[2023-06-05 18:00:43,190] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:00:43,198] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:00:43,199] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc2ed9c8-11b6-43e6-8ce8-4309d234ea07/dqc_reference
[2023-06-05 18:00:47,240] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:00:47,241] [INFO] Task started: Prodigal
[2023-06-05 18:00:47,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg386f9402-d4bc-4568-bee9-ea1ca0c03cc7/GCA_902617965.1_AG-919-P18_genomic.fna.gz | prodigal -d GCA_902617965.1_AG-919-P18_genomic.fna/cds.fna -a GCA_902617965.1_AG-919-P18_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:00:49,681] [INFO] Task succeeded: Prodigal
[2023-06-05 18:00:49,682] [INFO] Task started: HMMsearch
[2023-06-05 18:00:49,682] [INFO] Running command: hmmsearch --tblout GCA_902617965.1_AG-919-P18_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc2ed9c8-11b6-43e6-8ce8-4309d234ea07/dqc_reference/reference_markers.hmm GCA_902617965.1_AG-919-P18_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:00:49,902] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:00:49,905] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg386f9402-d4bc-4568-bee9-ea1ca0c03cc7/GCA_902617965.1_AG-919-P18_genomic.fna.gz]
[2023-06-05 18:00:49,957] [INFO] Query marker FASTA was written to GCA_902617965.1_AG-919-P18_genomic.fna/markers.fasta
[2023-06-05 18:00:49,957] [INFO] Task started: Blastn
[2023-06-05 18:00:49,957] [INFO] Running command: blastn -query GCA_902617965.1_AG-919-P18_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc2ed9c8-11b6-43e6-8ce8-4309d234ea07/dqc_reference/reference_markers.fasta -out GCA_902617965.1_AG-919-P18_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:00:58,542] [INFO] Task succeeded: Blastn
[2023-06-05 18:00:58,548] [INFO] Selected 12 target genomes.
[2023-06-05 18:00:58,549] [INFO] Target genome list was writen to GCA_902617965.1_AG-919-P18_genomic.fna/target_genomes.txt
[2023-06-05 18:00:58,569] [INFO] Task started: fastANI
[2023-06-05 18:00:58,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg386f9402-d4bc-4568-bee9-ea1ca0c03cc7/GCA_902617965.1_AG-919-P18_genomic.fna.gz --refList GCA_902617965.1_AG-919-P18_genomic.fna/target_genomes.txt --output GCA_902617965.1_AG-919-P18_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:01:02,659] [INFO] Task succeeded: fastANI
[2023-06-05 18:01:02,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc2ed9c8-11b6-43e6-8ce8-4309d234ea07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:01:02,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc2ed9c8-11b6-43e6-8ce8-4309d234ea07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:01:02,665] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:01:02,665] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:01:02,665] [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	78.6486	118	246	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:01:02,668] [INFO] DFAST Taxonomy check result was written to GCA_902617965.1_AG-919-P18_genomic.fna/tc_result.tsv
[2023-06-05 18:01:02,669] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:01:02,669] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:01:02,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc2ed9c8-11b6-43e6-8ce8-4309d234ea07/dqc_reference/checkm_data
[2023-06-05 18:01:02,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:01:02,685] [INFO] Task started: CheckM
[2023-06-05 18:01:02,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902617965.1_AG-919-P18_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902617965.1_AG-919-P18_genomic.fna/checkm_input GCA_902617965.1_AG-919-P18_genomic.fna/checkm_result
[2023-06-05 18:01:19,065] [INFO] Task succeeded: CheckM
[2023-06-05 18:01:19,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:01:19,086] [INFO] ===== Completeness check finished =====
[2023-06-05 18:01:19,086] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:01:19,087] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902617965.1_AG-919-P18_genomic.fna/markers.fasta)
[2023-06-05 18:01:19,087] [INFO] Task started: Blastn
[2023-06-05 18:01:19,087] [INFO] Running command: blastn -query GCA_902617965.1_AG-919-P18_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc2ed9c8-11b6-43e6-8ce8-4309d234ea07/dqc_reference/reference_markers_gtdb.fasta -out GCA_902617965.1_AG-919-P18_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:01:20,006] [INFO] Task succeeded: Blastn
[2023-06-05 18:01:20,010] [INFO] Selected 13 target genomes.
[2023-06-05 18:01:20,010] [INFO] Target genome list was writen to GCA_902617965.1_AG-919-P18_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:01:20,021] [INFO] Task started: fastANI
[2023-06-05 18:01:20,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg386f9402-d4bc-4568-bee9-ea1ca0c03cc7/GCA_902617965.1_AG-919-P18_genomic.fna.gz --refList GCA_902617965.1_AG-919-P18_genomic.fna/target_genomes_gtdb.txt --output GCA_902617965.1_AG-919-P18_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:01:22,944] [INFO] Task succeeded: fastANI
[2023-06-05 18:01:22,957] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:01:22,957] [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_902597675.1	s__Pelagibacter sp902597675	95.9451	176	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.60	95.15	0.72	0.69	5	conclusive
GCA_902518155.1	s__Pelagibacter sp902518155	94.9621	212	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.58	95.45	0.87	0.84	3	-
GCA_902616725.1	s__Pelagibacter sp902616725	94.6776	194	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.39	95.04	0.85	0.83	5	-
GCA_003213155.1	s__Pelagibacter sp003213155	94.3959	167	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.52	95.06	0.83	0.73	7	-
GCA_902612325.1	s__Pelagibacter sp902612325	94.3007	217	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.45	95.30	0.90	0.90	3	-
GCA_902609685.1	s__Pelagibacter sp902609685	94.1688	205	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.69	95.28	0.90	0.86	8	-
GCA_902574345.1	s__Pelagibacter sp902574345	93.8617	153	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003212275.1	s__Pelagibacter sp003212275	93.7234	186	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902632935.1	s__Pelagibacter sp902632935	93.3344	126	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524865.1	s__Pelagibacter sp902524865	92.7429	121	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902586125.1	s__Pelagibacter sp902586125	92.7379	172	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.02	96.32	0.75	0.72	7	-
GCA_902626645.1	s__Pelagibacter sp902626645	92.0843	185	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902627805.1	s__Pelagibacter sp902627805	91.3928	186	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:01:22,960] [INFO] GTDB search result was written to GCA_902617965.1_AG-919-P18_genomic.fna/result_gtdb.tsv
[2023-06-05 18:01:22,960] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:01:22,981] [INFO] DFAST_QC result json was written to GCA_902617965.1_AG-919-P18_genomic.fna/dqc_result.json
[2023-06-05 18:01:22,982] [INFO] DFAST_QC completed!
[2023-06-05 18:01:22,982] [INFO] Total running time: 0h0m40s