[2023-03-19 00:19:08,845] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:19:08,845] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:19:08,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg10076a3f-61bc-455b-99dc-18f8dab708d3/dqc_reference
[2023-03-19 00:19:10,372] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:19:10,372] [INFO] Task started: Prodigal
[2023-03-19 00:19:10,372] [INFO] Running command: cat /var/lib/cwl/stg889517d6-7c2e-4145-9518-9bba59c71f0b/OceanDNA-b29526.fa | prodigal -d OceanDNA-b29526/cds.fna -a OceanDNA-b29526/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:19:27,221] [INFO] Task succeeded: Prodigal
[2023-03-19 00:19:27,221] [INFO] Task started: HMMsearch
[2023-03-19 00:19:27,221] [INFO] Running command: hmmsearch --tblout OceanDNA-b29526/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10076a3f-61bc-455b-99dc-18f8dab708d3/dqc_reference/reference_markers.hmm OceanDNA-b29526/protein.faa > /dev/null
[2023-03-19 00:19:27,425] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:19:27,426] [INFO] Found 6/6 markers.
[2023-03-19 00:19:27,449] [INFO] Query marker FASTA was written to OceanDNA-b29526/markers.fasta
[2023-03-19 00:19:27,449] [INFO] Task started: Blastn
[2023-03-19 00:19:27,449] [INFO] Running command: blastn -query OceanDNA-b29526/markers.fasta -db /var/lib/cwl/stg10076a3f-61bc-455b-99dc-18f8dab708d3/dqc_reference/reference_markers.fasta -out OceanDNA-b29526/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:19:28,229] [INFO] Task succeeded: Blastn
[2023-03-19 00:19:28,229] [INFO] Selected 16 target genomes.
[2023-03-19 00:19:28,230] [INFO] Target genome list was writen to OceanDNA-b29526/target_genomes.txt
[2023-03-19 00:19:28,241] [INFO] Task started: fastANI
[2023-03-19 00:19:28,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg889517d6-7c2e-4145-9518-9bba59c71f0b/OceanDNA-b29526.fa --refList OceanDNA-b29526/target_genomes.txt --output OceanDNA-b29526/fastani_result.tsv --threads 1
[2023-03-19 00:19:40,771] [INFO] Task succeeded: fastANI
[2023-03-19 00:19:40,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10076a3f-61bc-455b-99dc-18f8dab708d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:19:40,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10076a3f-61bc-455b-99dc-18f8dab708d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:19:40,781] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2023-03-19 00:19:40,782] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-19 00:19:40,782] [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
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	97.1775	869	902	95	inconclusive
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	97.1752	867	902	95	inconclusive
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	97.0758	854	902	95	inconclusive
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	82.1751	588	902	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.2568	323	902	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.2069	296	902	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.2043	297	902	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.0474	233	902	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.7954	246	902	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	77.76	265	902	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.7145	241	902	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.6096	244	902	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.3643	238	902	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	77.3544	238	902	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	77.3259	229	902	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.2243	167	902	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:19:40,782] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29526/tc_result.tsv
[2023-03-19 00:19:40,782] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:19:40,782] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:19:40,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10076a3f-61bc-455b-99dc-18f8dab708d3/dqc_reference/checkm_data
[2023-03-19 00:19:40,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:19:40,788] [INFO] Task started: CheckM
[2023-03-19 00:19:40,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29526/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29526/checkm_input OceanDNA-b29526/checkm_result
[2023-03-19 00:20:24,454] [INFO] Task succeeded: CheckM
[2023-03-19 00:20:24,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:20:24,458] [INFO] ===== Completeness check finished =====
[2023-03-19 00:20:24,458] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:20:24,458] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29526/markers.fasta)
[2023-03-19 00:20:24,459] [INFO] Task started: Blastn
[2023-03-19 00:20:24,459] [INFO] Running command: blastn -query OceanDNA-b29526/markers.fasta -db /var/lib/cwl/stg10076a3f-61bc-455b-99dc-18f8dab708d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29526/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:20:25,810] [INFO] Task succeeded: Blastn
[2023-03-19 00:20:25,811] [INFO] Selected 14 target genomes.
[2023-03-19 00:20:25,811] [INFO] Target genome list was writen to OceanDNA-b29526/target_genomes_gtdb.txt
[2023-03-19 00:20:25,861] [INFO] Task started: fastANI
[2023-03-19 00:20:25,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg889517d6-7c2e-4145-9518-9bba59c71f0b/OceanDNA-b29526.fa --refList OceanDNA-b29526/target_genomes_gtdb.txt --output OceanDNA-b29526/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:20:35,724] [INFO] Task succeeded: fastANI
[2023-03-19 00:20:35,733] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:20:35,733] [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_000152805.1	s__Maritimibacter alkaliphilus	97.1775	869	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	97.94	96.90	0.93	0.88	4	conclusive
GCA_002695005.1	s__Maritimibacter sp002695005	82.959	650	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009882975.1	s__Maritimibacter harenae	82.162	589	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218265.1	s__Maritimibacter sp019218265	80.9466	495	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001626765.1	s__Maritimibacter sp001626765	80.561	465	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.88	99.88	0.89	0.89	2	-
GCF_019218295.1	s__Maritimibacter sp019218295	80.3815	496	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003520545.1	s__Maritimibacter sp003520545	79.7443	388	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389895.1	s__Maritimibacter sp011389895	79.5634	436	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640115.1	s__Muriiphilus lacisalsi	78.8049	346	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177545.1	s__Muriiphilus sp900177545	78.5943	330	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	78.537	346	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711185.1	s__Paracoccus limosus	77.8374	198	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	77.5026	190	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_003709565.1	s__Paracoccus siganidrum	77.3541	238	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:20:35,733] [INFO] GTDB search result was written to OceanDNA-b29526/result_gtdb.tsv
[2023-03-19 00:20:35,733] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:20:35,735] [INFO] DFAST_QC result json was written to OceanDNA-b29526/dqc_result.json
[2023-03-19 00:20:35,735] [INFO] DFAST_QC completed!
[2023-03-19 00:20:35,735] [INFO] Total running time: 0h1m27s