[2023-06-08 12:27:46,684] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:27:46,686] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:27:46,686] [INFO] DQC Reference Directory: /var/lib/cwl/stg174e1dcc-ff4d-45e2-911e-7dcf6c0458b8/dqc_reference
[2023-06-08 12:27:48,056] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:27:48,057] [INFO] Task started: Prodigal
[2023-06-08 12:27:48,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg82ecf428-cfe4-495a-8ab3-1c046bd2b871/GCA_902520685.1_AG-333-J17_genomic.fna.gz | prodigal -d GCA_902520685.1_AG-333-J17_genomic.fna/cds.fna -a GCA_902520685.1_AG-333-J17_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:27:50,464] [INFO] Task succeeded: Prodigal
[2023-06-08 12:27:50,464] [INFO] Task started: HMMsearch
[2023-06-08 12:27:50,465] [INFO] Running command: hmmsearch --tblout GCA_902520685.1_AG-333-J17_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg174e1dcc-ff4d-45e2-911e-7dcf6c0458b8/dqc_reference/reference_markers.hmm GCA_902520685.1_AG-333-J17_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:27:50,674] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:27:50,676] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg82ecf428-cfe4-495a-8ab3-1c046bd2b871/GCA_902520685.1_AG-333-J17_genomic.fna.gz]
[2023-06-08 12:27:50,697] [INFO] Query marker FASTA was written to GCA_902520685.1_AG-333-J17_genomic.fna/markers.fasta
[2023-06-08 12:27:50,697] [INFO] Task started: Blastn
[2023-06-08 12:27:50,698] [INFO] Running command: blastn -query GCA_902520685.1_AG-333-J17_genomic.fna/markers.fasta -db /var/lib/cwl/stg174e1dcc-ff4d-45e2-911e-7dcf6c0458b8/dqc_reference/reference_markers.fasta -out GCA_902520685.1_AG-333-J17_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:51,187] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:51,191] [INFO] Selected 10 target genomes.
[2023-06-08 12:27:51,191] [INFO] Target genome list was writen to GCA_902520685.1_AG-333-J17_genomic.fna/target_genomes.txt
[2023-06-08 12:27:51,199] [INFO] Task started: fastANI
[2023-06-08 12:27:51,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg82ecf428-cfe4-495a-8ab3-1c046bd2b871/GCA_902520685.1_AG-333-J17_genomic.fna.gz --refList GCA_902520685.1_AG-333-J17_genomic.fna/target_genomes.txt --output GCA_902520685.1_AG-333-J17_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:27:55,651] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:55,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg174e1dcc-ff4d-45e2-911e-7dcf6c0458b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:27:55,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg174e1dcc-ff4d-45e2-911e-7dcf6c0458b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:27:55,656] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:27:55,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:27:55,657] [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	78.7257	153	273	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:27:55,659] [INFO] DFAST Taxonomy check result was written to GCA_902520685.1_AG-333-J17_genomic.fna/tc_result.tsv
[2023-06-08 12:27:55,660] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:27:55,660] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:27:55,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg174e1dcc-ff4d-45e2-911e-7dcf6c0458b8/dqc_reference/checkm_data
[2023-06-08 12:27:55,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:27:55,679] [INFO] Task started: CheckM
[2023-06-08 12:27:55,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902520685.1_AG-333-J17_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902520685.1_AG-333-J17_genomic.fna/checkm_input GCA_902520685.1_AG-333-J17_genomic.fna/checkm_result
[2023-06-08 12:28:11,601] [INFO] Task succeeded: CheckM
[2023-06-08 12:28:11,602] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:28:11,620] [INFO] ===== Completeness check finished =====
[2023-06-08 12:28:11,621] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:28:11,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902520685.1_AG-333-J17_genomic.fna/markers.fasta)
[2023-06-08 12:28:11,622] [INFO] Task started: Blastn
[2023-06-08 12:28:11,622] [INFO] Running command: blastn -query GCA_902520685.1_AG-333-J17_genomic.fna/markers.fasta -db /var/lib/cwl/stg174e1dcc-ff4d-45e2-911e-7dcf6c0458b8/dqc_reference/reference_markers_gtdb.fasta -out GCA_902520685.1_AG-333-J17_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:28:12,204] [INFO] Task succeeded: Blastn
[2023-06-08 12:28:12,208] [INFO] Selected 12 target genomes.
[2023-06-08 12:28:12,209] [INFO] Target genome list was writen to GCA_902520685.1_AG-333-J17_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:28:12,220] [INFO] Task started: fastANI
[2023-06-08 12:28:12,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg82ecf428-cfe4-495a-8ab3-1c046bd2b871/GCA_902520685.1_AG-333-J17_genomic.fna.gz --refList GCA_902520685.1_AG-333-J17_genomic.fna/target_genomes_gtdb.txt --output GCA_902520685.1_AG-333-J17_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:28:14,828] [INFO] Task succeeded: fastANI
[2023-06-08 12:28:14,844] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:28:14,844] [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_902520685.1	s__Pelagibacter sp902520685	100.0	271	273	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_902571235.1	s__Pelagibacter sp902571235	84.9094	172	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654245.1	s__Pelagibacter sp014654245	84.5079	118	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622805.1	s__Pelagibacter sp902622805	83.4233	156	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.81	99.81	0.79	0.79	2	-
GCA_902578775.1	s__Pelagibacter sp902578775	83.2026	202	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177485.1	s__Pelagibacter sp900177485	81.092	184	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638165.1	s__Pelagibacter sp008638165	81.041	145	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.93	98.78	0.83	0.76	5	-
GCA_003279685.1	s__Pelagibacter sp003279685	80.3388	148	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902558795.1	s__Pelagibacter sp902558795	80.1171	93	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905616465.1	s__Pelagibacter sp905616465	80.0305	124	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556905.1	s__Pelagibacter sp902556905	79.9458	156	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000299095.1	s__Pelagibacter sp000299095	79.306	163	273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:28:14,847] [INFO] GTDB search result was written to GCA_902520685.1_AG-333-J17_genomic.fna/result_gtdb.tsv
[2023-06-08 12:28:14,847] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:28:14,851] [INFO] DFAST_QC result json was written to GCA_902520685.1_AG-333-J17_genomic.fna/dqc_result.json
[2023-06-08 12:28:14,851] [INFO] DFAST_QC completed!
[2023-06-08 12:28:14,851] [INFO] Total running time: 0h0m28s