[2023-03-18 05:05:08,017] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:05:08,021] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:05:08,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ac3624e-40b0-4d59-bb50-6c361ce8b5bd/dqc_reference
[2023-03-18 05:05:09,097] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:05:09,099] [INFO] Task started: Prodigal
[2023-03-18 05:05:09,099] [INFO] Running command: cat /var/lib/cwl/stg5c8cd946-b160-4bce-8d99-8a9b3cb55604/OceanDNA-b43761.fa | prodigal -d OceanDNA-b43761/cds.fna -a OceanDNA-b43761/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:05:24,456] [INFO] Task succeeded: Prodigal
[2023-03-18 05:05:24,457] [INFO] Task started: HMMsearch
[2023-03-18 05:05:24,457] [INFO] Running command: hmmsearch --tblout OceanDNA-b43761/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ac3624e-40b0-4d59-bb50-6c361ce8b5bd/dqc_reference/reference_markers.hmm OceanDNA-b43761/protein.faa > /dev/null
[2023-03-18 05:05:24,653] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:05:24,654] [INFO] Found 6/6 markers.
[2023-03-18 05:05:24,702] [INFO] Query marker FASTA was written to OceanDNA-b43761/markers.fasta
[2023-03-18 05:05:24,703] [INFO] Task started: Blastn
[2023-03-18 05:05:24,703] [INFO] Running command: blastn -query OceanDNA-b43761/markers.fasta -db /var/lib/cwl/stg5ac3624e-40b0-4d59-bb50-6c361ce8b5bd/dqc_reference/reference_markers.fasta -out OceanDNA-b43761/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:05:25,312] [INFO] Task succeeded: Blastn
[2023-03-18 05:05:25,321] [INFO] Selected 26 target genomes.
[2023-03-18 05:05:25,321] [INFO] Target genome list was writen to OceanDNA-b43761/target_genomes.txt
[2023-03-18 05:05:25,341] [INFO] Task started: fastANI
[2023-03-18 05:05:25,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c8cd946-b160-4bce-8d99-8a9b3cb55604/OceanDNA-b43761.fa --refList OceanDNA-b43761/target_genomes.txt --output OceanDNA-b43761/fastani_result.tsv --threads 1
[2023-03-18 05:05:40,110] [INFO] Task succeeded: fastANI
[2023-03-18 05:05:40,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ac3624e-40b0-4d59-bb50-6c361ce8b5bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:05:40,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ac3624e-40b0-4d59-bb50-6c361ce8b5bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:05:40,110] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:05:40,110] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:05:40,111] [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 05:05:40,114] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43761/tc_result.tsv
[2023-03-18 05:05:40,119] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:05:40,120] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:05:40,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ac3624e-40b0-4d59-bb50-6c361ce8b5bd/dqc_reference/checkm_data
[2023-03-18 05:05:40,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:05:40,136] [INFO] Task started: CheckM
[2023-03-18 05:05:40,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43761/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43761/checkm_input OceanDNA-b43761/checkm_result
[2023-03-18 05:06:21,968] [INFO] Task succeeded: CheckM
[2023-03-18 05:06:21,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 8.80%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 05:06:22,012] [INFO] ===== Completeness check finished =====
[2023-03-18 05:06:22,012] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:06:22,012] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43761/markers.fasta)
[2023-03-18 05:06:22,013] [INFO] Task started: Blastn
[2023-03-18 05:06:22,013] [INFO] Running command: blastn -query OceanDNA-b43761/markers.fasta -db /var/lib/cwl/stg5ac3624e-40b0-4d59-bb50-6c361ce8b5bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43761/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:06:23,079] [INFO] Task succeeded: Blastn
[2023-03-18 05:06:23,091] [INFO] Selected 11 target genomes.
[2023-03-18 05:06:23,091] [INFO] Target genome list was writen to OceanDNA-b43761/target_genomes_gtdb.txt
[2023-03-18 05:06:23,230] [INFO] Task started: fastANI
[2023-03-18 05:06:23,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c8cd946-b160-4bce-8d99-8a9b3cb55604/OceanDNA-b43761.fa --refList OceanDNA-b43761/target_genomes_gtdb.txt --output OceanDNA-b43761/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:06:28,436] [INFO] Task succeeded: fastANI
[2023-03-18 05:06:28,441] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:06:28,441] [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_002694065.1	s__UBA868 sp002694065	96.0812	493	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	97.83	97.76	0.76	0.75	3	conclusive
GCA_011523045.1	s__UBA868 sp011523045	90.0824	593	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477475.1	s__UBA868 sp002477475	90.016	605	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.71	99.58	0.88	0.75	11	-
GCA_002713825.1	s__UBA868 sp002713825	87.8076	397	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346525.1	s__UBA868 sp002346525	86.3336	430	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845525.1	s__UBA868 sp016845525	85.7239	431	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002327725.1	s__UBA868 sp002327725	77.6388	216	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.85	99.69	0.88	0.82	5	-
--------------------------------------------------------------------------------
[2023-03-18 05:06:28,445] [INFO] GTDB search result was written to OceanDNA-b43761/result_gtdb.tsv
[2023-03-18 05:06:28,453] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:06:28,458] [INFO] DFAST_QC result json was written to OceanDNA-b43761/dqc_result.json
[2023-03-18 05:06:28,458] [INFO] DFAST_QC completed!
[2023-03-18 05:06:28,458] [INFO] Total running time: 0h1m20s