[2023-03-14 14:16:15,406] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:16:15,406] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:16:15,406] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1aaa99a-cea9-493d-a143-a0bba20f9d81/dqc_reference
[2023-03-14 14:16:16,483] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:16:16,483] [INFO] Task started: Prodigal
[2023-03-14 14:16:16,483] [INFO] Running command: cat /var/lib/cwl/stge4ab927c-80f7-4068-ac06-e7f7130c3ba2/OceanDNA-b28170.fa | prodigal -d OceanDNA-b28170/cds.fna -a OceanDNA-b28170/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:16:50,860] [INFO] Task succeeded: Prodigal
[2023-03-14 14:16:50,860] [INFO] Task started: HMMsearch
[2023-03-14 14:16:50,860] [INFO] Running command: hmmsearch --tblout OceanDNA-b28170/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1aaa99a-cea9-493d-a143-a0bba20f9d81/dqc_reference/reference_markers.hmm OceanDNA-b28170/protein.faa > /dev/null
[2023-03-14 14:16:51,336] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:16:51,337] [INFO] Found 6/6 markers.
[2023-03-14 14:16:51,373] [INFO] Query marker FASTA was written to OceanDNA-b28170/markers.fasta
[2023-03-14 14:16:51,383] [INFO] Task started: Blastn
[2023-03-14 14:16:51,383] [INFO] Running command: blastn -query OceanDNA-b28170/markers.fasta -db /var/lib/cwl/stgf1aaa99a-cea9-493d-a143-a0bba20f9d81/dqc_reference/reference_markers.fasta -out OceanDNA-b28170/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:16:52,697] [INFO] Task succeeded: Blastn
[2023-03-14 14:16:52,699] [INFO] Selected 29 target genomes.
[2023-03-14 14:16:52,699] [INFO] Target genome list was writen to OceanDNA-b28170/target_genomes.txt
[2023-03-14 14:16:52,786] [INFO] Task started: fastANI
[2023-03-14 14:16:52,786] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ab927c-80f7-4068-ac06-e7f7130c3ba2/OceanDNA-b28170.fa --refList OceanDNA-b28170/target_genomes.txt --output OceanDNA-b28170/fastani_result.tsv --threads 1
[2023-03-14 14:17:23,378] [INFO] Task succeeded: fastANI
[2023-03-14 14:17:23,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1aaa99a-cea9-493d-a143-a0bba20f9d81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:17:23,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1aaa99a-cea9-493d-a143-a0bba20f9d81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:17:23,395] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:17:23,395] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:17:23,396] [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
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.7536	522	1196	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.7456	529	1196	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.6636	496	1196	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.5751	498	1196	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.5737	498	1196	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.5529	445	1196	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.5361	446	1196	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.5151	417	1196	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.4869	466	1196	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	78.3452	408	1196	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.3451	408	1196	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.2448	405	1196	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.2089	434	1196	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.1865	414	1196	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.1727	410	1196	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	78.1566	403	1196	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.1257	449	1196	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.1138	405	1196	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.9399	420	1196	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.9258	426	1196	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	77.9126	347	1196	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	77.8732	376	1196	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.7412	402	1196	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	77.7104	321	1196	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	77.6937	378	1196	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6465	345	1196	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.482	368	1196	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.4341	290	1196	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	77.22	275	1196	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:17:23,396] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28170/tc_result.tsv
[2023-03-14 14:17:23,396] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:17:23,396] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:17:23,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1aaa99a-cea9-493d-a143-a0bba20f9d81/dqc_reference/checkm_data
[2023-03-14 14:17:23,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:17:23,421] [INFO] Task started: CheckM
[2023-03-14 14:17:23,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28170/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28170/checkm_input OceanDNA-b28170/checkm_result
[2023-03-14 14:18:33,922] [INFO] Task succeeded: CheckM
[2023-03-14 14:18:33,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:18:33,925] [INFO] ===== Completeness check finished =====
[2023-03-14 14:18:33,925] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:18:33,925] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28170/markers.fasta)
[2023-03-14 14:18:33,926] [INFO] Task started: Blastn
[2023-03-14 14:18:33,926] [INFO] Running command: blastn -query OceanDNA-b28170/markers.fasta -db /var/lib/cwl/stgf1aaa99a-cea9-493d-a143-a0bba20f9d81/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28170/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:18:35,616] [INFO] Task succeeded: Blastn
[2023-03-14 14:18:35,617] [INFO] Selected 24 target genomes.
[2023-03-14 14:18:35,618] [INFO] Target genome list was writen to OceanDNA-b28170/target_genomes_gtdb.txt
[2023-03-14 14:18:35,734] [INFO] Task started: fastANI
[2023-03-14 14:18:35,734] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ab927c-80f7-4068-ac06-e7f7130c3ba2/OceanDNA-b28170.fa --refList OceanDNA-b28170/target_genomes_gtdb.txt --output OceanDNA-b28170/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:18:57,043] [INFO] Task succeeded: fastANI
[2023-03-14 14:18:57,058] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:18:57,058] [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
GCA_002282555.1	s__EhC02 sp002282555	86.2762	436	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	84.2533	917	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.4948	577	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009857745.1	s__Thalassobius mangrovi	78.7583	528	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	78.5776	468	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.5457	502	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	78.5236	448	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_900129345.1	s__Ruegeria intermedia	78.5151	417	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.5102	441	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	78.3954	355	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	78.364	404	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCA_011048875.1	s__Rhodovulum sp011048875	78.2244	308	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	78.2175	433	1196	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_004339675.1	s__Rhodovulum steppense	78.1927	412	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.1111	406	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.027	416	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	78.0113	390	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002073975.1	s__Rhodovulum sp002073975	77.9931	338	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.9507	418	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003651245.1	s__Roseovarius spongiae	77.7961	388	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	77.7602	405	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_004342445.1	s__Rhodovulum euryhalinum	77.7308	402	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.5281	356	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCA_018524345.1	s__KMM-3653 sp018524345	76.8374	255	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMM-3653	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:18:57,059] [INFO] GTDB search result was written to OceanDNA-b28170/result_gtdb.tsv
[2023-03-14 14:18:57,064] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:18:57,069] [INFO] DFAST_QC result json was written to OceanDNA-b28170/dqc_result.json
[2023-03-14 14:18:57,070] [INFO] DFAST_QC completed!
[2023-03-14 14:18:57,070] [INFO] Total running time: 0h2m42s