[2023-03-18 05:05:06,221] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:05:06,226] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:05:06,226] [INFO] DQC Reference Directory: /var/lib/cwl/stg6eceb73d-272a-4ccf-a7e3-d174c080d68d/dqc_reference
[2023-03-18 05:05:07,334] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:05:07,334] [INFO] Task started: Prodigal
[2023-03-18 05:05:07,335] [INFO] Running command: cat /var/lib/cwl/stg1c7576c7-6fcb-4d7b-9730-4530ce87bb4f/OceanDNA-b20538.fa | prodigal -d OceanDNA-b20538/cds.fna -a OceanDNA-b20538/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:05:13,869] [INFO] Task succeeded: Prodigal
[2023-03-18 05:05:13,869] [INFO] Task started: HMMsearch
[2023-03-18 05:05:13,869] [INFO] Running command: hmmsearch --tblout OceanDNA-b20538/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6eceb73d-272a-4ccf-a7e3-d174c080d68d/dqc_reference/reference_markers.hmm OceanDNA-b20538/protein.faa > /dev/null
[2023-03-18 05:05:14,036] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:05:14,037] [INFO] Found 6/6 markers.
[2023-03-18 05:05:14,081] [INFO] Query marker FASTA was written to OceanDNA-b20538/markers.fasta
[2023-03-18 05:05:14,082] [INFO] Task started: Blastn
[2023-03-18 05:05:14,082] [INFO] Running command: blastn -query OceanDNA-b20538/markers.fasta -db /var/lib/cwl/stg6eceb73d-272a-4ccf-a7e3-d174c080d68d/dqc_reference/reference_markers.fasta -out OceanDNA-b20538/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:05:14,592] [INFO] Task succeeded: Blastn
[2023-03-18 05:05:14,600] [INFO] Selected 16 target genomes.
[2023-03-18 05:05:14,600] [INFO] Target genome list was writen to OceanDNA-b20538/target_genomes.txt
[2023-03-18 05:05:14,612] [INFO] Task started: fastANI
[2023-03-18 05:05:14,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c7576c7-6fcb-4d7b-9730-4530ce87bb4f/OceanDNA-b20538.fa --refList OceanDNA-b20538/target_genomes.txt --output OceanDNA-b20538/fastani_result.tsv --threads 1
[2023-03-18 05:05:21,378] [INFO] Task succeeded: fastANI
[2023-03-18 05:05:21,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6eceb73d-272a-4ccf-a7e3-d174c080d68d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:05:21,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6eceb73d-272a-4ccf-a7e3-d174c080d68d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:05:21,378] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:05:21,378] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:05:21,378] [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 05:05:21,382] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20538/tc_result.tsv
[2023-03-18 05:05:21,387] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:05:21,388] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:05:21,388] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6eceb73d-272a-4ccf-a7e3-d174c080d68d/dqc_reference/checkm_data
[2023-03-18 05:05:21,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:05:21,437] [INFO] Task started: CheckM
[2023-03-18 05:05:21,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20538/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20538/checkm_input OceanDNA-b20538/checkm_result
[2023-03-18 05:05:43,417] [INFO] Task succeeded: CheckM
[2023-03-18 05:05:43,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 05:05:43,448] [INFO] ===== Completeness check finished =====
[2023-03-18 05:05:43,448] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:05:43,448] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20538/markers.fasta)
[2023-03-18 05:05:43,449] [INFO] Task started: Blastn
[2023-03-18 05:05:43,449] [INFO] Running command: blastn -query OceanDNA-b20538/markers.fasta -db /var/lib/cwl/stg6eceb73d-272a-4ccf-a7e3-d174c080d68d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20538/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:05:44,151] [INFO] Task succeeded: Blastn
[2023-03-18 05:05:44,172] [INFO] Selected 13 target genomes.
[2023-03-18 05:05:44,172] [INFO] Target genome list was writen to OceanDNA-b20538/target_genomes_gtdb.txt
[2023-03-18 05:05:44,276] [INFO] Task started: fastANI
[2023-03-18 05:05:44,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c7576c7-6fcb-4d7b-9730-4530ce87bb4f/OceanDNA-b20538.fa --refList OceanDNA-b20538/target_genomes_gtdb.txt --output OceanDNA-b20538/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:05:47,895] [INFO] Task succeeded: fastANI
[2023-03-18 05:05:47,899] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:05:47,899] [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_002693365.1	s__GCA-002707645 sp002693365	98.5568	330	419	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	conclusive
GCA_002704685.1	s__GCA-002707645 sp002704685	93.7916	368	419	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	80.1081	236	419	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_002705605.1	s__GCA-002707645 sp002705605	79.874	275	419	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_002717625.1	s__GCA-2717625 sp002717625	75.931	83	419	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_002718585.1	s__GCA-002718585 sp002718585	75.9237	60	419	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	-
--------------------------------------------------------------------------------
[2023-03-18 05:05:47,904] [INFO] GTDB search result was written to OceanDNA-b20538/result_gtdb.tsv
[2023-03-18 05:05:47,915] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:05:47,920] [INFO] DFAST_QC result json was written to OceanDNA-b20538/dqc_result.json
[2023-03-18 05:05:47,921] [INFO] DFAST_QC completed!
[2023-03-18 05:05:47,921] [INFO] Total running time: 0h0m42s