[2023-03-16 08:34:18,644] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:34:18,645] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:34:18,645] [INFO] DQC Reference Directory: /var/lib/cwl/stgec35bf14-2561-4e7b-aeac-3e4314490ff1/dqc_reference
[2023-03-16 08:34:19,745] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:34:19,745] [INFO] Task started: Prodigal
[2023-03-16 08:34:19,745] [INFO] Running command: cat /var/lib/cwl/stg4ed51ded-2b48-48af-b83d-6adec3a5b197/OceanDNA-b25722.fa | prodigal -d OceanDNA-b25722/cds.fna -a OceanDNA-b25722/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:34:24,151] [INFO] Task succeeded: Prodigal
[2023-03-16 08:34:24,151] [INFO] Task started: HMMsearch
[2023-03-16 08:34:24,151] [INFO] Running command: hmmsearch --tblout OceanDNA-b25722/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec35bf14-2561-4e7b-aeac-3e4314490ff1/dqc_reference/reference_markers.hmm OceanDNA-b25722/protein.faa > /dev/null
[2023-03-16 08:34:24,296] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:34:24,297] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4ed51ded-2b48-48af-b83d-6adec3a5b197/OceanDNA-b25722.fa]
[2023-03-16 08:34:24,308] [INFO] Query marker FASTA was written to OceanDNA-b25722/markers.fasta
[2023-03-16 08:34:24,310] [INFO] Task started: Blastn
[2023-03-16 08:34:24,310] [INFO] Running command: blastn -query OceanDNA-b25722/markers.fasta -db /var/lib/cwl/stgec35bf14-2561-4e7b-aeac-3e4314490ff1/dqc_reference/reference_markers.fasta -out OceanDNA-b25722/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:34:24,864] [INFO] Task succeeded: Blastn
[2023-03-16 08:34:24,867] [INFO] Selected 12 target genomes.
[2023-03-16 08:34:24,867] [INFO] Target genome list was writen to OceanDNA-b25722/target_genomes.txt
[2023-03-16 08:34:24,873] [INFO] Task started: fastANI
[2023-03-16 08:34:24,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ed51ded-2b48-48af-b83d-6adec3a5b197/OceanDNA-b25722.fa --refList OceanDNA-b25722/target_genomes.txt --output OceanDNA-b25722/fastani_result.tsv --threads 1
[2023-03-16 08:34:29,828] [INFO] Task succeeded: fastANI
[2023-03-16 08:34:29,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec35bf14-2561-4e7b-aeac-3e4314490ff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:34:29,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec35bf14-2561-4e7b-aeac-3e4314490ff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:34:29,872] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:34:29,872] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:34:29,872] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	77.3647	100	209	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:34:29,874] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25722/tc_result.tsv
[2023-03-16 08:34:29,875] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:34:29,875] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:34:29,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec35bf14-2561-4e7b-aeac-3e4314490ff1/dqc_reference/checkm_data
[2023-03-16 08:34:29,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:34:29,880] [INFO] Task started: CheckM
[2023-03-16 08:34:29,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25722/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25722/checkm_input OceanDNA-b25722/checkm_result
[2023-03-16 08:34:49,946] [INFO] Task succeeded: CheckM
[2023-03-16 08:34:49,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.26%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 08:34:49,957] [INFO] ===== Completeness check finished =====
[2023-03-16 08:34:49,957] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:34:49,957] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25722/markers.fasta)
[2023-03-16 08:34:49,958] [INFO] Task started: Blastn
[2023-03-16 08:34:49,958] [INFO] Running command: blastn -query OceanDNA-b25722/markers.fasta -db /var/lib/cwl/stgec35bf14-2561-4e7b-aeac-3e4314490ff1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25722/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:34:51,033] [INFO] Task succeeded: Blastn
[2023-03-16 08:34:51,037] [INFO] Selected 14 target genomes.
[2023-03-16 08:34:51,037] [INFO] Target genome list was writen to OceanDNA-b25722/target_genomes_gtdb.txt
[2023-03-16 08:34:51,095] [INFO] Task started: fastANI
[2023-03-16 08:34:51,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ed51ded-2b48-48af-b83d-6adec3a5b197/OceanDNA-b25722.fa --refList OceanDNA-b25722/target_genomes_gtdb.txt --output OceanDNA-b25722/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:34:53,742] [INFO] Task succeeded: fastANI
[2023-03-16 08:34:53,751] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:34:53,751] [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_011526385.1	s__Pelagibacter sp011526385	98.0559	181	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.04	98.04	0.83	0.83	2	conclusive
GCA_902625715.1	s__Pelagibacter sp902625715	80.9914	134	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.20	95.77	0.80	0.79	3	-
GCF_002101295.1	s__Pelagibacter sp002101295	80.926	172	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.97	95.60	0.92	0.90	4	-
GCA_902634885.1	s__Pelagibacter sp902634885	80.6979	124	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.47	97.62	0.77	0.76	3	-
GCA_902614125.1	s__Pelagibacter sp902614125	80.6675	146	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546765.1	s__Pelagibacter sp902546765	80.5431	120	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.47	97.47	0.71	0.71	2	-
GCA_902592445.1	s__Pelagibacter sp902592445	80.4389	132	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.56	95.56	0.78	0.78	2	-
GCA_902634935.1	s__Pelagibacter sp902634935	80.3416	121	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601315.1	s__Pelagibacter sp902601315	80.3071	141	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576045.1	s__Pelagibacter sp902576045	80.1591	137	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.81	95.50	0.75	0.71	6	-
GCA_902595635.1	s__Pelagibacter sp902595635	78.424	87	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519255.1	s__Pelagibacter sp902519255	78.0869	90	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.11	99.05	0.75	0.74	3	-
GCA_902609705.1	s__Pelagibacter sp902609705	77.9651	89	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902577875.1	s__Pelagibacter sp902577875	77.6094	73	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:34:53,753] [INFO] GTDB search result was written to OceanDNA-b25722/result_gtdb.tsv
[2023-03-16 08:34:53,754] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:34:53,757] [INFO] DFAST_QC result json was written to OceanDNA-b25722/dqc_result.json
[2023-03-16 08:34:53,757] [INFO] DFAST_QC completed!
[2023-03-16 08:34:53,757] [INFO] Total running time: 0h0m35s