[2023-03-16 06:12:34,971] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:12:34,972] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:12:34,972] [INFO] DQC Reference Directory: /var/lib/cwl/stg532083f9-6e65-43e3-9b61-624b2330427a/dqc_reference
[2023-03-16 06:12:36,624] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:12:36,625] [INFO] Task started: Prodigal
[2023-03-16 06:12:36,625] [INFO] Running command: cat /var/lib/cwl/stg258942d1-def9-4d9c-847a-b3051e4ae45e/OceanDNA-b33298.fa | prodigal -d OceanDNA-b33298/cds.fna -a OceanDNA-b33298/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:12:52,280] [INFO] Task succeeded: Prodigal
[2023-03-16 06:12:52,280] [INFO] Task started: HMMsearch
[2023-03-16 06:12:52,280] [INFO] Running command: hmmsearch --tblout OceanDNA-b33298/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg532083f9-6e65-43e3-9b61-624b2330427a/dqc_reference/reference_markers.hmm OceanDNA-b33298/protein.faa > /dev/null
[2023-03-16 06:12:52,457] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:12:52,458] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg258942d1-def9-4d9c-847a-b3051e4ae45e/OceanDNA-b33298.fa]
[2023-03-16 06:12:52,491] [INFO] Query marker FASTA was written to OceanDNA-b33298/markers.fasta
[2023-03-16 06:12:52,491] [INFO] Task started: Blastn
[2023-03-16 06:12:52,491] [INFO] Running command: blastn -query OceanDNA-b33298/markers.fasta -db /var/lib/cwl/stg532083f9-6e65-43e3-9b61-624b2330427a/dqc_reference/reference_markers.fasta -out OceanDNA-b33298/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:12:53,151] [INFO] Task succeeded: Blastn
[2023-03-16 06:12:53,156] [INFO] Selected 18 target genomes.
[2023-03-16 06:12:53,157] [INFO] Target genome list was writen to OceanDNA-b33298/target_genomes.txt
[2023-03-16 06:12:53,167] [INFO] Task started: fastANI
[2023-03-16 06:12:53,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg258942d1-def9-4d9c-847a-b3051e4ae45e/OceanDNA-b33298.fa --refList OceanDNA-b33298/target_genomes.txt --output OceanDNA-b33298/fastani_result.tsv --threads 1
[2023-03-16 06:13:08,624] [INFO] Task succeeded: fastANI
[2023-03-16 06:13:08,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg532083f9-6e65-43e3-9b61-624b2330427a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:13:08,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg532083f9-6e65-43e3-9b61-624b2330427a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:13:08,635] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:13:08,635] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:13:08,635] [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
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	81.4284	463	798	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	81.3745	327	798	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	80.8122	505	798	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	80.4991	480	798	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	80.4116	459	798	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	80.0472	451	798	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	79.9941	440	798	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	79.9772	441	798	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	79.9566	444	798	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.8653	444	798	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.5223	393	798	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	79.4979	483	798	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	79.4459	405	798	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	79.1012	337	798	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.0999	362	798	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	79.0935	424	798	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.8456	414	798	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.0807	304	798	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:13:08,638] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33298/tc_result.tsv
[2023-03-16 06:13:08,659] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:13:08,659] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:13:08,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg532083f9-6e65-43e3-9b61-624b2330427a/dqc_reference/checkm_data
[2023-03-16 06:13:08,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:13:08,672] [INFO] Task started: CheckM
[2023-03-16 06:13:08,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33298/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33298/checkm_input OceanDNA-b33298/checkm_result
[2023-03-16 06:13:53,413] [INFO] Task succeeded: CheckM
[2023-03-16 06:13:53,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:13:53,435] [INFO] ===== Completeness check finished =====
[2023-03-16 06:13:53,435] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:13:53,435] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33298/markers.fasta)
[2023-03-16 06:13:53,435] [INFO] Task started: Blastn
[2023-03-16 06:13:53,436] [INFO] Running command: blastn -query OceanDNA-b33298/markers.fasta -db /var/lib/cwl/stg532083f9-6e65-43e3-9b61-624b2330427a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33298/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:13:54,451] [INFO] Task succeeded: Blastn
[2023-03-16 06:13:54,455] [INFO] Selected 14 target genomes.
[2023-03-16 06:13:54,455] [INFO] Target genome list was writen to OceanDNA-b33298/target_genomes_gtdb.txt
[2023-03-16 06:13:54,469] [INFO] Task started: fastANI
[2023-03-16 06:13:54,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg258942d1-def9-4d9c-847a-b3051e4ae45e/OceanDNA-b33298.fa --refList OceanDNA-b33298/target_genomes_gtdb.txt --output OceanDNA-b33298/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:14:04,379] [INFO] Task succeeded: fastANI
[2023-03-16 06:14:04,387] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:14:04,388] [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_001725255.1	s__Comamonas_C sp001725255	85.1193	578	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	98.57	95.76	0.95	0.89	4	-
GCF_007954405.1	s__Comamonas_C sp007954405	84.3453	589	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000484635.1	s__Comamonas_C badia	84.024	599	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	98.01	98.01	0.89	0.89	2	-
GCF_019195435.1	s__Comamonas_C sp019195435	84.0129	551	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724135.1	s__Comamonas_C sp001724135	83.2601	582	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204645.1	s__Alicycliphilus denitrificans	81.8945	520	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCF_000282995.1	s__Melaminivora alkalimesophila	81.3952	326	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora	95.0	99.95	99.95	0.97	0.97	2	-
GCA_017307865.1	s__Ottowia sp017307865	81.2194	488	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	98.48	98.25	0.89	0.83	4	-
GCF_900103645.1	s__Oryzisolibacter propanilivorax	81.1806	488	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oryzisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240925.1	s__Ottowia sp018240925	80.9166	431	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.08	99.08	0.81	0.81	2	-
GCA_018240985.1	s__Alicycliphilus sp018240985	80.7502	448	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.65	99.65	0.85	0.85	2	-
GCA_001897615.1	s__Ottowia sp001897615	80.5152	451	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	96.20	96.20	0.84	0.84	2	-
GCA_018241325.1	s__Ottowia sp018241325	80.4475	469	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240995.1	s__Alicycliphilus sp018240995	80.1671	373	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:14:04,389] [INFO] GTDB search result was written to OceanDNA-b33298/result_gtdb.tsv
[2023-03-16 06:14:04,393] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:14:04,397] [INFO] DFAST_QC result json was written to OceanDNA-b33298/dqc_result.json
[2023-03-16 06:14:04,397] [INFO] DFAST_QC completed!
[2023-03-16 06:14:04,397] [INFO] Total running time: 0h1m29s