[2023-03-19 04:59:58,321] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:59:58,321] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:59:58,321] [INFO] DQC Reference Directory: /var/lib/cwl/stg56807840-8894-4fd8-99ba-a381ccea2ca3/dqc_reference
[2023-03-19 04:59:59,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:59:59,404] [INFO] Task started: Prodigal
[2023-03-19 04:59:59,404] [INFO] Running command: cat /var/lib/cwl/stgae8d3a1f-8fd9-49be-923c-d840e2d1384e/OceanDNA-b25685.fa | prodigal -d OceanDNA-b25685/cds.fna -a OceanDNA-b25685/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:00:05,109] [INFO] Task succeeded: Prodigal
[2023-03-19 05:00:05,109] [INFO] Task started: HMMsearch
[2023-03-19 05:00:05,109] [INFO] Running command: hmmsearch --tblout OceanDNA-b25685/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56807840-8894-4fd8-99ba-a381ccea2ca3/dqc_reference/reference_markers.hmm OceanDNA-b25685/protein.faa > /dev/null
[2023-03-19 05:00:05,273] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:00:05,273] [INFO] Found 6/6 markers.
[2023-03-19 05:00:05,282] [INFO] Query marker FASTA was written to OceanDNA-b25685/markers.fasta
[2023-03-19 05:00:05,284] [INFO] Task started: Blastn
[2023-03-19 05:00:05,284] [INFO] Running command: blastn -query OceanDNA-b25685/markers.fasta -db /var/lib/cwl/stg56807840-8894-4fd8-99ba-a381ccea2ca3/dqc_reference/reference_markers.fasta -out OceanDNA-b25685/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:00:05,831] [INFO] Task succeeded: Blastn
[2023-03-19 05:00:05,831] [INFO] Selected 15 target genomes.
[2023-03-19 05:00:05,831] [INFO] Target genome list was writen to OceanDNA-b25685/target_genomes.txt
[2023-03-19 05:00:05,841] [INFO] Task started: fastANI
[2023-03-19 05:00:05,841] [INFO] Running command: fastANI --query /var/lib/cwl/stgae8d3a1f-8fd9-49be-923c-d840e2d1384e/OceanDNA-b25685.fa --refList OceanDNA-b25685/target_genomes.txt --output OceanDNA-b25685/fastani_result.tsv --threads 1
[2023-03-19 05:00:12,402] [INFO] Task succeeded: fastANI
[2023-03-19 05:00:12,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56807840-8894-4fd8-99ba-a381ccea2ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:00:12,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56807840-8894-4fd8-99ba-a381ccea2ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:00:12,403] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:00:12,403] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:00:12,403] [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
--------------------------------------------------------------------------------
[2023-03-19 05:00:12,900] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25685/tc_result.tsv
[2023-03-19 05:00:12,902] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:00:12,902] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:00:12,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56807840-8894-4fd8-99ba-a381ccea2ca3/dqc_reference/checkm_data
[2023-03-19 05:00:12,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:00:13,079] [INFO] Task started: CheckM
[2023-03-19 05:00:13,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25685/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25685/checkm_input OceanDNA-b25685/checkm_result
[2023-03-19 05:00:32,956] [INFO] Task succeeded: CheckM
[2023-03-19 05:00:32,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:00:32,958] [INFO] ===== Completeness check finished =====
[2023-03-19 05:00:32,958] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:00:32,959] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25685/markers.fasta)
[2023-03-19 05:00:32,960] [INFO] Task started: Blastn
[2023-03-19 05:00:32,960] [INFO] Running command: blastn -query OceanDNA-b25685/markers.fasta -db /var/lib/cwl/stg56807840-8894-4fd8-99ba-a381ccea2ca3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25685/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:00:33,679] [INFO] Task succeeded: Blastn
[2023-03-19 05:00:33,680] [INFO] Selected 23 target genomes.
[2023-03-19 05:00:33,680] [INFO] Target genome list was writen to OceanDNA-b25685/target_genomes_gtdb.txt
[2023-03-19 05:00:33,693] [INFO] Task started: fastANI
[2023-03-19 05:00:33,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgae8d3a1f-8fd9-49be-923c-d840e2d1384e/OceanDNA-b25685.fa --refList OceanDNA-b25685/target_genomes_gtdb.txt --output OceanDNA-b25685/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:00:38,351] [INFO] Task succeeded: fastANI
[2023-03-19 05:00:38,356] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:00:38,356] [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
GCF_000195085.1	s__IMCC9063 sp000195085	94.8464	263	284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638205.1	s__IMCC9063 sp008638205	93.4634	252	284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	97.30	96.70	0.84	0.65	4	-
GCA_008638015.1	s__IMCC9063 sp008638015	78.101	121	284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	99.18	98.68	0.91	0.88	9	-
GCA_008638225.1	s__IMCC9063 sp008638225	77.8536	114	284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	99.77	99.77	0.92	0.92	2	-
GCA_018402735.1	s__IMCC9063 sp000750175	77.769	130	284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	99.21	99.21	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-19 05:00:38,356] [INFO] GTDB search result was written to OceanDNA-b25685/result_gtdb.tsv
[2023-03-19 05:00:38,356] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:00:38,357] [INFO] DFAST_QC result json was written to OceanDNA-b25685/dqc_result.json
[2023-03-19 05:00:38,357] [INFO] DFAST_QC completed!
[2023-03-19 05:00:38,357] [INFO] Total running time: 0h0m40s