input OceanDNA-b14563/checkm_result
[2023-03-15 10:35:30,763] [INFO] Task succeeded: CheckM
[2023-03-15 10:35:30,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:35:31,110] [INFO] ===== Completeness check finished =====
[2023-03-15 10:35:31,110] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:35:31,110] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14563/markers.fasta)
[2023-03-15 10:35:31,111] [INFO] Task started: Blastn
[2023-03-15 10:35:31,111] [INFO] Running command: blastn -query OceanDNA-b14563/markers.fasta -db /var/lib/cwl/stgc1d4bc1a-4bed-40be-9437-bd4c9d892c6e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14563/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:35:31,821] [INFO] Task succeeded: Blastn
[2023-03-15 10:35:31,825] [INFO] Selected 11 target genomes.
[2023-03-15 10:35:31,826] [INFO] Target genome list was writen to OceanDNA-b14563/target_genomes_gtdb.txt
[2023-03-15 10:35:32,243] [INFO] Task started: fastANI
[2023-03-15 10:35:32,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg77600633-e5ca-4c0a-afbd-e15ef86f8f52/OceanDNA-b14563.fa --refList OceanDNA-b14563/target_genomes_gtdb.txt --output OceanDNA-b14563/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:35:36,521] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:36,526] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:35:36,526] [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_905614375.1	s__UBA1328 sp905614375	91.5165	248	528	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673955.1	s__UBA1328 sp018673955	84.6046	436	528	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.55	99.47	0.91	0.89	13	-
GCA_018649665.1	s__UBA1328 sp018649665	84.2302	395	528	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650845.1	s__UBA1328 sp018650845	79.3348	266	528	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.74	99.74	0.93	0.93	2	-
GCA_012959765.1	s__UBA1328 sp012959765	78.6198	215	528	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.88	99.88	0.97	0.97	2	-
GCA_002501045.1	s__UBA1328 sp002501045	77.7584	149	528	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.73	99.73	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-15 10:35:36,530] [INFO] GTDB search result was written to OceanDNA-b14563/result_gtdb.tsv
[2023-03-15 10:35:36,530] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:35:36,533] [INFO] DFAST_QC result json was written to OceanDNA-b14563/dqc_result.json
[2023-03-15 10:35:36,533] [INFO] DFAST_QC completed!
[2023-03-15 10:35:36,533] [INFO] Total running time: 0h0m49s