[2023-03-17 02:49:37,507] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:49:37,507] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:49:37,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg42e87ad3-5bce-4eae-bb21-11d5f8e5ff17/dqc_reference
[2023-03-17 02:49:38,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:49:38,701] [INFO] Task started: Prodigal
[2023-03-17 02:49:38,701] [INFO] Running command: cat /var/lib/cwl/stgdbe9bac5-e24c-4b62-adba-b0a4f2455a3a/OceanDNA-b39559.fa | prodigal -d OceanDNA-b39559/cds.fna -a OceanDNA-b39559/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:49:52,202] [INFO] Task succeeded: Prodigal
[2023-03-17 02:49:52,203] [INFO] Task started: HMMsearch
[2023-03-17 02:49:52,203] [INFO] Running command: hmmsearch --tblout OceanDNA-b39559/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42e87ad3-5bce-4eae-bb21-11d5f8e5ff17/dqc_reference/reference_markers.hmm OceanDNA-b39559/protein.faa > /dev/null
[2023-03-17 02:49:52,397] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:49:52,398] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdbe9bac5-e24c-4b62-adba-b0a4f2455a3a/OceanDNA-b39559.fa]
[2023-03-17 02:49:52,412] [INFO] Query marker FASTA was written to OceanDNA-b39559/markers.fasta
[2023-03-17 02:49:52,412] [INFO] Task started: Blastn
[2023-03-17 02:49:52,412] [INFO] Running command: blastn -query OceanDNA-b39559/markers.fasta -db /var/lib/cwl/stg42e87ad3-5bce-4eae-bb21-11d5f8e5ff17/dqc_reference/reference_markers.fasta -out OceanDNA-b39559/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:49:53,020] [INFO] Task succeeded: Blastn
[2023-03-17 02:49:53,021] [INFO] Selected 26 target genomes.
[2023-03-17 02:49:53,022] [INFO] Target genome list was writen to OceanDNA-b39559/target_genomes.txt
[2023-03-17 02:49:53,105] [INFO] Task started: fastANI
[2023-03-17 02:49:53,105] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbe9bac5-e24c-4b62-adba-b0a4f2455a3a/OceanDNA-b39559.fa --refList OceanDNA-b39559/target_genomes.txt --output OceanDNA-b39559/fastani_result.tsv --threads 1
[2023-03-17 02:50:09,698] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:09,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42e87ad3-5bce-4eae-bb21-11d5f8e5ff17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:50:09,698] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42e87ad3-5bce-4eae-bb21-11d5f8e5ff17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:50:09,699] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:50:09,699] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:50:09,699] [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
--------------------------------------------------------------------------------
[2023-03-17 02:50:09,699] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39559/tc_result.tsv
[2023-03-17 02:50:09,699] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:50:09,699] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:50:09,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42e87ad3-5bce-4eae-bb21-11d5f8e5ff17/dqc_reference/checkm_data
[2023-03-17 02:50:09,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:50:09,706] [INFO] Task started: CheckM
[2023-03-17 02:50:09,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39559/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39559/checkm_input OceanDNA-b39559/checkm_result
[2023-03-17 02:50:45,671] [INFO] Task succeeded: CheckM
[2023-03-17 02:50:45,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:50:45,717] [INFO] ===== Completeness check finished =====
[2023-03-17 02:50:45,717] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:50:45,718] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39559/markers.fasta)
[2023-03-17 02:50:45,719] [INFO] Task started: Blastn
[2023-03-17 02:50:45,719] [INFO] Running command: blastn -query OceanDNA-b39559/markers.fasta -db /var/lib/cwl/stg42e87ad3-5bce-4eae-bb21-11d5f8e5ff17/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39559/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:50:46,710] [INFO] Task succeeded: Blastn
[2023-03-17 02:50:46,713] [INFO] Selected 15 target genomes.
[2023-03-17 02:50:46,713] [INFO] Target genome list was writen to OceanDNA-b39559/target_genomes_gtdb.txt
[2023-03-17 02:50:46,797] [INFO] Task started: fastANI
[2023-03-17 02:50:46,798] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbe9bac5-e24c-4b62-adba-b0a4f2455a3a/OceanDNA-b39559.fa --refList OceanDNA-b39559/target_genomes_gtdb.txt --output OceanDNA-b39559/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:50:54,265] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:54,271] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:50:54,272] [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_002335945.1	s__HTCC2207 sp002335945	80.3352	428	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_905182245.1	s__HTCC2207 sp905182245	80.3195	258	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664075.1	s__HTCC2207 sp018664075	78.6107	233	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_002378645.1	s__HTCC2207 sp002378645	78.4543	218	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
GCA_002334915.1	s__HTCC2207 sp002334915	78.1368	234	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_905182855.1	s__HTCC2207 sp905182855	77.9335	173	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478975.1	s__HTCC2207 sp905478975	77.7483	152	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018663035.1	s__HTCC2207 sp018663035	77.3979	175	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
GCA_012960115.1	s__HTCC2207 sp012960115	76.8151	68	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.92	99.92	0.91	0.91	2	-
GCA_018607545.1	s__HTCC2207 sp018607545	76.7643	63	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:50:54,274] [INFO] GTDB search result was written to OceanDNA-b39559/result_gtdb.tsv
[2023-03-17 02:50:54,276] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:50:54,279] [INFO] DFAST_QC result json was written to OceanDNA-b39559/dqc_result.json
[2023-03-17 02:50:54,279] [INFO] DFAST_QC completed!
[2023-03-17 02:50:54,279] [INFO] Total running time: 0h1m17s