[2023-03-16 08:30:41,844] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:30:41,844] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:30:41,845] [INFO] DQC Reference Directory: /var/lib/cwl/stgda382625-7e10-493a-aa0b-aafdd0a89eea/dqc_reference
[2023-03-16 08:30:42,938] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:30:42,939] [INFO] Task started: Prodigal
[2023-03-16 08:30:42,939] [INFO] Running command: cat /var/lib/cwl/stg0b3926e0-8fbc-45d1-b332-571239b33e2e/OceanDNA-b30136.fa | prodigal -d OceanDNA-b30136/cds.fna -a OceanDNA-b30136/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:30:57,533] [INFO] Task succeeded: Prodigal
[2023-03-16 08:30:57,533] [INFO] Task started: HMMsearch
[2023-03-16 08:30:57,533] [INFO] Running command: hmmsearch --tblout OceanDNA-b30136/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda382625-7e10-493a-aa0b-aafdd0a89eea/dqc_reference/reference_markers.hmm OceanDNA-b30136/protein.faa > /dev/null
[2023-03-16 08:30:57,710] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:30:57,711] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0b3926e0-8fbc-45d1-b332-571239b33e2e/OceanDNA-b30136.fa]
[2023-03-16 08:30:57,749] [INFO] Query marker FASTA was written to OceanDNA-b30136/markers.fasta
[2023-03-16 08:30:57,750] [INFO] Task started: Blastn
[2023-03-16 08:30:57,751] [INFO] Running command: blastn -query OceanDNA-b30136/markers.fasta -db /var/lib/cwl/stgda382625-7e10-493a-aa0b-aafdd0a89eea/dqc_reference/reference_markers.fasta -out OceanDNA-b30136/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:30:58,513] [INFO] Task succeeded: Blastn
[2023-03-16 08:30:58,526] [INFO] Selected 20 target genomes.
[2023-03-16 08:30:58,526] [INFO] Target genome list was writen to OceanDNA-b30136/target_genomes.txt
[2023-03-16 08:30:58,551] [INFO] Task started: fastANI
[2023-03-16 08:30:58,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b3926e0-8fbc-45d1-b332-571239b33e2e/OceanDNA-b30136.fa --refList OceanDNA-b30136/target_genomes.txt --output OceanDNA-b30136/fastani_result.tsv --threads 1
[2023-03-16 08:31:13,490] [INFO] Task succeeded: fastANI
[2023-03-16 08:31:13,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda382625-7e10-493a-aa0b-aafdd0a89eea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:31:13,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda382625-7e10-493a-aa0b-aafdd0a89eea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:31:13,502] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:31:13,502] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:31:13,502] [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
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	91.1282	703	773	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	84.2712	594	773	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	80.981	497	773	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	80.9749	479	773	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	80.8259	496	773	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	80.7689	505	773	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	80.6069	493	773	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	79.6833	446	773	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.4225	388	773	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	79.0382	427	773	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	78.6378	356	773	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	78.4407	325	773	95	below_threshold
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	78.3504	281	773	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	78.3008	281	773	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.1068	304	773	95	below_threshold
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	78.0177	316	773	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0013	288	773	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.906	290	773	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6428	236	773	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.6097	232	773	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:31:13,506] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30136/tc_result.tsv
[2023-03-16 08:31:13,515] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:31:13,515] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:31:13,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda382625-7e10-493a-aa0b-aafdd0a89eea/dqc_reference/checkm_data
[2023-03-16 08:31:13,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:31:13,521] [INFO] Task started: CheckM
[2023-03-16 08:31:13,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30136/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30136/checkm_input OceanDNA-b30136/checkm_result
[2023-03-16 08:31:52,185] [INFO] Task succeeded: CheckM
[2023-03-16 08:31:52,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.56%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 08:31:52,220] [INFO] ===== Completeness check finished =====
[2023-03-16 08:31:52,220] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:31:52,220] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30136/markers.fasta)
[2023-03-16 08:31:52,221] [INFO] Task started: Blastn
[2023-03-16 08:31:52,221] [INFO] Running command: blastn -query OceanDNA-b30136/markers.fasta -db /var/lib/cwl/stgda382625-7e10-493a-aa0b-aafdd0a89eea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30136/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:31:53,600] [INFO] Task succeeded: Blastn
[2023-03-16 08:31:53,605] [INFO] Selected 18 target genomes.
[2023-03-16 08:31:53,605] [INFO] Target genome list was writen to OceanDNA-b30136/target_genomes_gtdb.txt
[2023-03-16 08:31:53,676] [INFO] Task started: fastANI
[2023-03-16 08:31:53,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b3926e0-8fbc-45d1-b332-571239b33e2e/OceanDNA-b30136.fa --refList OceanDNA-b30136/target_genomes_gtdb.txt --output OceanDNA-b30136/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:32:07,826] [INFO] Task succeeded: fastANI
[2023-03-16 08:32:07,836] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:32:07,836] [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_000011965.2	s__Ruegeria_B pomeroyi	91.1282	703	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_010500245.1	s__Ruegeria_B sp010500245	86.0846	656	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	84.2421	596	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	81.1201	547	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	80.986	497	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	80.9748	479	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	80.8385	495	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	80.8254	469	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013032855.1	s__Ruegeria arenilitoris	80.2871	442	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCA_003511785.1	s__UBA7951 sp003511785	79.8687	322	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	79.6693	448	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	79.2987	272	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	78.7741	382	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017743995.1	s__Ruegeria sp017743995	78.7325	373	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318255.1	s__Ruegeria sp003318255	78.4816	342	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458195.1	s__Ruegeria atlantica	78.4237	325	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.59	95.51	0.84	0.83	3	-
GCF_017872555.1	s__Ruegeria sp017872555	78.3626	361	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.26	98.59	0.96	0.95	3	-
GCF_900106805.1	s__Ruegeria halocynthiae	78.0054	317	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:32:07,842] [INFO] GTDB search result was written to OceanDNA-b30136/result_gtdb.tsv
[2023-03-16 08:32:07,855] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:32:07,863] [INFO] DFAST_QC result json was written to OceanDNA-b30136/dqc_result.json
[2023-03-16 08:32:07,863] [INFO] DFAST_QC completed!
[2023-03-16 08:32:07,863] [INFO] Total running time: 0h1m26s