[2023-03-15 07:03:38,648] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,648] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg42e8ab85-b24f-4a65-bb29-4b313558714c/dqc_reference
[2023-03-15 07:03:39,821] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:39,822] [INFO] Task started: Prodigal
[2023-03-15 07:03:39,822] [INFO] Running command: cat /var/lib/cwl/stg51179f10-452b-400a-9e05-be95c5e57063/OceanDNA-b11578.fa | prodigal -d OceanDNA-b11578/cds.fna -a OceanDNA-b11578/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:03:45,114] [INFO] Task succeeded: Prodigal
[2023-03-15 07:03:45,114] [INFO] Task started: HMMsearch
[2023-03-15 07:03:45,114] [INFO] Running command: hmmsearch --tblout OceanDNA-b11578/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42e8ab85-b24f-4a65-bb29-4b313558714c/dqc_reference/reference_markers.hmm OceanDNA-b11578/protein.faa > /dev/null
[2023-03-15 07:03:45,297] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:03:45,298] [INFO] Found 6/6 markers.
[2023-03-15 07:03:45,327] [INFO] Query marker FASTA was written to OceanDNA-b11578/markers.fasta
[2023-03-15 07:03:45,328] [INFO] Task started: Blastn
[2023-03-15 07:03:45,328] [INFO] Running command: blastn -query OceanDNA-b11578/markers.fasta -db /var/lib/cwl/stg42e8ab85-b24f-4a65-bb29-4b313558714c/dqc_reference/reference_markers.fasta -out OceanDNA-b11578/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:03:45,871] [INFO] Task succeeded: Blastn
[2023-03-15 07:03:45,878] [INFO] Selected 37 target genomes.
[2023-03-15 07:03:45,879] [INFO] Target genome list was writen to OceanDNA-b11578/target_genomes.txt
[2023-03-15 07:03:45,893] [INFO] Task started: fastANI
[2023-03-15 07:03:45,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg51179f10-452b-400a-9e05-be95c5e57063/OceanDNA-b11578.fa --refList OceanDNA-b11578/target_genomes.txt --output OceanDNA-b11578/fastani_result.tsv --threads 1
[2023-03-15 07:04:09,929] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:09,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42e8ab85-b24f-4a65-bb29-4b313558714c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:04:09,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42e8ab85-b24f-4a65-bb29-4b313558714c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:04:09,930] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:04:09,930] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:04:09,930] [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
--------------------------------------------------------------------------------
[2023-03-15 07:04:09,931] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11578/tc_result.tsv
[2023-03-15 07:04:09,931] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:04:09,932] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:04:09,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42e8ab85-b24f-4a65-bb29-4b313558714c/dqc_reference/checkm_data
[2023-03-15 07:04:09,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:04:09,942] [INFO] Task started: CheckM
[2023-03-15 07:04:09,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11578/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11578/checkm_input OceanDNA-b11578/checkm_result
[2023-03-15 07:04:29,396] [INFO] Task succeeded: CheckM
[2023-03-15 07:04:29,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:04:29,426] [INFO] ===== Completeness check finished =====
[2023-03-15 07:04:29,426] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:04:29,427] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11578/markers.fasta)
[2023-03-15 07:04:29,427] [INFO] Task started: Blastn
[2023-03-15 07:04:29,427] [INFO] Running command: blastn -query OceanDNA-b11578/markers.fasta -db /var/lib/cwl/stg42e8ab85-b24f-4a65-bb29-4b313558714c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11578/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:30,222] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:30,229] [INFO] Selected 25 target genomes.
[2023-03-15 07:04:30,229] [INFO] Target genome list was writen to OceanDNA-b11578/target_genomes_gtdb.txt
[2023-03-15 07:04:30,353] [INFO] Task started: fastANI
[2023-03-15 07:04:30,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg51179f10-452b-400a-9e05-be95c5e57063/OceanDNA-b11578.fa --refList OceanDNA-b11578/target_genomes_gtdb.txt --output OceanDNA-b11578/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:04:38,029] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:38,035] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:04:38,035] [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_002707245.1	s__GCA-002707245 sp002707245	99.5275	204	259	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002698365.1	s__GCA-002707245 sp002698365	88.2585	183	259	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713285.1	s__SP256 sp002713285	77.3766	98	259	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714185.1	s__SP256 sp002714185	77.0913	87	259	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722215.1	s__SP256 sp002722215	76.9601	83	259	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701365.1	s__GCA-002701365 sp002701365	76.9566	85	259	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002701365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171975.2	s__GCA-2696965 sp002171975	76.9239	77	259	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2696965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718895.1	s__GCA-2718895 sp002718895	76.7688	59	259	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718895	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:04:38,038] [INFO] GTDB search result was written to OceanDNA-b11578/result_gtdb.tsv
[2023-03-15 07:04:38,041] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:04:38,046] [INFO] DFAST_QC result json was written to OceanDNA-b11578/dqc_result.json
[2023-03-15 07:04:38,047] [INFO] DFAST_QC completed!
[2023-03-15 07:04:38,047] [INFO] Total running time: 0h0m59s