[2023-03-18 01:59:39,744] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:59:39,744] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:59:39,744] [INFO] DQC Reference Directory: /var/lib/cwl/stg466ccecb-dfa8-4d30-a770-ccc8620ff0dc/dqc_reference
[2023-03-18 01:59:40,972] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:59:40,972] [INFO] Task started: Prodigal
[2023-03-18 01:59:40,972] [INFO] Running command: cat /var/lib/cwl/stg06ac8c71-59e1-47a1-92a2-de6878ff0bf0/OceanDNA-b19130.fa | prodigal -d OceanDNA-b19130/cds.fna -a OceanDNA-b19130/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:59:51,585] [INFO] Task succeeded: Prodigal
[2023-03-18 01:59:51,585] [INFO] Task started: HMMsearch
[2023-03-18 01:59:51,585] [INFO] Running command: hmmsearch --tblout OceanDNA-b19130/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg466ccecb-dfa8-4d30-a770-ccc8620ff0dc/dqc_reference/reference_markers.hmm OceanDNA-b19130/protein.faa > /dev/null
[2023-03-18 01:59:51,744] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:59:51,745] [INFO] Found 6/6 markers.
[2023-03-18 01:59:51,761] [INFO] Query marker FASTA was written to OceanDNA-b19130/markers.fasta
[2023-03-18 01:59:51,762] [INFO] Task started: Blastn
[2023-03-18 01:59:51,762] [INFO] Running command: blastn -query OceanDNA-b19130/markers.fasta -db /var/lib/cwl/stg466ccecb-dfa8-4d30-a770-ccc8620ff0dc/dqc_reference/reference_markers.fasta -out OceanDNA-b19130/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:59:52,271] [INFO] Task succeeded: Blastn
[2023-03-18 01:59:52,275] [INFO] Selected 14 target genomes.
[2023-03-18 01:59:52,275] [INFO] Target genome list was writen to OceanDNA-b19130/target_genomes.txt
[2023-03-18 01:59:52,288] [INFO] Task started: fastANI
[2023-03-18 01:59:52,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg06ac8c71-59e1-47a1-92a2-de6878ff0bf0/OceanDNA-b19130.fa --refList OceanDNA-b19130/target_genomes.txt --output OceanDNA-b19130/fastani_result.tsv --threads 1
[2023-03-18 01:59:59,980] [INFO] Task succeeded: fastANI
[2023-03-18 01:59:59,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg466ccecb-dfa8-4d30-a770-ccc8620ff0dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:59:59,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg466ccecb-dfa8-4d30-a770-ccc8620ff0dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:59:59,981] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:59:59,981] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:59:59,981] [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 01:59:59,984] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19130/tc_result.tsv
[2023-03-18 01:59:59,989] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:59:59,989] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:59:59,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg466ccecb-dfa8-4d30-a770-ccc8620ff0dc/dqc_reference/checkm_data
[2023-03-18 01:59:59,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:59:59,996] [INFO] Task started: CheckM
[2023-03-18 01:59:59,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19130/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19130/checkm_input OceanDNA-b19130/checkm_result
[2023-03-18 02:00:31,168] [INFO] Task succeeded: CheckM
[2023-03-18 02:00:31,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:00:31,200] [INFO] ===== Completeness check finished =====
[2023-03-18 02:00:31,200] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:00:31,200] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19130/markers.fasta)
[2023-03-18 02:00:31,202] [INFO] Task started: Blastn
[2023-03-18 02:00:31,202] [INFO] Running command: blastn -query OceanDNA-b19130/markers.fasta -db /var/lib/cwl/stg466ccecb-dfa8-4d30-a770-ccc8620ff0dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19130/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:00:31,952] [INFO] Task succeeded: Blastn
[2023-03-18 02:00:31,956] [INFO] Selected 14 target genomes.
[2023-03-18 02:00:31,957] [INFO] Target genome list was writen to OceanDNA-b19130/target_genomes_gtdb.txt
[2023-03-18 02:00:31,973] [INFO] Task started: fastANI
[2023-03-18 02:00:31,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg06ac8c71-59e1-47a1-92a2-de6878ff0bf0/OceanDNA-b19130.fa --refList OceanDNA-b19130/target_genomes_gtdb.txt --output OceanDNA-b19130/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:00:36,246] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:36,252] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:00:36,252] [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_001577025.1	s__TCS55 sp001577025	95.047	437	613	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	95.80	95.01	0.79	0.74	7	conclusive
GCA_016845785.1	s__TCS55 sp016845785	81.7274	360	613	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704905.1	s__TCS55 sp002704905	77.2467	78	613	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647265.1	s__TCS55 sp018647265	76.9472	148	613	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.87	99.79	0.92	0.89	15	-
GCA_018674655.1	s__TCS55 sp018674655	76.8472	114	613	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.73	99.62	0.91	0.80	15	-
GCA_002716525.1	s__TCS55 sp002716525	76.7052	69	613	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715035.1	s__TCS55 sp002715035	76.6954	84	613	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	96.36	95.92	0.81	0.67	4	-
GCA_014382015.1	s__TCS55 sp014382015	76.5664	138	613	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.95	99.95	0.97	0.96	3	-
GCA_012964665.1	s__TCS55 sp012964665	76.405	79	613	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.32	99.03	0.83	0.81	3	-
--------------------------------------------------------------------------------
[2023-03-18 02:00:36,254] [INFO] GTDB search result was written to OceanDNA-b19130/result_gtdb.tsv
[2023-03-18 02:00:36,259] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:00:36,262] [INFO] DFAST_QC result json was written to OceanDNA-b19130/dqc_result.json
[2023-03-18 02:00:36,262] [INFO] DFAST_QC completed!
[2023-03-18 02:00:36,262] [INFO] Total running time: 0h0m57s