[2023-03-16 08:22:25,416] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:22:25,417] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:22:25,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg681814f1-3c2e-4d9d-8115-79d87217e98c/dqc_reference
[2023-03-16 08:22:27,106] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:22:27,107] [INFO] Task started: Prodigal
[2023-03-16 08:22:27,107] [INFO] Running command: cat /var/lib/cwl/stg5993b802-c4db-4679-b7a9-c690127b6553/OceanDNA-b44445.fa | prodigal -d OceanDNA-b44445/cds.fna -a OceanDNA-b44445/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:22:42,580] [INFO] Task succeeded: Prodigal
[2023-03-16 08:22:42,581] [INFO] Task started: HMMsearch
[2023-03-16 08:22:42,581] [INFO] Running command: hmmsearch --tblout OceanDNA-b44445/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg681814f1-3c2e-4d9d-8115-79d87217e98c/dqc_reference/reference_markers.hmm OceanDNA-b44445/protein.faa > /dev/null
[2023-03-16 08:22:42,768] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:22:42,768] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5993b802-c4db-4679-b7a9-c690127b6553/OceanDNA-b44445.fa]
[2023-03-16 08:22:42,796] [INFO] Query marker FASTA was written to OceanDNA-b44445/markers.fasta
[2023-03-16 08:22:42,797] [INFO] Task started: Blastn
[2023-03-16 08:22:42,798] [INFO] Running command: blastn -query OceanDNA-b44445/markers.fasta -db /var/lib/cwl/stg681814f1-3c2e-4d9d-8115-79d87217e98c/dqc_reference/reference_markers.fasta -out OceanDNA-b44445/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:22:43,344] [INFO] Task succeeded: Blastn
[2023-03-16 08:22:43,348] [INFO] Selected 25 target genomes.
[2023-03-16 08:22:43,348] [INFO] Target genome list was writen to OceanDNA-b44445/target_genomes.txt
[2023-03-16 08:22:43,362] [INFO] Task started: fastANI
[2023-03-16 08:22:43,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg5993b802-c4db-4679-b7a9-c690127b6553/OceanDNA-b44445.fa --refList OceanDNA-b44445/target_genomes.txt --output OceanDNA-b44445/fastani_result.tsv --threads 1
[2023-03-16 08:22:58,828] [INFO] Task succeeded: fastANI
[2023-03-16 08:22:58,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg681814f1-3c2e-4d9d-8115-79d87217e98c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:22:58,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg681814f1-3c2e-4d9d-8115-79d87217e98c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:22:58,837] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:22:58,837] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:22:58,837] [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
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.2031	53	807	95	below_threshold
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	75.912	58	807	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	75.8823	65	807	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.8222	60	807	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.7775	72	807	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	75.7548	59	807	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.7355	75	807	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	75.6542	52	807	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	75.599	74	807	95	below_threshold
Metallibacterium scheffleri	strain=DKE6	GCA_002077135.1	993689	993689	type	True	75.1732	51	807	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	75.1732	51	807	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:22:58,839] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44445/tc_result.tsv
[2023-03-16 08:22:58,839] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:22:58,840] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:22:58,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg681814f1-3c2e-4d9d-8115-79d87217e98c/dqc_reference/checkm_data
[2023-03-16 08:22:58,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:22:58,846] [INFO] Task started: CheckM
[2023-03-16 08:22:58,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44445/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44445/checkm_input OceanDNA-b44445/checkm_result
[2023-03-16 08:23:39,491] [INFO] Task succeeded: CheckM
[2023-03-16 08:23:39,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.78%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 08:23:39,497] [INFO] ===== Completeness check finished =====
[2023-03-16 08:23:39,497] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:23:39,498] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44445/markers.fasta)
[2023-03-16 08:23:39,499] [INFO] Task started: Blastn
[2023-03-16 08:23:39,499] [INFO] Running command: blastn -query OceanDNA-b44445/markers.fasta -db /var/lib/cwl/stg681814f1-3c2e-4d9d-8115-79d87217e98c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44445/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:23:40,315] [INFO] Task succeeded: Blastn
[2023-03-16 08:23:40,315] [INFO] Selected 22 target genomes.
[2023-03-16 08:23:40,315] [INFO] Target genome list was writen to OceanDNA-b44445/target_genomes_gtdb.txt
[2023-03-16 08:23:40,367] [INFO] Task started: fastANI
[2023-03-16 08:23:40,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg5993b802-c4db-4679-b7a9-c690127b6553/OceanDNA-b44445.fa --refList OceanDNA-b44445/target_genomes_gtdb.txt --output OceanDNA-b44445/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:23:52,840] [INFO] Task succeeded: fastANI
[2023-03-16 08:23:52,850] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:23:52,850] [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_013042375.1	s__UBA1847 sp013042375	76.9092	92	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.79	99.73	0.92	0.88	6	-
GCA_016789885.1	s__SHZI01 sp016789885	76.6868	90	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__SHZI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704655.1	s__RPQJ01 sp016704655	76.6291	76	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	98.97	98.97	0.93	0.93	2	-
GCA_011391405.1	s__RPQJ01 sp011391405	76.3743	63	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136105.1	s__RPQJ01 sp019136105	76.3376	62	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242685.1	s__ZC4RG24 sp003242685	76.3313	78	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709695.1	s__QUBU01 sp015709695	76.2217	70	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__QUBU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127715.1	s__PWYM01 sp007127715	76.1524	71	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PWYM01;f__PWYM01;g__PWYM01	95.0	99.45	99.43	0.90	0.89	3	-
GCA_002995625.1	s__UDEA-SF1 sp002995625	75.9583	62	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__UDEA-SF1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011089885.1	s__XN24 sp011089885	75.924	85	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923475.1	s__UBA964 sp009923475	75.9087	66	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054615.1	s__FEN-1219 sp011054615	75.5711	87	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6522;f__UBA6522;g__FEN-1219	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839465.1	s__CAIKMS01 sp903839465	75.5673	64	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIKMS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799035.1	s__Rhodanobacter lindaniclasticus	75.5167	56	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426885.1	s__Pelomonas sp001426885	75.3945	54	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284255.1	s__Rubrivivax gelatinosus_A	75.1546	80	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	98.28	98.28	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:23:52,850] [INFO] GTDB search result was written to OceanDNA-b44445/result_gtdb.tsv
[2023-03-16 08:23:52,850] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:23:52,852] [INFO] DFAST_QC result json was written to OceanDNA-b44445/dqc_result.json
[2023-03-16 08:23:52,852] [INFO] DFAST_QC completed!
[2023-03-16 08:23:52,852] [INFO] Total running time: 0h1m27s