[2023-03-17 10:08:39,092] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:08:39,092] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:08:39,092] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2d44e31-cef2-46d5-b442-8b52a410a1fb/dqc_reference
[2023-03-17 10:08:40,236] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:08:40,236] [INFO] Task started: Prodigal
[2023-03-17 10:08:40,236] [INFO] Running command: cat /var/lib/cwl/stg7d32c09e-7908-4128-8dc0-cb83c67ac293/OceanDNA-b42285.fa | prodigal -d OceanDNA-b42285/cds.fna -a OceanDNA-b42285/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:08:44,224] [INFO] Task succeeded: Prodigal
[2023-03-17 10:08:44,224] [INFO] Task started: HMMsearch
[2023-03-17 10:08:44,224] [INFO] Running command: hmmsearch --tblout OceanDNA-b42285/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2d44e31-cef2-46d5-b442-8b52a410a1fb/dqc_reference/reference_markers.hmm OceanDNA-b42285/protein.faa > /dev/null
[2023-03-17 10:08:44,374] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:08:44,375] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7d32c09e-7908-4128-8dc0-cb83c67ac293/OceanDNA-b42285.fa]
[2023-03-17 10:08:44,381] [INFO] Query marker FASTA was written to OceanDNA-b42285/markers.fasta
[2023-03-17 10:08:44,383] [INFO] Task started: Blastn
[2023-03-17 10:08:44,383] [INFO] Running command: blastn -query OceanDNA-b42285/markers.fasta -db /var/lib/cwl/stgf2d44e31-cef2-46d5-b442-8b52a410a1fb/dqc_reference/reference_markers.fasta -out OceanDNA-b42285/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:08:45,114] [INFO] Task succeeded: Blastn
[2023-03-17 10:08:45,114] [INFO] Selected 11 target genomes.
[2023-03-17 10:08:45,114] [INFO] Target genome list was writen to OceanDNA-b42285/target_genomes.txt
[2023-03-17 10:08:45,125] [INFO] Task started: fastANI
[2023-03-17 10:08:45,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d32c09e-7908-4128-8dc0-cb83c67ac293/OceanDNA-b42285.fa --refList OceanDNA-b42285/target_genomes.txt --output OceanDNA-b42285/fastani_result.tsv --threads 1
[2023-03-17 10:08:48,503] [INFO] Task succeeded: fastANI
[2023-03-17 10:08:48,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2d44e31-cef2-46d5-b442-8b52a410a1fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:08:48,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2d44e31-cef2-46d5-b442-8b52a410a1fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:08:48,504] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:08:48,504] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:08:48,504] [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 10:08:48,504] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42285/tc_result.tsv
[2023-03-17 10:08:48,504] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:08:48,504] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:08:48,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2d44e31-cef2-46d5-b442-8b52a410a1fb/dqc_reference/checkm_data
[2023-03-17 10:08:48,562] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:08:48,564] [INFO] Task started: CheckM
[2023-03-17 10:08:48,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42285/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42285/checkm_input OceanDNA-b42285/checkm_result
[2023-03-17 10:09:08,724] [INFO] Task succeeded: CheckM
[2023-03-17 10:09:08,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:09:08,726] [INFO] ===== Completeness check finished =====
[2023-03-17 10:09:08,726] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:09:08,726] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42285/markers.fasta)
[2023-03-17 10:09:08,727] [INFO] Task started: Blastn
[2023-03-17 10:09:08,728] [INFO] Running command: blastn -query OceanDNA-b42285/markers.fasta -db /var/lib/cwl/stgf2d44e31-cef2-46d5-b442-8b52a410a1fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42285/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:09:09,924] [INFO] Task succeeded: Blastn
[2023-03-17 10:09:09,925] [INFO] Selected 19 target genomes.
[2023-03-17 10:09:09,925] [INFO] Target genome list was writen to OceanDNA-b42285/target_genomes_gtdb.txt
[2023-03-17 10:09:09,958] [INFO] Task started: fastANI
[2023-03-17 10:09:09,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d32c09e-7908-4128-8dc0-cb83c67ac293/OceanDNA-b42285.fa --refList OceanDNA-b42285/target_genomes_gtdb.txt --output OceanDNA-b42285/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:09:13,587] [INFO] Task succeeded: fastANI
[2023-03-17 10:09:13,595] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:09:13,596] [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_902557965.1	s__SAR86A sp902557965	97.938	221	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.42	97.04	0.73	0.71	3	conclusive
GCA_002710265.1	s__SAR86A sp002710265	83.9416	190	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626385.1	s__SAR86A sp902626385	78.9065	141	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721385.1	s__SAR86A sp002721385	78.6395	92	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000252525.1	s__SAR86A sp000252525	78.4632	138	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.49	95.25	0.88	0.84	16	-
GCA_902558095.1	s__SAR86A sp902558095	78.3741	110	264	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	78.2843	99	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_902559345.1	s__SAR86A sp902559345	78.13	95	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547295.1	s__SAR86A sp902547295	78.0728	106	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902551185.1	s__SAR86A sp902551185	77.9544	90	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.17	99.17	0.78	0.78	2	-
GCA_902520725.1	s__SAR86A sp902520725	77.824	106	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.82	99.82	0.73	0.73	2	-
GCA_002169625.2	s__SAR86A sp002169625	77.7656	82	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.57	98.54	0.85	0.74	4	-
GCA_003213495.1	s__SAR86A sp003213495	77.4076	124	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.20	96.41	0.97	0.94	3	-
GCA_902591665.1	s__SCGC-AAA076-P13 sp902591665	77.2192	61	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	99.81	99.81	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-17 10:09:13,596] [INFO] GTDB search result was written to OceanDNA-b42285/result_gtdb.tsv
[2023-03-17 10:09:13,596] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:09:13,597] [INFO] DFAST_QC result json was written to OceanDNA-b42285/dqc_result.json
[2023-03-17 10:09:13,597] [INFO] DFAST_QC completed!
[2023-03-17 10:09:13,597] [INFO] Total running time: 0h0m35s