[2023-03-18 22:53:23,464] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:53:23,465] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:53:23,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg75c5418d-62f2-48e5-95f5-d8945b1024db/dqc_reference
[2023-03-18 22:53:25,705] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:53:25,706] [INFO] Task started: Prodigal
[2023-03-18 22:53:25,706] [INFO] Running command: cat /var/lib/cwl/stgdeb2c84e-39df-4bbd-9117-1f21652178dd/OceanDNA-b20556.fa | prodigal -d OceanDNA-b20556/cds.fna -a OceanDNA-b20556/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:53:32,916] [INFO] Task succeeded: Prodigal
[2023-03-18 22:53:32,916] [INFO] Task started: HMMsearch
[2023-03-18 22:53:32,916] [INFO] Running command: hmmsearch --tblout OceanDNA-b20556/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75c5418d-62f2-48e5-95f5-d8945b1024db/dqc_reference/reference_markers.hmm OceanDNA-b20556/protein.faa > /dev/null
[2023-03-18 22:53:33,091] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:53:33,092] [INFO] Found 6/6 markers.
[2023-03-18 22:53:33,102] [INFO] Query marker FASTA was written to OceanDNA-b20556/markers.fasta
[2023-03-18 22:53:33,103] [INFO] Task started: Blastn
[2023-03-18 22:53:33,104] [INFO] Running command: blastn -query OceanDNA-b20556/markers.fasta -db /var/lib/cwl/stg75c5418d-62f2-48e5-95f5-d8945b1024db/dqc_reference/reference_markers.fasta -out OceanDNA-b20556/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:53:35,060] [INFO] Task succeeded: Blastn
[2023-03-18 22:53:35,061] [INFO] Selected 20 target genomes.
[2023-03-18 22:53:35,061] [INFO] Target genome list was writen to OceanDNA-b20556/target_genomes.txt
[2023-03-18 22:53:35,132] [INFO] Task started: fastANI
[2023-03-18 22:53:35,132] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeb2c84e-39df-4bbd-9117-1f21652178dd/OceanDNA-b20556.fa --refList OceanDNA-b20556/target_genomes.txt --output OceanDNA-b20556/fastani_result.tsv --threads 1
[2023-03-18 22:53:47,418] [INFO] Task succeeded: fastANI
[2023-03-18 22:53:47,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75c5418d-62f2-48e5-95f5-d8945b1024db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:53:47,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75c5418d-62f2-48e5-95f5-d8945b1024db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:53:47,419] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:53:47,419] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:53:47,419] [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 22:53:47,419] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20556/tc_result.tsv
[2023-03-18 22:53:47,420] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:53:47,420] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:53:47,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75c5418d-62f2-48e5-95f5-d8945b1024db/dqc_reference/checkm_data
[2023-03-18 22:53:47,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:53:47,478] [INFO] Task started: CheckM
[2023-03-18 22:53:47,479] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20556/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20556/checkm_input OceanDNA-b20556/checkm_result
[2023-03-18 22:54:12,421] [INFO] Task succeeded: CheckM
[2023-03-18 22:54:12,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:54:12,423] [INFO] ===== Completeness check finished =====
[2023-03-18 22:54:12,423] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:54:12,423] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20556/markers.fasta)
[2023-03-18 22:54:12,424] [INFO] Task started: Blastn
[2023-03-18 22:54:12,424] [INFO] Running command: blastn -query OceanDNA-b20556/markers.fasta -db /var/lib/cwl/stg75c5418d-62f2-48e5-95f5-d8945b1024db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20556/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:54:13,476] [INFO] Task succeeded: Blastn
[2023-03-18 22:54:13,477] [INFO] Selected 22 target genomes.
[2023-03-18 22:54:13,477] [INFO] Target genome list was writen to OceanDNA-b20556/target_genomes_gtdb.txt
[2023-03-18 22:54:13,506] [INFO] Task started: fastANI
[2023-03-18 22:54:13,506] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeb2c84e-39df-4bbd-9117-1f21652178dd/OceanDNA-b20556.fa --refList OceanDNA-b20556/target_genomes_gtdb.txt --output OceanDNA-b20556/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:54:20,353] [INFO] Task succeeded: fastANI
[2023-03-18 22:54:20,358] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:54:20,359] [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_002717625.1	s__GCA-2717625 sp002717625	78.2704	206	477	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-2717625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707765.1	s__GCA-002718585 sp002707765	77.6909	127	477	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002718585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718585.1	s__GCA-002718585 sp002718585	77.4688	167	477	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002718585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705605.1	s__GCA-002707645 sp002705605	76.3999	81	477	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707645.1	s__GCA-002707645 sp002707645	76.2038	67	477	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704685.1	s__GCA-002707645 sp002704685	76.127	80	477	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002693365.1	s__GCA-002707645 sp002693365	76.0023	66	477	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	98.01	98.01	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:54:20,359] [INFO] GTDB search result was written to OceanDNA-b20556/result_gtdb.tsv
[2023-03-18 22:54:20,359] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:54:20,360] [INFO] DFAST_QC result json was written to OceanDNA-b20556/dqc_result.json
[2023-03-18 22:54:20,360] [INFO] DFAST_QC completed!
[2023-03-18 22:54:20,360] [INFO] Total running time: 0h0m57s