[2023-03-15 23:38:54,794] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:38:54,801] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:38:54,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg84962539-ac72-4b40-b709-d2db543145e8/dqc_reference
[2023-03-15 23:38:55,908] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:38:55,908] [INFO] Task started: Prodigal
[2023-03-15 23:38:55,909] [INFO] Running command: cat /var/lib/cwl/stg5430cda7-3fd8-4eea-aa2c-2168f49f4424/OceanDNA-b37895.fa | prodigal -d OceanDNA-b37895/cds.fna -a OceanDNA-b37895/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:39:06,693] [INFO] Task succeeded: Prodigal
[2023-03-15 23:39:06,694] [INFO] Task started: HMMsearch
[2023-03-15 23:39:06,694] [INFO] Running command: hmmsearch --tblout OceanDNA-b37895/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84962539-ac72-4b40-b709-d2db543145e8/dqc_reference/reference_markers.hmm OceanDNA-b37895/protein.faa > /dev/null
[2023-03-15 23:39:06,874] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:39:06,875] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5430cda7-3fd8-4eea-aa2c-2168f49f4424/OceanDNA-b37895.fa]
[2023-03-15 23:39:06,987] [INFO] Query marker FASTA was written to OceanDNA-b37895/markers.fasta
[2023-03-15 23:39:06,988] [INFO] Task started: Blastn
[2023-03-15 23:39:06,988] [INFO] Running command: blastn -query OceanDNA-b37895/markers.fasta -db /var/lib/cwl/stg84962539-ac72-4b40-b709-d2db543145e8/dqc_reference/reference_markers.fasta -out OceanDNA-b37895/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:39:07,532] [INFO] Task succeeded: Blastn
[2023-03-15 23:39:07,557] [INFO] Selected 32 target genomes.
[2023-03-15 23:39:07,557] [INFO] Target genome list was writen to OceanDNA-b37895/target_genomes.txt
[2023-03-15 23:39:07,575] [INFO] Task started: fastANI
[2023-03-15 23:39:07,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg5430cda7-3fd8-4eea-aa2c-2168f49f4424/OceanDNA-b37895.fa --refList OceanDNA-b37895/target_genomes.txt --output OceanDNA-b37895/fastani_result.tsv --threads 1
[2023-03-15 23:39:26,467] [INFO] Task succeeded: fastANI
[2023-03-15 23:39:26,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84962539-ac72-4b40-b709-d2db543145e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:39:26,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84962539-ac72-4b40-b709-d2db543145e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:39:26,468] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:39:26,468] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:39:26,468] [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
--------------------------------------------------------------------------------
[2023-03-15 23:39:26,472] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37895/tc_result.tsv
[2023-03-15 23:39:26,478] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:39:26,479] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:39:26,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84962539-ac72-4b40-b709-d2db543145e8/dqc_reference/checkm_data
[2023-03-15 23:39:26,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:39:26,497] [INFO] Task started: CheckM
[2023-03-15 23:39:26,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37895/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37895/checkm_input OceanDNA-b37895/checkm_result
[2023-03-15 23:39:58,615] [INFO] Task succeeded: CheckM
[2023-03-15 23:39:58,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 5.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:39:58,738] [INFO] ===== Completeness check finished =====
[2023-03-15 23:39:58,738] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:39:58,738] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37895/markers.fasta)
[2023-03-15 23:39:58,739] [INFO] Task started: Blastn
[2023-03-15 23:39:58,739] [INFO] Running command: blastn -query OceanDNA-b37895/markers.fasta -db /var/lib/cwl/stg84962539-ac72-4b40-b709-d2db543145e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37895/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:39:59,422] [INFO] Task succeeded: Blastn
[2023-03-15 23:39:59,435] [INFO] Selected 21 target genomes.
[2023-03-15 23:39:59,435] [INFO] Target genome list was writen to OceanDNA-b37895/target_genomes_gtdb.txt
[2023-03-15 23:39:59,459] [INFO] Task started: fastANI
[2023-03-15 23:39:59,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg5430cda7-3fd8-4eea-aa2c-2168f49f4424/OceanDNA-b37895.fa --refList OceanDNA-b37895/target_genomes_gtdb.txt --output OceanDNA-b37895/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:40:09,690] [INFO] Task succeeded: fastANI
[2023-03-15 23:40:09,697] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:40:09,697] [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_002390485.1	s__Luminiphilus sp002390485	91.0884	508	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.01	96.90	0.92	0.88	5	-
GCA_018666295.1	s__Luminiphilus sp018666295	91.0567	447	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.15	99.01	0.84	0.82	4	-
GCA_009937065.1	s__Luminiphilus sp009937065	78.2771	93	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689915.1	s__Luminiphilus sp002689915	77.8001	68	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	100.00	100.00	0.97	0.97	2	-
GCA_902613175.1	s__Luminiphilus sp902613175	77.7126	64	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000227505.4	s__Luminiphilus sp000227505	77.465	81	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523185.1	s__Luminiphilus sp003523185	77.3434	97	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862405.1	s__Luminiphilus sp002862405	77.2257	76	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.70	95.58	0.78	0.76	4	-
GCA_902547755.1	s__Luminiphilus sp902547755	76.8672	81	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469785.1	s__Luminiphilus sp002469785	76.1523	70	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:40:09,701] [INFO] GTDB search result was written to OceanDNA-b37895/result_gtdb.tsv
[2023-03-15 23:40:09,704] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:40:09,715] [INFO] DFAST_QC result json was written to OceanDNA-b37895/dqc_result.json
[2023-03-15 23:40:09,715] [INFO] DFAST_QC completed!
[2023-03-15 23:40:09,715] [INFO] Total running time: 0h1m15s