[2023-03-17 07:47:46,526] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:47:46,526] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:47:46,526] [INFO] DQC Reference Directory: /var/lib/cwl/stgd486d9c5-90b7-4327-87ec-4bcdc87f9d46/dqc_reference
[2023-03-17 07:47:47,625] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:47:47,625] [INFO] Task started: Prodigal
[2023-03-17 07:47:47,625] [INFO] Running command: cat /var/lib/cwl/stg819f028c-3d1c-470f-8abf-3875940d2c1d/OceanDNA-b31279.fa | prodigal -d OceanDNA-b31279/cds.fna -a OceanDNA-b31279/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:48:07,293] [INFO] Task succeeded: Prodigal
[2023-03-17 07:48:07,294] [INFO] Task started: HMMsearch
[2023-03-17 07:48:07,294] [INFO] Running command: hmmsearch --tblout OceanDNA-b31279/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd486d9c5-90b7-4327-87ec-4bcdc87f9d46/dqc_reference/reference_markers.hmm OceanDNA-b31279/protein.faa > /dev/null
[2023-03-17 07:48:07,486] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:48:07,487] [INFO] Found 6/6 markers.
[2023-03-17 07:48:07,508] [INFO] Query marker FASTA was written to OceanDNA-b31279/markers.fasta
[2023-03-17 07:48:07,508] [INFO] Task started: Blastn
[2023-03-17 07:48:07,509] [INFO] Running command: blastn -query OceanDNA-b31279/markers.fasta -db /var/lib/cwl/stgd486d9c5-90b7-4327-87ec-4bcdc87f9d46/dqc_reference/reference_markers.fasta -out OceanDNA-b31279/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:48:08,137] [INFO] Task succeeded: Blastn
[2023-03-17 07:48:08,137] [INFO] Selected 30 target genomes.
[2023-03-17 07:48:08,138] [INFO] Target genome list was writen to OceanDNA-b31279/target_genomes.txt
[2023-03-17 07:48:08,151] [INFO] Task started: fastANI
[2023-03-17 07:48:08,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg819f028c-3d1c-470f-8abf-3875940d2c1d/OceanDNA-b31279.fa --refList OceanDNA-b31279/target_genomes.txt --output OceanDNA-b31279/fastani_result.tsv --threads 1
[2023-03-17 07:48:30,323] [INFO] Task succeeded: fastANI
[2023-03-17 07:48:30,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd486d9c5-90b7-4327-87ec-4bcdc87f9d46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:48:30,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd486d9c5-90b7-4327-87ec-4bcdc87f9d46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:48:30,324] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:48:30,324] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:48:30,324] [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 07:48:30,324] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31279/tc_result.tsv
[2023-03-17 07:48:30,324] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:48:30,324] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:48:30,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd486d9c5-90b7-4327-87ec-4bcdc87f9d46/dqc_reference/checkm_data
[2023-03-17 07:48:30,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:48:30,331] [INFO] Task started: CheckM
[2023-03-17 07:48:30,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31279/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31279/checkm_input OceanDNA-b31279/checkm_result
[2023-03-17 07:49:20,969] [INFO] Task succeeded: CheckM
[2023-03-17 07:49:20,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.36%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 07:49:20,972] [INFO] ===== Completeness check finished =====
[2023-03-17 07:49:20,972] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:49:20,972] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31279/markers.fasta)
[2023-03-17 07:49:20,972] [INFO] Task started: Blastn
[2023-03-17 07:49:20,972] [INFO] Running command: blastn -query OceanDNA-b31279/markers.fasta -db /var/lib/cwl/stgd486d9c5-90b7-4327-87ec-4bcdc87f9d46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31279/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:49:22,055] [INFO] Task succeeded: Blastn
[2023-03-17 07:49:22,056] [INFO] Selected 23 target genomes.
[2023-03-17 07:49:22,056] [INFO] Target genome list was writen to OceanDNA-b31279/target_genomes_gtdb.txt
[2023-03-17 07:49:22,428] [INFO] Task started: fastANI
[2023-03-17 07:49:22,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg819f028c-3d1c-470f-8abf-3875940d2c1d/OceanDNA-b31279.fa --refList OceanDNA-b31279/target_genomes_gtdb.txt --output OceanDNA-b31279/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:49:37,437] [INFO] Task succeeded: fastANI
[2023-03-17 07:49:37,441] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:49:37,441] [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_002389175.1	s__UBA4479 sp002389175	99.6537	832	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017857825.1	s__UBA4479 sp017857825	77.314	132	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389385.1	s__UBA4479 sp002389385	76.4838	84	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.63	99.57	0.92	0.85	8	-
GCA_017640505.1	s__UBA4479 sp017640505	76.2346	127	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.97	99.97	1.00	1.00	2	-
GCA_017644185.1	s__UBA4479 sp017644185	76.1507	113	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:49:37,442] [INFO] GTDB search result was written to OceanDNA-b31279/result_gtdb.tsv
[2023-03-17 07:49:37,442] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:49:37,442] [INFO] DFAST_QC result json was written to OceanDNA-b31279/dqc_result.json
[2023-03-17 07:49:37,442] [INFO] DFAST_QC completed!
[2023-03-17 07:49:37,442] [INFO] Total running time: 0h1m51s