[2023-06-07 20:25:28,953] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:25:28,954] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:25:28,955] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5e0f8b3-cfad-4f3f-8ec9-f110c6225574/dqc_reference
[2023-06-07 20:25:30,281] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:25:30,282] [INFO] Task started: Prodigal
[2023-06-07 20:25:30,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dead8bc-023e-404e-9df1-5e4db45d5298/GCA_902520355.1_AG-333-I10_genomic.fna.gz | prodigal -d GCA_902520355.1_AG-333-I10_genomic.fna/cds.fna -a GCA_902520355.1_AG-333-I10_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:25:32,475] [INFO] Task succeeded: Prodigal
[2023-06-07 20:25:32,476] [INFO] Task started: HMMsearch
[2023-06-07 20:25:32,476] [INFO] Running command: hmmsearch --tblout GCA_902520355.1_AG-333-I10_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5e0f8b3-cfad-4f3f-8ec9-f110c6225574/dqc_reference/reference_markers.hmm GCA_902520355.1_AG-333-I10_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:25:32,657] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:25:32,658] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0dead8bc-023e-404e-9df1-5e4db45d5298/GCA_902520355.1_AG-333-I10_genomic.fna.gz]
[2023-06-07 20:25:32,671] [INFO] Query marker FASTA was written to GCA_902520355.1_AG-333-I10_genomic.fna/markers.fasta
[2023-06-07 20:25:32,671] [INFO] Task started: Blastn
[2023-06-07 20:25:32,671] [INFO] Running command: blastn -query GCA_902520355.1_AG-333-I10_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5e0f8b3-cfad-4f3f-8ec9-f110c6225574/dqc_reference/reference_markers.fasta -out GCA_902520355.1_AG-333-I10_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:25:33,207] [INFO] Task succeeded: Blastn
[2023-06-07 20:25:33,211] [INFO] Selected 10 target genomes.
[2023-06-07 20:25:33,211] [INFO] Target genome list was writen to GCA_902520355.1_AG-333-I10_genomic.fna/target_genomes.txt
[2023-06-07 20:25:33,213] [INFO] Task started: fastANI
[2023-06-07 20:25:33,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dead8bc-023e-404e-9df1-5e4db45d5298/GCA_902520355.1_AG-333-I10_genomic.fna.gz --refList GCA_902520355.1_AG-333-I10_genomic.fna/target_genomes.txt --output GCA_902520355.1_AG-333-I10_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:25:38,229] [INFO] Task succeeded: fastANI
[2023-06-07 20:25:38,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5e0f8b3-cfad-4f3f-8ec9-f110c6225574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:25:38,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5e0f8b3-cfad-4f3f-8ec9-f110c6225574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:25:38,234] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:25:38,234] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 20:25:38,234] [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	78.701	108	235	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 20:25:38,236] [INFO] DFAST Taxonomy check result was written to GCA_902520355.1_AG-333-I10_genomic.fna/tc_result.tsv
[2023-06-07 20:25:38,237] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:25:38,237] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:25:38,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5e0f8b3-cfad-4f3f-8ec9-f110c6225574/dqc_reference/checkm_data
[2023-06-07 20:25:38,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:25:38,250] [INFO] Task started: CheckM
[2023-06-07 20:25:38,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902520355.1_AG-333-I10_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902520355.1_AG-333-I10_genomic.fna/checkm_input GCA_902520355.1_AG-333-I10_genomic.fna/checkm_result
[2023-06-07 20:25:53,441] [INFO] Task succeeded: CheckM
[2023-06-07 20:25:53,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:25:53,461] [INFO] ===== Completeness check finished =====
[2023-06-07 20:25:53,461] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:25:53,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902520355.1_AG-333-I10_genomic.fna/markers.fasta)
[2023-06-07 20:25:53,462] [INFO] Task started: Blastn
[2023-06-07 20:25:53,462] [INFO] Running command: blastn -query GCA_902520355.1_AG-333-I10_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5e0f8b3-cfad-4f3f-8ec9-f110c6225574/dqc_reference/reference_markers_gtdb.fasta -out GCA_902520355.1_AG-333-I10_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:25:54,236] [INFO] Task succeeded: Blastn
[2023-06-07 20:25:54,240] [INFO] Selected 11 target genomes.
[2023-06-07 20:25:54,241] [INFO] Target genome list was writen to GCA_902520355.1_AG-333-I10_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:25:54,242] [INFO] Task started: fastANI
[2023-06-07 20:25:54,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dead8bc-023e-404e-9df1-5e4db45d5298/GCA_902520355.1_AG-333-I10_genomic.fna.gz --refList GCA_902520355.1_AG-333-I10_genomic.fna/target_genomes_gtdb.txt --output GCA_902520355.1_AG-333-I10_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:25:56,421] [INFO] Task succeeded: fastANI
[2023-06-07 20:25:56,433] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:25:56,434] [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_902520355.1	s__Pelagibacter sp902520355	100.0	233	235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902625035.1	s__Pelagibacter sp902625035	89.742	170	235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596515.1	s__Pelagibacter sp902596515	89.3839	190	235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.03	95.14	0.85	0.80	9	-
GCA_902531765.1	s__Pelagibacter sp902531765	89.1674	162	235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557235.1	s__Pelagibacter sp902557235	89.1333	159	235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902541825.1	s__Pelagibacter sp902541825	89.1086	147	235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.36	95.25	0.66	0.63	4	-
GCF_002101315.1	s__Pelagibacter sp002101315	89.0378	196	235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902573465.1	s__Pelagibacter sp902573465	88.0475	170	235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.88	99.88	0.91	0.91	2	-
GCA_902572925.1	s__Pelagibacter sp902572925	87.7962	112	235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578265.1	s__Pelagibacter sp902578265	87.6815	179	235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.64	99.64	0.82	0.82	2	-
GCA_902579925.1	s__Pelagibacter sp902579925	83.5124	126	235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.80	96.31	0.69	0.68	3	-
--------------------------------------------------------------------------------
[2023-06-07 20:25:56,436] [INFO] GTDB search result was written to GCA_902520355.1_AG-333-I10_genomic.fna/result_gtdb.tsv
[2023-06-07 20:25:56,437] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:25:56,440] [INFO] DFAST_QC result json was written to GCA_902520355.1_AG-333-I10_genomic.fna/dqc_result.json
[2023-06-07 20:25:56,441] [INFO] DFAST_QC completed!
[2023-06-07 20:25:56,441] [INFO] Total running time: 0h0m27s