[2023-03-18 21:07:03,637] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:07:03,637] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:07:03,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ecda436-df0f-4447-835f-aacbad1cbc0f/dqc_reference
[2023-03-18 21:07:05,388] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:07:05,389] [INFO] Task started: Prodigal
[2023-03-18 21:07:05,389] [INFO] Running command: cat /var/lib/cwl/stg0119c3aa-d09c-4ac6-b1ef-ae3fc46dae92/OceanDNA-b25897.fa | prodigal -d OceanDNA-b25897/cds.fna -a OceanDNA-b25897/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:07:09,275] [INFO] Task succeeded: Prodigal
[2023-03-18 21:07:09,275] [INFO] Task started: HMMsearch
[2023-03-18 21:07:09,275] [INFO] Running command: hmmsearch --tblout OceanDNA-b25897/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ecda436-df0f-4447-835f-aacbad1cbc0f/dqc_reference/reference_markers.hmm OceanDNA-b25897/protein.faa > /dev/null
[2023-03-18 21:07:09,411] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:07:09,411] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0119c3aa-d09c-4ac6-b1ef-ae3fc46dae92/OceanDNA-b25897.fa]
[2023-03-18 21:07:09,420] [INFO] Query marker FASTA was written to OceanDNA-b25897/markers.fasta
[2023-03-18 21:07:09,420] [INFO] Task started: Blastn
[2023-03-18 21:07:09,420] [INFO] Running command: blastn -query OceanDNA-b25897/markers.fasta -db /var/lib/cwl/stg3ecda436-df0f-4447-835f-aacbad1cbc0f/dqc_reference/reference_markers.fasta -out OceanDNA-b25897/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:07:11,923] [INFO] Task succeeded: Blastn
[2023-03-18 21:07:11,924] [INFO] Selected 14 target genomes.
[2023-03-18 21:07:11,924] [INFO] Target genome list was writen to OceanDNA-b25897/target_genomes.txt
[2023-03-18 21:07:11,939] [INFO] Task started: fastANI
[2023-03-18 21:07:11,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg0119c3aa-d09c-4ac6-b1ef-ae3fc46dae92/OceanDNA-b25897.fa --refList OceanDNA-b25897/target_genomes.txt --output OceanDNA-b25897/fastani_result.tsv --threads 1
[2023-03-18 21:07:18,568] [INFO] Task succeeded: fastANI
[2023-03-18 21:07:18,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ecda436-df0f-4447-835f-aacbad1cbc0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:07:18,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ecda436-df0f-4447-835f-aacbad1cbc0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:07:18,572] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:07:18,572] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:07:18,572] [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	78.3887	89	159	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:07:18,572] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25897/tc_result.tsv
[2023-03-18 21:07:18,572] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:07:18,572] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:07:18,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ecda436-df0f-4447-835f-aacbad1cbc0f/dqc_reference/checkm_data
[2023-03-18 21:07:18,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:07:18,575] [INFO] Task started: CheckM
[2023-03-18 21:07:18,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25897/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25897/checkm_input OceanDNA-b25897/checkm_result
[2023-03-18 21:07:33,412] [INFO] Task succeeded: CheckM
[2023-03-18 21:07:33,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:07:33,423] [INFO] ===== Completeness check finished =====
[2023-03-18 21:07:33,424] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:07:33,424] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25897/markers.fasta)
[2023-03-18 21:07:33,425] [INFO] Task started: Blastn
[2023-03-18 21:07:33,425] [INFO] Running command: blastn -query OceanDNA-b25897/markers.fasta -db /var/lib/cwl/stg3ecda436-df0f-4447-835f-aacbad1cbc0f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25897/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:07:34,227] [INFO] Task succeeded: Blastn
[2023-03-18 21:07:34,228] [INFO] Selected 10 target genomes.
[2023-03-18 21:07:34,228] [INFO] Target genome list was writen to OceanDNA-b25897/target_genomes_gtdb.txt
[2023-03-18 21:07:34,240] [INFO] Task started: fastANI
[2023-03-18 21:07:34,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg0119c3aa-d09c-4ac6-b1ef-ae3fc46dae92/OceanDNA-b25897.fa --refList OceanDNA-b25897/target_genomes_gtdb.txt --output OceanDNA-b25897/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:07:36,069] [INFO] Task succeeded: fastANI
[2023-03-18 21:07:36,075] [INFO] Found 10 fastANI hits (3 hits with ANI > circumscription radius)
[2023-03-18 21:07:36,076] [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_003209915.1	s__Pelagibacter sp003209915	97.5776	137	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.70	95.04	0.84	0.76	80	inconclusive
GCA_902540595.1	s__Pelagibacter sp902540595	96.2307	129	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.43	95.31	0.77	0.75	3	inconclusive
GCA_014654235.1	s__Pelagibacter sp014654235	95.131	84	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_014653985.1	s__Pelagibacter sp014653985	92.9769	135	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902590915.1	s__Pelagibacter sp902590915	92.3632	117	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583295.1	s__Pelagibacter sp902583295	92.1262	124	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622795.1	s__Pelagibacter sp902622795	90.4635	120	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.61	99.61	0.85	0.85	2	-
GCA_902613855.1	s__Pelagibacter sp902613855	90.2379	134	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515625.1	s__Pelagibacter sp902515625	89.1157	101	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902539165.1	s__Pelagibacter sp902539165	88.3837	115	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.84	98.84	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:07:36,076] [INFO] GTDB search result was written to OceanDNA-b25897/result_gtdb.tsv
[2023-03-18 21:07:36,076] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:07:36,077] [INFO] DFAST_QC result json was written to OceanDNA-b25897/dqc_result.json
[2023-03-18 21:07:36,077] [INFO] DFAST_QC completed!
[2023-03-18 21:07:36,077] [INFO] Total running time: 0h0m32s