[2023-03-15 21:48:06,703] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:06,704] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:06,704] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfa2c1a9-d6d3-43f3-93a4-5b76217839f5/dqc_reference
[2023-03-15 21:48:07,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:07,852] [INFO] Task started: Prodigal
[2023-03-15 21:48:07,852] [INFO] Running command: cat /var/lib/cwl/stg17569b36-5fef-455a-9e53-4f52e641e1c4/OceanDNA-b26824.fa | prodigal -d OceanDNA-b26824/cds.fna -a OceanDNA-b26824/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:39,492] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:39,492] [INFO] Task started: HMMsearch
[2023-03-15 21:48:39,493] [INFO] Running command: hmmsearch --tblout OceanDNA-b26824/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfa2c1a9-d6d3-43f3-93a4-5b76217839f5/dqc_reference/reference_markers.hmm OceanDNA-b26824/protein.faa > /dev/null
[2023-03-15 21:48:39,738] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:39,738] [INFO] Found 6/6 markers.
[2023-03-15 21:48:39,770] [INFO] Query marker FASTA was written to OceanDNA-b26824/markers.fasta
[2023-03-15 21:48:39,771] [INFO] Task started: Blastn
[2023-03-15 21:48:39,771] [INFO] Running command: blastn -query OceanDNA-b26824/markers.fasta -db /var/lib/cwl/stgcfa2c1a9-d6d3-43f3-93a4-5b76217839f5/dqc_reference/reference_markers.fasta -out OceanDNA-b26824/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:40,699] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:40,706] [INFO] Selected 13 target genomes.
[2023-03-15 21:48:40,707] [INFO] Target genome list was writen to OceanDNA-b26824/target_genomes.txt
[2023-03-15 21:48:40,717] [INFO] Task started: fastANI
[2023-03-15 21:48:40,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg17569b36-5fef-455a-9e53-4f52e641e1c4/OceanDNA-b26824.fa --refList OceanDNA-b26824/target_genomes.txt --output OceanDNA-b26824/fastani_result.tsv --threads 1
[2023-03-15 21:48:54,171] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:54,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfa2c1a9-d6d3-43f3-93a4-5b76217839f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:54,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfa2c1a9-d6d3-43f3-93a4-5b76217839f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:54,181] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:54,181] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:48:54,181] [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
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	89.4356	1341	1707	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	84.3669	1102	1707	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	84.3012	1136	1707	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	80.8418	710	1707	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	80.7682	732	1707	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	80.7454	741	1707	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	80.5955	723	1707	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	80.5837	726	1707	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	80.5565	734	1707	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	79.2287	613	1707	95	below_threshold
Fulvimarina pelagi	strain=HTCC2506	GCA_000153705.1	217511	217511	type	True	78.2075	387	1707	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.0123	414	1707	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.9188	461	1707	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:48:54,182] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26824/tc_result.tsv
[2023-03-15 21:48:54,182] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:54,182] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:54,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfa2c1a9-d6d3-43f3-93a4-5b76217839f5/dqc_reference/checkm_data
[2023-03-15 21:48:54,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:54,211] [INFO] Task started: CheckM
[2023-03-15 21:48:54,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26824/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26824/checkm_input OceanDNA-b26824/checkm_result
[2023-03-15 21:50:10,551] [INFO] Task succeeded: CheckM
[2023-03-15 21:50:10,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:50:10,631] [INFO] ===== Completeness check finished =====
[2023-03-15 21:50:10,631] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:50:10,631] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26824/markers.fasta)
[2023-03-15 21:50:10,632] [INFO] Task started: Blastn
[2023-03-15 21:50:10,632] [INFO] Running command: blastn -query OceanDNA-b26824/markers.fasta -db /var/lib/cwl/stgcfa2c1a9-d6d3-43f3-93a4-5b76217839f5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26824/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:50:12,527] [INFO] Task succeeded: Blastn
[2023-03-15 21:50:12,530] [INFO] Selected 7 target genomes.
[2023-03-15 21:50:12,530] [INFO] Target genome list was writen to OceanDNA-b26824/target_genomes_gtdb.txt
[2023-03-15 21:50:12,536] [INFO] Task started: fastANI
[2023-03-15 21:50:12,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg17569b36-5fef-455a-9e53-4f52e641e1c4/OceanDNA-b26824.fa --refList OceanDNA-b26824/target_genomes_gtdb.txt --output OceanDNA-b26824/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:50:22,070] [INFO] Task succeeded: fastANI
[2023-03-15 21:50:22,076] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:50:22,076] [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
GCF_010500815.1	s__Jiella pacifica	89.4152	1343	1707	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	85.4395	1176	1707	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	85.361	1146	1707	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	84.3729	1100	1707	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	84.2997	1136	1707	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815135.1	s__Jiella sp017815135	83.5298	1027	1707	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349315.1	s__Jiella sp017349315	81.461	828	1707	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:50:22,077] [INFO] GTDB search result was written to OceanDNA-b26824/result_gtdb.tsv
[2023-03-15 21:50:22,078] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:50:22,081] [INFO] DFAST_QC result json was written to OceanDNA-b26824/dqc_result.json
[2023-03-15 21:50:22,081] [INFO] DFAST_QC completed!
[2023-03-15 21:50:22,081] [INFO] Total running time: 0h2m15s