[2023-06-05 03:59:54,222] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:59:54,225] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:59:54,225] [INFO] DQC Reference Directory: /var/lib/cwl/stg635494c9-7dfe-4b93-88a3-63721a058e14/dqc_reference
[2023-06-05 03:59:55,616] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:59:55,618] [INFO] Task started: Prodigal
[2023-06-05 03:59:55,618] [INFO] Running command: gunzip -c /var/lib/cwl/stg68bde10e-f6ca-461b-9a05-3fd95c41ec61/GCA_902617475.1_AG-919-N15_genomic.fna.gz | prodigal -d GCA_902617475.1_AG-919-N15_genomic.fna/cds.fna -a GCA_902617475.1_AG-919-N15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:59:57,249] [INFO] Task succeeded: Prodigal
[2023-06-05 03:59:57,250] [INFO] Task started: HMMsearch
[2023-06-05 03:59:57,250] [INFO] Running command: hmmsearch --tblout GCA_902617475.1_AG-919-N15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg635494c9-7dfe-4b93-88a3-63721a058e14/dqc_reference/reference_markers.hmm GCA_902617475.1_AG-919-N15_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:59:57,488] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:59:57,489] [INFO] Found 6/6 markers.
[2023-06-05 03:59:57,526] [INFO] Query marker FASTA was written to GCA_902617475.1_AG-919-N15_genomic.fna/markers.fasta
[2023-06-05 03:59:57,527] [INFO] Task started: Blastn
[2023-06-05 03:59:57,527] [INFO] Running command: blastn -query GCA_902617475.1_AG-919-N15_genomic.fna/markers.fasta -db /var/lib/cwl/stg635494c9-7dfe-4b93-88a3-63721a058e14/dqc_reference/reference_markers.fasta -out GCA_902617475.1_AG-919-N15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:59:58,523] [INFO] Task succeeded: Blastn
[2023-06-05 03:59:58,527] [INFO] Selected 20 target genomes.
[2023-06-05 03:59:58,528] [INFO] Target genome list was writen to GCA_902617475.1_AG-919-N15_genomic.fna/target_genomes.txt
[2023-06-05 03:59:58,531] [INFO] Task started: fastANI
[2023-06-05 03:59:58,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg68bde10e-f6ca-461b-9a05-3fd95c41ec61/GCA_902617475.1_AG-919-N15_genomic.fna.gz --refList GCA_902617475.1_AG-919-N15_genomic.fna/target_genomes.txt --output GCA_902617475.1_AG-919-N15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:00:07,663] [INFO] Task succeeded: fastANI
[2023-06-05 04:00:07,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg635494c9-7dfe-4b93-88a3-63721a058e14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:00:07,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg635494c9-7dfe-4b93-88a3-63721a058e14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:00:07,666] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:00:07,666] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 04:00:07,666] [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
--------------------------------------------------------------------------------
[2023-06-05 04:00:07,669] [INFO] DFAST Taxonomy check result was written to GCA_902617475.1_AG-919-N15_genomic.fna/tc_result.tsv
[2023-06-05 04:00:07,669] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:00:07,670] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:00:07,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg635494c9-7dfe-4b93-88a3-63721a058e14/dqc_reference/checkm_data
[2023-06-05 04:00:07,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:00:07,693] [INFO] Task started: CheckM
[2023-06-05 04:00:07,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902617475.1_AG-919-N15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902617475.1_AG-919-N15_genomic.fna/checkm_input GCA_902617475.1_AG-919-N15_genomic.fna/checkm_result
[2023-06-05 04:00:21,472] [INFO] Task succeeded: CheckM
[2023-06-05 04:00:21,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:00:21,494] [INFO] ===== Completeness check finished =====
[2023-06-05 04:00:21,495] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:00:21,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902617475.1_AG-919-N15_genomic.fna/markers.fasta)
[2023-06-05 04:00:21,496] [INFO] Task started: Blastn
[2023-06-05 04:00:21,496] [INFO] Running command: blastn -query GCA_902617475.1_AG-919-N15_genomic.fna/markers.fasta -db /var/lib/cwl/stg635494c9-7dfe-4b93-88a3-63721a058e14/dqc_reference/reference_markers_gtdb.fasta -out GCA_902617475.1_AG-919-N15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:00:22,451] [INFO] Task succeeded: Blastn
[2023-06-05 04:00:22,455] [INFO] Selected 15 target genomes.
[2023-06-05 04:00:22,455] [INFO] Target genome list was writen to GCA_902617475.1_AG-919-N15_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:00:22,461] [INFO] Task started: fastANI
[2023-06-05 04:00:22,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg68bde10e-f6ca-461b-9a05-3fd95c41ec61/GCA_902617475.1_AG-919-N15_genomic.fna.gz --refList GCA_902617475.1_AG-919-N15_genomic.fna/target_genomes_gtdb.txt --output GCA_902617475.1_AG-919-N15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:00:25,861] [INFO] Task succeeded: fastANI
[2023-06-05 04:00:25,873] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 04:00:25,873] [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_902591925.1	s__SAR86A sp902591925	97.3619	264	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	conclusive
GCA_902617045.1	s__SAR86A sp902617045	91.1085	210	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_004212975.1	s__SAR86A sp004212975	90.8587	159	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.30	95.02	0.85	0.76	8	-
GCA_902612915.1	s__SAR86A sp902612915	90.6596	202	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.80	95.61	0.84	0.75	10	-
GCA_902541175.1	s__SAR86A sp902541175	90.5739	216	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.65	95.31	0.89	0.85	3	-
GCA_902547295.1	s__SAR86A sp902547295	90.4898	184	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902630885.1	s__SAR86A sp902630885	82.9051	188	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902631785.1	s__SAR86A sp902631785	82.8843	173	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_000252525.1	s__SAR86A sp000252525	82.4236	135	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.49	95.25	0.88	0.84	16	-
GCA_902579825.1	s__SAR86A sp902579825	79.5984	114	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559345.1	s__SAR86A sp902559345	79.1121	95	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516285.1	s__SAR86A sp902516285	78.1071	97	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.51	96.51	0.92	0.92	2	-
GCA_902557705.1	s__SCGC-AAA076-P13 sp902557705	77.5659	51	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 04:00:25,875] [INFO] GTDB search result was written to GCA_902617475.1_AG-919-N15_genomic.fna/result_gtdb.tsv
[2023-06-05 04:00:25,876] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:00:25,879] [INFO] DFAST_QC result json was written to GCA_902617475.1_AG-919-N15_genomic.fna/dqc_result.json
[2023-06-05 04:00:25,879] [INFO] DFAST_QC completed!
[2023-06-05 04:00:25,879] [INFO] Total running time: 0h0m32s