[2023-03-18 07:54:30,544] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:30,544] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:30,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d53dd7c-e5b1-42c0-9d86-d1366b1544e2/dqc_reference
[2023-03-18 07:54:32,281] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:32,281] [INFO] Task started: Prodigal
[2023-03-18 07:54:32,282] [INFO] Running command: cat /var/lib/cwl/stg047f0274-0fba-4aa3-a30a-05215369844f/OceanDNA-b26816.fa | prodigal -d OceanDNA-b26816/cds.fna -a OceanDNA-b26816/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:53,277] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:53,277] [INFO] Task started: HMMsearch
[2023-03-18 07:54:53,277] [INFO] Running command: hmmsearch --tblout OceanDNA-b26816/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d53dd7c-e5b1-42c0-9d86-d1366b1544e2/dqc_reference/reference_markers.hmm OceanDNA-b26816/protein.faa > /dev/null
[2023-03-18 07:54:53,476] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:53,476] [INFO] Found 6/6 markers.
[2023-03-18 07:54:53,500] [INFO] Query marker FASTA was written to OceanDNA-b26816/markers.fasta
[2023-03-18 07:54:53,501] [INFO] Task started: Blastn
[2023-03-18 07:54:53,501] [INFO] Running command: blastn -query OceanDNA-b26816/markers.fasta -db /var/lib/cwl/stg1d53dd7c-e5b1-42c0-9d86-d1366b1544e2/dqc_reference/reference_markers.fasta -out OceanDNA-b26816/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:54,492] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:54,492] [INFO] Selected 10 target genomes.
[2023-03-18 07:54:54,493] [INFO] Target genome list was writen to OceanDNA-b26816/target_genomes.txt
[2023-03-18 07:54:54,499] [INFO] Task started: fastANI
[2023-03-18 07:54:54,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg047f0274-0fba-4aa3-a30a-05215369844f/OceanDNA-b26816.fa --refList OceanDNA-b26816/target_genomes.txt --output OceanDNA-b26816/fastani_result.tsv --threads 1
[2023-03-18 07:55:04,416] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:04,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d53dd7c-e5b1-42c0-9d86-d1366b1544e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:55:04,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d53dd7c-e5b1-42c0-9d86-d1366b1544e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:55:04,424] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2023-03-18 07:55:04,424] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-18 07:55:04,424] [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
Aurantimonas coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	96.8825	1086	1127	95	inconclusive
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	96.8312	1080	1127	95	inconclusive
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	95.3407	1026	1127	95	inconclusive
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	95.2719	1056	1127	95	inconclusive
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	82.5704	748	1127	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	82.482	749	1127	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	81.64	685	1127	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	80.9249	683	1127	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.7637	427	1127	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.1068	388	1127	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:55:04,424] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26816/tc_result.tsv
[2023-03-18 07:55:04,425] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:55:04,425] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:55:04,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d53dd7c-e5b1-42c0-9d86-d1366b1544e2/dqc_reference/checkm_data
[2023-03-18 07:55:04,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:55:04,431] [INFO] Task started: CheckM
[2023-03-18 07:55:04,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26816/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26816/checkm_input OceanDNA-b26816/checkm_result
[2023-03-18 07:55:56,187] [INFO] Task succeeded: CheckM
[2023-03-18 07:55:56,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:55:56,190] [INFO] ===== Completeness check finished =====
[2023-03-18 07:55:56,190] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:55:56,190] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26816/markers.fasta)
[2023-03-18 07:55:56,191] [INFO] Task started: Blastn
[2023-03-18 07:55:56,191] [INFO] Running command: blastn -query OceanDNA-b26816/markers.fasta -db /var/lib/cwl/stg1d53dd7c-e5b1-42c0-9d86-d1366b1544e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26816/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:55:58,194] [INFO] Task succeeded: Blastn
[2023-03-18 07:55:58,195] [INFO] Selected 10 target genomes.
[2023-03-18 07:55:58,195] [INFO] Target genome list was writen to OceanDNA-b26816/target_genomes_gtdb.txt
[2023-03-18 07:55:58,208] [INFO] Task started: fastANI
[2023-03-18 07:55:58,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg047f0274-0fba-4aa3-a30a-05215369844f/OceanDNA-b26816.fa --refList OceanDNA-b26816/target_genomes_gtdb.txt --output OceanDNA-b26816/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:56:08,054] [INFO] Task succeeded: fastANI
[2023-03-18 07:56:08,060] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:56:08,060] [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_000421645.1	s__Aurantimonas coralicida	96.8825	1086	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	conclusive
GCF_000153465.1	s__Aurantimonas manganoxydans	95.2916	1055	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_010500835.1	s__Aurantimonas aggregata	82.5704	748	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196845.1	s__Aurantimonas endophytica	82.4908	753	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	81.6704	694	1127	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	81.6452	712	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017183135.1	s__Aurantimonas sp017183135	81.6398	685	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050685.1	s__Aurantimonas coralicida_A	81.5926	664	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	99.96	99.96	0.91	0.91	2	-
GCF_017353515.1	s__Jiella sp017353515	80.9299	681	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425575.1	s__Leaf443 sp001425575	80.7328	610	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Leaf443	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:56:08,061] [INFO] GTDB search result was written to OceanDNA-b26816/result_gtdb.tsv
[2023-03-18 07:56:08,061] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:56:08,062] [INFO] DFAST_QC result json was written to OceanDNA-b26816/dqc_result.json
[2023-03-18 07:56:08,062] [INFO] DFAST_QC completed!
[2023-03-18 07:56:08,062] [INFO] Total running time: 0h1m38s