[2023-03-18 09:53:10,260] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:53:10,260] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:53:10,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg0869df21-c5fa-49cd-a267-ac99d1de554f/dqc_reference
[2023-03-18 09:53:11,353] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:53:11,353] [INFO] Task started: Prodigal
[2023-03-18 09:53:11,354] [INFO] Running command: cat /var/lib/cwl/stg187554c4-a9be-4b94-9e36-ee9289a7fcf1/OceanDNA-b29563.fa | prodigal -d OceanDNA-b29563/cds.fna -a OceanDNA-b29563/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:53:33,411] [INFO] Task succeeded: Prodigal
[2023-03-18 09:53:33,411] [INFO] Task started: HMMsearch
[2023-03-18 09:53:33,411] [INFO] Running command: hmmsearch --tblout OceanDNA-b29563/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0869df21-c5fa-49cd-a267-ac99d1de554f/dqc_reference/reference_markers.hmm OceanDNA-b29563/protein.faa > /dev/null
[2023-03-18 09:53:33,610] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:53:33,610] [INFO] Found 6/6 markers.
[2023-03-18 09:53:33,632] [INFO] Query marker FASTA was written to OceanDNA-b29563/markers.fasta
[2023-03-18 09:53:33,632] [INFO] Task started: Blastn
[2023-03-18 09:53:33,632] [INFO] Running command: blastn -query OceanDNA-b29563/markers.fasta -db /var/lib/cwl/stg0869df21-c5fa-49cd-a267-ac99d1de554f/dqc_reference/reference_markers.fasta -out OceanDNA-b29563/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:53:34,552] [INFO] Task succeeded: Blastn
[2023-03-18 09:53:34,553] [INFO] Selected 19 target genomes.
[2023-03-18 09:53:34,553] [INFO] Target genome list was writen to OceanDNA-b29563/target_genomes.txt
[2023-03-18 09:53:34,566] [INFO] Task started: fastANI
[2023-03-18 09:53:34,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg187554c4-a9be-4b94-9e36-ee9289a7fcf1/OceanDNA-b29563.fa --refList OceanDNA-b29563/target_genomes.txt --output OceanDNA-b29563/fastani_result.tsv --threads 1
[2023-03-18 09:53:48,172] [INFO] Task succeeded: fastANI
[2023-03-18 09:53:48,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0869df21-c5fa-49cd-a267-ac99d1de554f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:53:48,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0869df21-c5fa-49cd-a267-ac99d1de554f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:53:48,183] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:53:48,183] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:53:48,183] [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
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	80.7332	766	1168	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	80.5803	710	1168	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	79.9751	712	1168	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.0417	566	1168	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.0381	560	1168	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.9774	552	1168	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	78.8345	468	1168	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.7013	448	1168	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.5984	464	1168	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	78.5032	509	1168	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	78.5013	485	1168	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.3904	406	1168	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	78.2731	386	1168	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.2648	419	1168	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	78.2112	391	1168	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.9967	389	1168	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.9373	413	1168	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.8179	367	1168	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.7587	396	1168	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:53:48,183] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29563/tc_result.tsv
[2023-03-18 09:53:48,184] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:53:48,184] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:53:48,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0869df21-c5fa-49cd-a267-ac99d1de554f/dqc_reference/checkm_data
[2023-03-18 09:53:48,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:53:48,241] [INFO] Task started: CheckM
[2023-03-18 09:53:48,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29563/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29563/checkm_input OceanDNA-b29563/checkm_result
[2023-03-18 09:54:46,679] [INFO] Task succeeded: CheckM
[2023-03-18 09:54:46,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:54:46,682] [INFO] ===== Completeness check finished =====
[2023-03-18 09:54:46,682] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:54:46,683] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29563/markers.fasta)
[2023-03-18 09:54:46,684] [INFO] Task started: Blastn
[2023-03-18 09:54:46,684] [INFO] Running command: blastn -query OceanDNA-b29563/markers.fasta -db /var/lib/cwl/stg0869df21-c5fa-49cd-a267-ac99d1de554f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29563/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:54:48,504] [INFO] Task succeeded: Blastn
[2023-03-18 09:54:48,505] [INFO] Selected 13 target genomes.
[2023-03-18 09:54:48,505] [INFO] Target genome list was writen to OceanDNA-b29563/target_genomes_gtdb.txt
[2023-03-18 09:54:48,518] [INFO] Task started: fastANI
[2023-03-18 09:54:48,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg187554c4-a9be-4b94-9e36-ee9289a7fcf1/OceanDNA-b29563.fa --refList OceanDNA-b29563/target_genomes_gtdb.txt --output OceanDNA-b29563/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:54:58,810] [INFO] Task succeeded: fastANI
[2023-03-18 09:54:58,818] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:54:58,818] [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_013155465.1	s__Alterinioella nitratireducens	98.4728	1122	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	conclusive
GCF_004000255.1	s__Nioella ostreopsis	80.722	766	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	80.5942	708	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003428585.1	s__Nioella sp003428585	80.3534	693	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783145.1	s__Nioella sp002783145	80.18	538	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879715.1	s__Nioella nitratireducens	79.9597	714	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	79.4835	589	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.3163	504	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	78.9975	549	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644125.1	s__Rhodophyticola sp017644125	78.9342	542	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	99.99	99.99	0.99	0.98	3	-
GCF_003944755.1	s__Rhodovulum robiginosum	78.8442	467	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688285.1	s__Rhodophyticola porphyridii	78.4927	511	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.3436	474	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:54:59,008] [INFO] GTDB search result was written to OceanDNA-b29563/result_gtdb.tsv
[2023-03-18 09:54:59,008] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:54:59,010] [INFO] DFAST_QC result json was written to OceanDNA-b29563/dqc_result.json
[2023-03-18 09:54:59,010] [INFO] DFAST_QC completed!
[2023-03-18 09:54:59,010] [INFO] Total running time: 0h1m49s