[2023-03-17 05:59:11,088] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:59:11,088] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:59:11,088] [INFO] DQC Reference Directory: /var/lib/cwl/stg29a751e8-c49c-4747-8ad5-52d934893d9b/dqc_reference
[2023-03-17 05:59:12,193] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:59:12,193] [INFO] Task started: Prodigal
[2023-03-17 05:59:12,193] [INFO] Running command: cat /var/lib/cwl/stg559346d5-2ea2-408c-a3b0-aa508e00633e/OceanDNA-b25738.fa | prodigal -d OceanDNA-b25738/cds.fna -a OceanDNA-b25738/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:59:17,089] [INFO] Task succeeded: Prodigal
[2023-03-17 05:59:17,089] [INFO] Task started: HMMsearch
[2023-03-17 05:59:17,089] [INFO] Running command: hmmsearch --tblout OceanDNA-b25738/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29a751e8-c49c-4747-8ad5-52d934893d9b/dqc_reference/reference_markers.hmm OceanDNA-b25738/protein.faa > /dev/null
[2023-03-17 05:59:17,234] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:59:17,234] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg559346d5-2ea2-408c-a3b0-aa508e00633e/OceanDNA-b25738.fa]
[2023-03-17 05:59:17,243] [INFO] Query marker FASTA was written to OceanDNA-b25738/markers.fasta
[2023-03-17 05:59:17,243] [INFO] Task started: Blastn
[2023-03-17 05:59:17,243] [INFO] Running command: blastn -query OceanDNA-b25738/markers.fasta -db /var/lib/cwl/stg29a751e8-c49c-4747-8ad5-52d934893d9b/dqc_reference/reference_markers.fasta -out OceanDNA-b25738/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:17,844] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:17,845] [INFO] Selected 11 target genomes.
[2023-03-17 05:59:17,845] [INFO] Target genome list was writen to OceanDNA-b25738/target_genomes.txt
[2023-03-17 05:59:17,851] [INFO] Task started: fastANI
[2023-03-17 05:59:17,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg559346d5-2ea2-408c-a3b0-aa508e00633e/OceanDNA-b25738.fa --refList OceanDNA-b25738/target_genomes.txt --output OceanDNA-b25738/fastani_result.tsv --threads 1
[2023-03-17 05:59:21,234] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:21,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29a751e8-c49c-4747-8ad5-52d934893d9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:59:21,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29a751e8-c49c-4747-8ad5-52d934893d9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:59:21,237] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:59:21,237] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:59:21,237] [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	77.3277	72	221	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:59:21,238] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25738/tc_result.tsv
[2023-03-17 05:59:21,238] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:59:21,238] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:59:21,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29a751e8-c49c-4747-8ad5-52d934893d9b/dqc_reference/checkm_data
[2023-03-17 05:59:21,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:59:21,241] [INFO] Task started: CheckM
[2023-03-17 05:59:21,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25738/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25738/checkm_input OceanDNA-b25738/checkm_result
[2023-03-17 05:59:39,618] [INFO] Task succeeded: CheckM
[2023-03-17 05:59:39,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.81%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:59:39,620] [INFO] ===== Completeness check finished =====
[2023-03-17 05:59:39,620] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:59:39,620] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25738/markers.fasta)
[2023-03-17 05:59:39,621] [INFO] Task started: Blastn
[2023-03-17 05:59:39,621] [INFO] Running command: blastn -query OceanDNA-b25738/markers.fasta -db /var/lib/cwl/stg29a751e8-c49c-4747-8ad5-52d934893d9b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25738/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:40,485] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:40,486] [INFO] Selected 14 target genomes.
[2023-03-17 05:59:40,486] [INFO] Target genome list was writen to OceanDNA-b25738/target_genomes_gtdb.txt
[2023-03-17 05:59:40,678] [INFO] Task started: fastANI
[2023-03-17 05:59:40,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg559346d5-2ea2-408c-a3b0-aa508e00633e/OceanDNA-b25738.fa --refList OceanDNA-b25738/target_genomes_gtdb.txt --output OceanDNA-b25738/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:59:43,648] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:43,657] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:59:43,657] [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_902567045.1	s__Pelagibacter sp902567045	97.8362	177	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.91	97.30	0.81	0.77	7	conclusive
GCA_902596915.1	s__Pelagibacter sp902596915	94.6846	151	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902611465.1	s__Pelagibacter sp902611465	93.1827	176	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902579465.1	s__Pelagibacter sp902579465	92.417	161	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608845.1	s__Pelagibacter sp902608845	92.3182	137	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902518235.1	s__Pelagibacter sp902518235	92.0894	139	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902614055.1	s__Pelagibacter sp902614055	92.0492	178	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902555585.1	s__Pelagibacter sp902555585	91.7992	195	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.37	98.37	0.93	0.91	5	-
GCA_902604975.1	s__Pelagibacter sp902604975	90.8729	151	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583075.1	s__Pelagibacter sp902583075	90.7361	175	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902527215.1	s__Pelagibacter sp902527215	90.3932	193	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902555275.1	s__Pelagibacter sp902555275	90.241	183	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.10	98.10	0.78	0.78	2	-
GCA_902520695.1	s__Pelagibacter sp902520695	90.2165	187	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902551985.1	s__Pelagibacter sp902551985	83.9895	169	221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:59:43,657] [INFO] GTDB search result was written to OceanDNA-b25738/result_gtdb.tsv
[2023-03-17 05:59:43,657] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:59:43,658] [INFO] DFAST_QC result json was written to OceanDNA-b25738/dqc_result.json
[2023-03-17 05:59:43,658] [INFO] DFAST_QC completed!
[2023-03-17 05:59:43,659] [INFO] Total running time: 0h0m33s