[2023-03-18 01:24:39,915] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:24:39,915] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:24:39,915] [INFO] DQC Reference Directory: /var/lib/cwl/stge6f7063f-e81b-4139-9439-8c2a46ef6c50/dqc_reference
[2023-03-18 01:24:41,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:24:41,193] [INFO] Task started: Prodigal
[2023-03-18 01:24:41,193] [INFO] Running command: cat /var/lib/cwl/stg028ff19f-001c-4a96-a861-d819faf2c892/OceanDNA-b39347.fa | prodigal -d OceanDNA-b39347/cds.fna -a OceanDNA-b39347/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:24:51,329] [INFO] Task succeeded: Prodigal
[2023-03-18 01:24:51,329] [INFO] Task started: HMMsearch
[2023-03-18 01:24:51,329] [INFO] Running command: hmmsearch --tblout OceanDNA-b39347/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6f7063f-e81b-4139-9439-8c2a46ef6c50/dqc_reference/reference_markers.hmm OceanDNA-b39347/protein.faa > /dev/null
[2023-03-18 01:24:51,510] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:24:51,511] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg028ff19f-001c-4a96-a861-d819faf2c892/OceanDNA-b39347.fa]
[2023-03-18 01:24:51,524] [INFO] Query marker FASTA was written to OceanDNA-b39347/markers.fasta
[2023-03-18 01:24:51,525] [INFO] Task started: Blastn
[2023-03-18 01:24:51,525] [INFO] Running command: blastn -query OceanDNA-b39347/markers.fasta -db /var/lib/cwl/stge6f7063f-e81b-4139-9439-8c2a46ef6c50/dqc_reference/reference_markers.fasta -out OceanDNA-b39347/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:24:52,121] [INFO] Task succeeded: Blastn
[2023-03-18 01:24:52,122] [INFO] Selected 33 target genomes.
[2023-03-18 01:24:52,122] [INFO] Target genome list was writen to OceanDNA-b39347/target_genomes.txt
[2023-03-18 01:24:52,133] [INFO] Task started: fastANI
[2023-03-18 01:24:52,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg028ff19f-001c-4a96-a861-d819faf2c892/OceanDNA-b39347.fa --refList OceanDNA-b39347/target_genomes.txt --output OceanDNA-b39347/fastani_result.tsv --threads 1
[2023-03-18 01:25:10,578] [INFO] Task succeeded: fastANI
[2023-03-18 01:25:10,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6f7063f-e81b-4139-9439-8c2a46ef6c50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:25:10,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6f7063f-e81b-4139-9439-8c2a46ef6c50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:25:10,579] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:25:10,579] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:25:10,579] [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
--------------------------------------------------------------------------------
[2023-03-18 01:25:10,579] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39347/tc_result.tsv
[2023-03-18 01:25:10,579] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:25:10,579] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:25:10,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6f7063f-e81b-4139-9439-8c2a46ef6c50/dqc_reference/checkm_data
[2023-03-18 01:25:10,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:25:10,591] [INFO] Task started: CheckM
[2023-03-18 01:25:10,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39347/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39347/checkm_input OceanDNA-b39347/checkm_result
[2023-03-18 01:25:39,874] [INFO] Task succeeded: CheckM
[2023-03-18 01:25:39,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:25:39,876] [INFO] ===== Completeness check finished =====
[2023-03-18 01:25:39,876] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:25:39,877] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39347/markers.fasta)
[2023-03-18 01:25:39,878] [INFO] Task started: Blastn
[2023-03-18 01:25:39,878] [INFO] Running command: blastn -query OceanDNA-b39347/markers.fasta -db /var/lib/cwl/stge6f7063f-e81b-4139-9439-8c2a46ef6c50/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39347/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:25:40,847] [INFO] Task succeeded: Blastn
[2023-03-18 01:25:40,847] [INFO] Selected 18 target genomes.
[2023-03-18 01:25:40,848] [INFO] Target genome list was writen to OceanDNA-b39347/target_genomes_gtdb.txt
[2023-03-18 01:25:40,937] [INFO] Task started: fastANI
[2023-03-18 01:25:40,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg028ff19f-001c-4a96-a861-d819faf2c892/OceanDNA-b39347.fa --refList OceanDNA-b39347/target_genomes_gtdb.txt --output OceanDNA-b39347/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:25:48,047] [INFO] Task succeeded: fastANI
[2023-03-18 01:25:48,055] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:25:48,055] [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_018607545.1	s__HTCC2207 sp018607545	82.849	250	600	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	78.3531	228	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153445.1	s__HTCC2207 sp000153445	78.3084	244	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_017858135.1	s__HTCC2207 sp017858135	78.2763	215	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.94	0.87	0.86	3	-
GCA_905478725.1	s__HTCC2207 sp905478725	78.1659	180	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000511875.1	s__HTCC2207 sp000511875	77.9236	242	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858295.1	s__HTCC2207 sp017858295	77.8582	176	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_002335945.1	s__HTCC2207 sp002335945	77.8367	155	600	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	77.6933	87	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002334915.1	s__HTCC2207 sp002334915	77.4135	146	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_905182265.1	s__HTCC2207 sp905182265	77.3359	130	600	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	77.2187	140	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_002685715.1	s__HTCC2207 sp002685715	76.673	69	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:25:48,056] [INFO] GTDB search result was written to OceanDNA-b39347/result_gtdb.tsv
[2023-03-18 01:25:48,056] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:25:48,057] [INFO] DFAST_QC result json was written to OceanDNA-b39347/dqc_result.json
[2023-03-18 01:25:48,057] [INFO] DFAST_QC completed!
[2023-03-18 01:25:48,057] [INFO] Total running time: 0h1m8s