[2023-03-16 04:05:21,950] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:21,951] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:21,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e7ea5c7-8a1b-4c3e-a1ae-ccc86889797e/dqc_reference
[2023-03-16 04:05:23,029] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:23,029] [INFO] Task started: Prodigal
[2023-03-16 04:05:23,029] [INFO] Running command: cat /var/lib/cwl/stg9f06c32f-9811-4079-9887-b195edd3d619/OceanDNA-b39405.fa | prodigal -d OceanDNA-b39405/cds.fna -a OceanDNA-b39405/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:34,805] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:34,805] [INFO] Task started: HMMsearch
[2023-03-16 04:05:34,805] [INFO] Running command: hmmsearch --tblout OceanDNA-b39405/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e7ea5c7-8a1b-4c3e-a1ae-ccc86889797e/dqc_reference/reference_markers.hmm OceanDNA-b39405/protein.faa > /dev/null
[2023-03-16 04:05:34,999] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:34,999] [INFO] Found 6/6 markers.
[2023-03-16 04:05:35,012] [INFO] Query marker FASTA was written to OceanDNA-b39405/markers.fasta
[2023-03-16 04:05:35,012] [INFO] Task started: Blastn
[2023-03-16 04:05:35,013] [INFO] Running command: blastn -query OceanDNA-b39405/markers.fasta -db /var/lib/cwl/stg7e7ea5c7-8a1b-4c3e-a1ae-ccc86889797e/dqc_reference/reference_markers.fasta -out OceanDNA-b39405/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:35,623] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:35,624] [INFO] Selected 38 target genomes.
[2023-03-16 04:05:35,624] [INFO] Target genome list was writen to OceanDNA-b39405/target_genomes.txt
[2023-03-16 04:05:35,642] [INFO] Task started: fastANI
[2023-03-16 04:05:35,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f06c32f-9811-4079-9887-b195edd3d619/OceanDNA-b39405.fa --refList OceanDNA-b39405/target_genomes.txt --output OceanDNA-b39405/fastani_result.tsv --threads 1
[2023-03-16 04:06:00,424] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:00,424] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e7ea5c7-8a1b-4c3e-a1ae-ccc86889797e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:06:00,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e7ea5c7-8a1b-4c3e-a1ae-ccc86889797e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:06:00,425] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:06:00,425] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:06:00,425] [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
--------------------------------------------------------------------------------
[2023-03-16 04:06:00,425] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39405/tc_result.tsv
[2023-03-16 04:06:00,425] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:06:00,425] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:06:00,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e7ea5c7-8a1b-4c3e-a1ae-ccc86889797e/dqc_reference/checkm_data
[2023-03-16 04:06:00,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:06:00,431] [INFO] Task started: CheckM
[2023-03-16 04:06:00,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39405/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39405/checkm_input OceanDNA-b39405/checkm_result
[2023-03-16 04:06:33,569] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:33,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:33,571] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:33,571] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:33,571] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39405/markers.fasta)
[2023-03-16 04:06:33,571] [INFO] Task started: Blastn
[2023-03-16 04:06:33,571] [INFO] Running command: blastn -query OceanDNA-b39405/markers.fasta -db /var/lib/cwl/stg7e7ea5c7-8a1b-4c3e-a1ae-ccc86889797e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39405/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:34,599] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:34,600] [INFO] Selected 24 target genomes.
[2023-03-16 04:06:34,600] [INFO] Target genome list was writen to OceanDNA-b39405/target_genomes_gtdb.txt
[2023-03-16 04:06:34,698] [INFO] Task started: fastANI
[2023-03-16 04:06:34,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f06c32f-9811-4079-9887-b195edd3d619/OceanDNA-b39405.fa --refList OceanDNA-b39405/target_genomes_gtdb.txt --output OceanDNA-b39405/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:45,551] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:45,561] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:06:45,561] [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_017858135.1	s__HTCC2207 sp017858135	78.7295	298	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.94	0.87	0.86	3	-
GCA_000153445.1	s__HTCC2207 sp000153445	77.9807	261	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_000511875.1	s__HTCC2207 sp000511875	77.9392	250	660	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	77.8288	187	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_905478725.1	s__HTCC2207 sp905478725	77.7237	176	660	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	77.6593	227	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001438605.1	s__HTCC2207 sp001438605	77.2162	147	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.34	98.71	0.91	0.87	10	-
GCA_905182265.1	s__HTCC2207 sp905182265	77.1813	110	660	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	77.0738	123	660	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	77.0385	69	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018654575.1	s__HTCC2207 sp018654575	77.0302	50	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.63	99.50	0.93	0.91	15	-
GCA_018607545.1	s__HTCC2207 sp018607545	76.9369	97	660	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	76.8487	123	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_905182245.1	s__HTCC2207 sp905182245	76.809	74	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335945.1	s__HTCC2207 sp002335945	76.5805	130	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_002378645.1	s__HTCC2207 sp002378645	76.3883	131	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:45,561] [INFO] GTDB search result was written to OceanDNA-b39405/result_gtdb.tsv
[2023-03-16 04:06:45,561] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:45,562] [INFO] DFAST_QC result json was written to OceanDNA-b39405/dqc_result.json
[2023-03-16 04:06:45,563] [INFO] DFAST_QC completed!
[2023-03-16 04:06:45,563] [INFO] Total running time: 0h1m24s