[2023-03-18 04:54:25,335] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:54:25,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:54:25,335] [INFO] DQC Reference Directory: /var/lib/cwl/stga701cb16-83d5-46c0-9790-2e3a552e8fca/dqc_reference
[2023-03-18 04:54:26,988] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:54:26,989] [INFO] Task started: Prodigal
[2023-03-18 04:54:26,989] [INFO] Running command: cat /var/lib/cwl/stg8649f9be-cb01-4006-ab22-b80b7fe1095d/OceanDNA-b18842.fa | prodigal -d OceanDNA-b18842/cds.fna -a OceanDNA-b18842/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:54:35,889] [INFO] Task succeeded: Prodigal
[2023-03-18 04:54:35,890] [INFO] Task started: HMMsearch
[2023-03-18 04:54:35,890] [INFO] Running command: hmmsearch --tblout OceanDNA-b18842/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga701cb16-83d5-46c0-9790-2e3a552e8fca/dqc_reference/reference_markers.hmm OceanDNA-b18842/protein.faa > /dev/null
[2023-03-18 04:54:36,050] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:54:36,051] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8649f9be-cb01-4006-ab22-b80b7fe1095d/OceanDNA-b18842.fa]
[2023-03-18 04:54:36,064] [INFO] Query marker FASTA was written to OceanDNA-b18842/markers.fasta
[2023-03-18 04:54:36,065] [INFO] Task started: Blastn
[2023-03-18 04:54:36,065] [INFO] Running command: blastn -query OceanDNA-b18842/markers.fasta -db /var/lib/cwl/stga701cb16-83d5-46c0-9790-2e3a552e8fca/dqc_reference/reference_markers.fasta -out OceanDNA-b18842/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:54:36,549] [INFO] Task succeeded: Blastn
[2023-03-18 04:54:36,549] [INFO] Selected 10 target genomes.
[2023-03-18 04:54:36,550] [INFO] Target genome list was writen to OceanDNA-b18842/target_genomes.txt
[2023-03-18 04:54:36,558] [INFO] Task started: fastANI
[2023-03-18 04:54:36,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg8649f9be-cb01-4006-ab22-b80b7fe1095d/OceanDNA-b18842.fa --refList OceanDNA-b18842/target_genomes.txt --output OceanDNA-b18842/fastani_result.tsv --threads 1
[2023-03-18 04:54:42,260] [INFO] Task succeeded: fastANI
[2023-03-18 04:54:42,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga701cb16-83d5-46c0-9790-2e3a552e8fca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:54:42,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga701cb16-83d5-46c0-9790-2e3a552e8fca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:54:42,261] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:54:42,261] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:54:42,261] [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 04:54:42,261] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18842/tc_result.tsv
[2023-03-18 04:54:42,261] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:54:42,261] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:54:42,261] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga701cb16-83d5-46c0-9790-2e3a552e8fca/dqc_reference/checkm_data
[2023-03-18 04:54:42,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:54:42,413] [INFO] Task started: CheckM
[2023-03-18 04:54:42,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18842/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18842/checkm_input OceanDNA-b18842/checkm_result
[2023-03-18 04:55:09,316] [INFO] Task succeeded: CheckM
[2023-03-18 04:55:09,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:55:09,331] [INFO] ===== Completeness check finished =====
[2023-03-18 04:55:09,331] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:55:09,331] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18842/markers.fasta)
[2023-03-18 04:55:09,332] [INFO] Task started: Blastn
[2023-03-18 04:55:09,333] [INFO] Running command: blastn -query OceanDNA-b18842/markers.fasta -db /var/lib/cwl/stga701cb16-83d5-46c0-9790-2e3a552e8fca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18842/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:55:09,978] [INFO] Task succeeded: Blastn
[2023-03-18 04:55:10,012] [INFO] Selected 13 target genomes.
[2023-03-18 04:55:10,013] [INFO] Target genome list was writen to OceanDNA-b18842/target_genomes_gtdb.txt
[2023-03-18 04:55:10,049] [INFO] Task started: fastANI
[2023-03-18 04:55:10,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg8649f9be-cb01-4006-ab22-b80b7fe1095d/OceanDNA-b18842.fa --refList OceanDNA-b18842/target_genomes_gtdb.txt --output OceanDNA-b18842/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:55:14,961] [INFO] Task succeeded: fastANI
[2023-03-18 04:55:14,966] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:55:14,966] [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_002716525.1	s__TCS55 sp002716525	92.8481	306	536	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964665.1	s__TCS55 sp012964665	90.9002	403	536	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.32	99.03	0.83	0.81	3	-
GCA_002471845.1	s__TCS55 sp002471845	78.2387	137	536	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.96	99.93	0.96	0.96	5	-
GCA_002715035.1	s__TCS55 sp002715035	77.8552	74	536	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	96.36	95.92	0.81	0.67	4	-
GCA_001577025.1	s__TCS55 sp001577025	77.5493	79	536	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	95.80	95.01	0.79	0.74	7	-
GCA_018647265.1	s__TCS55 sp018647265	76.9585	100	536	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.87	99.79	0.92	0.89	15	-
GCA_014382015.1	s__TCS55 sp014382015	76.6951	120	536	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.95	99.95	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-18 04:55:14,975] [INFO] GTDB search result was written to OceanDNA-b18842/result_gtdb.tsv
[2023-03-18 04:55:14,977] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:55:14,978] [INFO] DFAST_QC result json was written to OceanDNA-b18842/dqc_result.json
[2023-03-18 04:55:14,978] [INFO] DFAST_QC completed!
[2023-03-18 04:55:14,978] [INFO] Total running time: 0h0m50s