[2023-03-18 06:37:01,798] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:37:01,798] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:37:01,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg8529a322-01af-4e1c-ad4c-5c3466eab741/dqc_reference
[2023-03-18 06:37:03,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:37:03,369] [INFO] Task started: Prodigal
[2023-03-18 06:37:03,369] [INFO] Running command: cat /var/lib/cwl/stg2ef10da4-d318-4bcd-860d-69ef587b6eb8/OceanDNA-b10403.fa | prodigal -d OceanDNA-b10403/cds.fna -a OceanDNA-b10403/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:37:12,154] [INFO] Task succeeded: Prodigal
[2023-03-18 06:37:12,155] [INFO] Task started: HMMsearch
[2023-03-18 06:37:12,155] [INFO] Running command: hmmsearch --tblout OceanDNA-b10403/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8529a322-01af-4e1c-ad4c-5c3466eab741/dqc_reference/reference_markers.hmm OceanDNA-b10403/protein.faa > /dev/null
[2023-03-18 06:37:12,341] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:37:12,342] [INFO] Found 6/6 markers.
[2023-03-18 06:37:12,354] [INFO] Query marker FASTA was written to OceanDNA-b10403/markers.fasta
[2023-03-18 06:37:12,355] [INFO] Task started: Blastn
[2023-03-18 06:37:12,355] [INFO] Running command: blastn -query OceanDNA-b10403/markers.fasta -db /var/lib/cwl/stg8529a322-01af-4e1c-ad4c-5c3466eab741/dqc_reference/reference_markers.fasta -out OceanDNA-b10403/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:12,931] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:12,932] [INFO] Selected 27 target genomes.
[2023-03-18 06:37:12,932] [INFO] Target genome list was writen to OceanDNA-b10403/target_genomes.txt
[2023-03-18 06:37:12,948] [INFO] Task started: fastANI
[2023-03-18 06:37:12,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef10da4-d318-4bcd-860d-69ef587b6eb8/OceanDNA-b10403.fa --refList OceanDNA-b10403/target_genomes.txt --output OceanDNA-b10403/fastani_result.tsv --threads 1
[2023-03-18 06:37:26,817] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:26,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8529a322-01af-4e1c-ad4c-5c3466eab741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:37:26,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8529a322-01af-4e1c-ad4c-5c3466eab741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:37:26,818] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:37:26,818] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:37:26,818] [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 06:37:26,818] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10403/tc_result.tsv
[2023-03-18 06:37:26,818] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:37:26,819] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:37:26,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8529a322-01af-4e1c-ad4c-5c3466eab741/dqc_reference/checkm_data
[2023-03-18 06:37:26,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:37:26,825] [INFO] Task started: CheckM
[2023-03-18 06:37:26,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10403/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10403/checkm_input OceanDNA-b10403/checkm_result
[2023-03-18 06:37:53,640] [INFO] Task succeeded: CheckM
[2023-03-18 06:37:53,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 06:37:53,642] [INFO] ===== Completeness check finished =====
[2023-03-18 06:37:53,643] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:37:53,643] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10403/markers.fasta)
[2023-03-18 06:37:53,644] [INFO] Task started: Blastn
[2023-03-18 06:37:53,644] [INFO] Running command: blastn -query OceanDNA-b10403/markers.fasta -db /var/lib/cwl/stg8529a322-01af-4e1c-ad4c-5c3466eab741/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10403/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:54,592] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:54,593] [INFO] Selected 9 target genomes.
[2023-03-18 06:37:54,593] [INFO] Target genome list was writen to OceanDNA-b10403/target_genomes_gtdb.txt
[2023-03-18 06:37:54,626] [INFO] Task started: fastANI
[2023-03-18 06:37:54,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef10da4-d318-4bcd-860d-69ef587b6eb8/OceanDNA-b10403.fa --refList OceanDNA-b10403/target_genomes_gtdb.txt --output OceanDNA-b10403/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:37:57,528] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:57,534] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:37:57,534] [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_002171475.2	s__TMED96 sp002171475	99.2728	441	475	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	99.27	99.27	0.93	0.93	2	conclusive
GCA_002728075.1	s__TMED96 sp002728075	94.5881	366	475	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593075.1	s__TMED96 sp902593075	88.1499	309	475	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902582405.1	s__TMED96 sp902582405	87.3268	300	475	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	99.80	99.80	0.73	0.73	2	-
GCA_902598305.1	s__TMED96 sp902598305	86.3218	414	475	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595825.1	s__TMED96 sp902595825	86.0357	289	475	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628605.1	s__TMED96 sp902628605	85.8106	196	475	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902635965.1	s__TMED96 sp902635965	85.1297	383	475	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	97.75	95.54	0.87	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-18 06:37:57,534] [INFO] GTDB search result was written to OceanDNA-b10403/result_gtdb.tsv
[2023-03-18 06:37:57,534] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:37:57,535] [INFO] DFAST_QC result json was written to OceanDNA-b10403/dqc_result.json
[2023-03-18 06:37:57,535] [INFO] DFAST_QC completed!
[2023-03-18 06:37:57,535] [INFO] Total running time: 0h0m56s