[2023-03-18 03:09:35,379] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:35,379] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:35,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg45526827-0f76-455a-b25b-d11abb12a074/dqc_reference
[2023-03-18 03:09:36,481] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:36,481] [INFO] Task started: Prodigal
[2023-03-18 03:09:36,481] [INFO] Running command: cat /var/lib/cwl/stgaafb499a-d592-4c66-bc82-c9a3910a556c/OceanDNA-b33530.fa | prodigal -d OceanDNA-b33530/cds.fna -a OceanDNA-b33530/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:53,985] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:53,985] [INFO] Task started: HMMsearch
[2023-03-18 03:09:53,985] [INFO] Running command: hmmsearch --tblout OceanDNA-b33530/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45526827-0f76-455a-b25b-d11abb12a074/dqc_reference/reference_markers.hmm OceanDNA-b33530/protein.faa > /dev/null
[2023-03-18 03:09:54,284] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:54,285] [INFO] Found 6/6 markers.
[2023-03-18 03:09:54,306] [INFO] Query marker FASTA was written to OceanDNA-b33530/markers.fasta
[2023-03-18 03:09:54,306] [INFO] Task started: Blastn
[2023-03-18 03:09:54,306] [INFO] Running command: blastn -query OceanDNA-b33530/markers.fasta -db /var/lib/cwl/stg45526827-0f76-455a-b25b-d11abb12a074/dqc_reference/reference_markers.fasta -out OceanDNA-b33530/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:54,975] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:54,976] [INFO] Selected 31 target genomes.
[2023-03-18 03:09:54,976] [INFO] Target genome list was writen to OceanDNA-b33530/target_genomes.txt
[2023-03-18 03:09:54,994] [INFO] Task started: fastANI
[2023-03-18 03:09:54,994] [INFO] Running command: fastANI --query /var/lib/cwl/stgaafb499a-d592-4c66-bc82-c9a3910a556c/OceanDNA-b33530.fa --refList OceanDNA-b33530/target_genomes.txt --output OceanDNA-b33530/fastani_result.tsv --threads 1
[2023-03-18 03:10:19,252] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:19,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45526827-0f76-455a-b25b-d11abb12a074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:10:19,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45526827-0f76-455a-b25b-d11abb12a074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:10:19,260] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:10:19,260] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:10:19,260] [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
Zwartia hollandica	strain=LF4-65	GCA_019923725.1	324606	324606	type	True	77.3566	126	928	95	below_threshold
Jezberella montanilacus	strain=MWH-P2sevCIIIb	GCA_003003055.1	323426	323426	type	True	76.9827	92	928	95	below_threshold
Sheuella amnicola	strain=NBD-18	GCA_010499255.1	2707330	2707330	type	True	76.7473	95	928	95	below_threshold
Achromobacter pestifer	strain=LMG 3431	GCA_902859625.1	1353889	1353889	type	True	75.7397	59	928	95	below_threshold
Achromobacter kerstersii	strain=LMG 3441	GCA_902859595.1	1353890	1353890	type	True	75.7314	64	928	95	below_threshold
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	75.7058	55	928	95	below_threshold
Achromobacter piechaudii	strain=NBRC 102461	GCA_001571245.1	72556	72556	type	True	75.7058	55	928	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	75.617	53	928	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	75.617	53	928	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	75.617	53	928	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	75.4734	56	928	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:10:19,260] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33530/tc_result.tsv
[2023-03-18 03:10:19,260] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:10:19,260] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:10:19,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45526827-0f76-455a-b25b-d11abb12a074/dqc_reference/checkm_data
[2023-03-18 03:10:19,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:10:19,265] [INFO] Task started: CheckM
[2023-03-18 03:10:19,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33530/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33530/checkm_input OceanDNA-b33530/checkm_result
[2023-03-18 03:11:05,327] [INFO] Task succeeded: CheckM
[2023-03-18 03:11:05,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 2.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:11:05,330] [INFO] ===== Completeness check finished =====
[2023-03-18 03:11:05,330] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:11:05,330] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33530/markers.fasta)
[2023-03-18 03:11:05,330] [INFO] Task started: Blastn
[2023-03-18 03:11:05,330] [INFO] Running command: blastn -query OceanDNA-b33530/markers.fasta -db /var/lib/cwl/stg45526827-0f76-455a-b25b-d11abb12a074/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33530/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:11:06,405] [INFO] Task succeeded: Blastn
[2023-03-18 03:11:06,406] [INFO] Selected 13 target genomes.
[2023-03-18 03:11:06,406] [INFO] Target genome list was writen to OceanDNA-b33530/target_genomes_gtdb.txt
[2023-03-18 03:11:06,455] [INFO] Task started: fastANI
[2023-03-18 03:11:06,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgaafb499a-d592-4c66-bc82-c9a3910a556c/OceanDNA-b33530.fa --refList OceanDNA-b33530/target_genomes_gtdb.txt --output OceanDNA-b33530/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:11:14,972] [INFO] Task succeeded: fastANI
[2023-03-18 03:11:14,978] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:11:14,978] [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_013205565.1	s__NBD-18 sp013205565	83.0784	547	928	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737415.1	s__NBD-18 sp002737415	82.4063	590	928	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903932425.1	s__NBD-18 sp903932425	81.5569	586	928	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924715.1	s__NBD-18 sp903924715	79.7038	353	928	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958565.1	s__NBD-18 sp903958565	77.306	128	928	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.16	98.92	0.86	0.85	5	-
GCA_903903735.1	s__NBD-18 sp903903735	76.9907	81	928	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847325.1	s__NBD-18 sp903847325	76.9025	111	928	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929925.1	s__NBD-18 sp903929925	76.5985	88	928	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:11:14,978] [INFO] GTDB search result was written to OceanDNA-b33530/result_gtdb.tsv
[2023-03-18 03:11:14,978] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:11:14,979] [INFO] DFAST_QC result json was written to OceanDNA-b33530/dqc_result.json
[2023-03-18 03:11:14,979] [INFO] DFAST_QC completed!
[2023-03-18 03:11:14,979] [INFO] Total running time: 0h1m40s