[2023-03-16 08:59:43,909] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:59:43,909] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:59:43,909] [INFO] DQC Reference Directory: /var/lib/cwl/stgabeecb2d-a0c9-46de-90c8-d586449b3cbb/dqc_reference
[2023-03-16 08:59:45,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:59:45,387] [INFO] Task started: Prodigal
[2023-03-16 08:59:45,387] [INFO] Running command: cat /var/lib/cwl/stg2d293a0a-deb0-4551-95d7-5e3532238ac3/OceanDNA-b30085.fa | prodigal -d OceanDNA-b30085/cds.fna -a OceanDNA-b30085/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:59:59,719] [INFO] Task succeeded: Prodigal
[2023-03-16 08:59:59,719] [INFO] Task started: HMMsearch
[2023-03-16 08:59:59,719] [INFO] Running command: hmmsearch --tblout OceanDNA-b30085/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabeecb2d-a0c9-46de-90c8-d586449b3cbb/dqc_reference/reference_markers.hmm OceanDNA-b30085/protein.faa > /dev/null
[2023-03-16 08:59:59,906] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:59:59,907] [INFO] Found 6/6 markers.
[2023-03-16 08:59:59,928] [INFO] Query marker FASTA was written to OceanDNA-b30085/markers.fasta
[2023-03-16 08:59:59,929] [INFO] Task started: Blastn
[2023-03-16 08:59:59,929] [INFO] Running command: blastn -query OceanDNA-b30085/markers.fasta -db /var/lib/cwl/stgabeecb2d-a0c9-46de-90c8-d586449b3cbb/dqc_reference/reference_markers.fasta -out OceanDNA-b30085/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:00:00,699] [INFO] Task succeeded: Blastn
[2023-03-16 09:00:00,700] [INFO] Selected 27 target genomes.
[2023-03-16 09:00:00,700] [INFO] Target genome list was writen to OceanDNA-b30085/target_genomes.txt
[2023-03-16 09:00:00,713] [INFO] Task started: fastANI
[2023-03-16 09:00:00,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d293a0a-deb0-4551-95d7-5e3532238ac3/OceanDNA-b30085.fa --refList OceanDNA-b30085/target_genomes.txt --output OceanDNA-b30085/fastani_result.tsv --threads 1
[2023-03-16 09:00:19,341] [INFO] Task succeeded: fastANI
[2023-03-16 09:00:19,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabeecb2d-a0c9-46de-90c8-d586449b3cbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:00:19,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabeecb2d-a0c9-46de-90c8-d586449b3cbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:00:19,356] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:00:19,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:00:19,357] [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
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	82.6409	580	773	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	81.1187	532	773	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	78.3226	347	773	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	78.3137	353	773	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.2163	331	773	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.2108	335	773	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	78.1223	344	773	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	77.9194	328	773	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	77.8937	365	773	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.8933	337	773	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	77.8709	292	773	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.84	284	773	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	77.5633	222	773	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.4615	257	773	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.46	263	773	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.4567	265	773	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.4462	301	773	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.442	199	773	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	77.422	291	773	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	77.3859	225	773	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	77.3205	208	773	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.3147	255	773	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	77.286	231	773	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.1976	223	773	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.1941	229	773	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	76.9992	237	773	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.7234	145	773	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:00:19,357] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30085/tc_result.tsv
[2023-03-16 09:00:19,357] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:00:19,357] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:00:19,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabeecb2d-a0c9-46de-90c8-d586449b3cbb/dqc_reference/checkm_data
[2023-03-16 09:00:19,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:00:19,531] [INFO] Task started: CheckM
[2023-03-16 09:00:19,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30085/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30085/checkm_input OceanDNA-b30085/checkm_result
[2023-03-16 09:00:58,001] [INFO] Task succeeded: CheckM
[2023-03-16 09:00:58,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:00:58,044] [INFO] ===== Completeness check finished =====
[2023-03-16 09:00:58,044] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:00:58,044] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30085/markers.fasta)
[2023-03-16 09:00:58,045] [INFO] Task started: Blastn
[2023-03-16 09:00:58,045] [INFO] Running command: blastn -query OceanDNA-b30085/markers.fasta -db /var/lib/cwl/stgabeecb2d-a0c9-46de-90c8-d586449b3cbb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30085/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:00:59,336] [INFO] Task succeeded: Blastn
[2023-03-16 09:00:59,337] [INFO] Selected 12 target genomes.
[2023-03-16 09:00:59,337] [INFO] Target genome list was writen to OceanDNA-b30085/target_genomes_gtdb.txt
[2023-03-16 09:00:59,357] [INFO] Task started: fastANI
[2023-03-16 09:00:59,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d293a0a-deb0-4551-95d7-5e3532238ac3/OceanDNA-b30085.fa --refList OceanDNA-b30085/target_genomes_gtdb.txt --output OceanDNA-b30085/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:01:08,588] [INFO] Task succeeded: fastANI
[2023-03-16 09:01:08,595] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:01:08,596] [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_900156535.1	s__Roseovarius nanhaiticus	83.1204	607	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003072125.1	s__Roseovarius sediminicola	82.6409	580	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316635.1	s__Roseovarius dicentrarchi	81.1446	530	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006125015.1	s__Roseovarius arcticus	80.5588	516	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	79.3783	431	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	78.2276	330	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCA_002720475.1	s__Roseovarius sp002720475	77.9854	229	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCA_006226775.1	s__Marinovum sp006226775	77.9675	309	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	77.5091	316	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	77.4736	261	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	77.2389	233	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	76.9988	181	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:01:08,608] [INFO] GTDB search result was written to OceanDNA-b30085/result_gtdb.tsv
[2023-03-16 09:01:08,608] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:01:08,610] [INFO] DFAST_QC result json was written to OceanDNA-b30085/dqc_result.json
[2023-03-16 09:01:08,611] [INFO] DFAST_QC completed!
[2023-03-16 09:01:08,611] [INFO] Total running time: 0h1m25s