[2023-03-15 21:01:44,348] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,349] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,349] [INFO] DQC Reference Directory: /var/lib/cwl/stgf029620f-88e6-401d-9b19-edc6eaa87a26/dqc_reference
[2023-03-15 21:01:45,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,597] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,597] [INFO] Running command: cat /var/lib/cwl/stgb6a26832-3787-43ce-a765-f71df5592847/OceanDNA-b28032.fa | prodigal -d OceanDNA-b28032/cds.fna -a OceanDNA-b28032/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:01,025] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:01,025] [INFO] Task started: HMMsearch
[2023-03-15 21:02:01,025] [INFO] Running command: hmmsearch --tblout OceanDNA-b28032/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf029620f-88e6-401d-9b19-edc6eaa87a26/dqc_reference/reference_markers.hmm OceanDNA-b28032/protein.faa > /dev/null
[2023-03-15 21:02:01,211] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:01,212] [INFO] Found 6/6 markers.
[2023-03-15 21:02:01,228] [INFO] Query marker FASTA was written to OceanDNA-b28032/markers.fasta
[2023-03-15 21:02:01,229] [INFO] Task started: Blastn
[2023-03-15 21:02:01,229] [INFO] Running command: blastn -query OceanDNA-b28032/markers.fasta -db /var/lib/cwl/stgf029620f-88e6-401d-9b19-edc6eaa87a26/dqc_reference/reference_markers.fasta -out OceanDNA-b28032/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:01,851] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:01,851] [INFO] Selected 26 target genomes.
[2023-03-15 21:02:01,852] [INFO] Target genome list was writen to OceanDNA-b28032/target_genomes.txt
[2023-03-15 21:02:01,869] [INFO] Task started: fastANI
[2023-03-15 21:02:01,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6a26832-3787-43ce-a765-f71df5592847/OceanDNA-b28032.fa --refList OceanDNA-b28032/target_genomes.txt --output OceanDNA-b28032/fastani_result.tsv --threads 1
[2023-03-15 21:02:16,750] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:16,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf029620f-88e6-401d-9b19-edc6eaa87a26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:16,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf029620f-88e6-401d-9b19-edc6eaa87a26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:16,764] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:16,764] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:16,764] [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
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	77.4114	189	811	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	77.1129	108	811	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	77.0806	132	811	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	77.0354	92	811	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.9868	107	811	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	76.9662	133	811	95	below_threshold
Cochlodiniinecator piscidefendens	strain=M26A2M	GCA_011326755.1	2715756	2715756	type	True	76.7657	68	811	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.7384	117	811	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.6667	115	811	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	76.5802	89	811	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	76.4408	76	811	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	76.3143	92	811	95	below_threshold
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	76.2931	74	811	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.245	63	811	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	76.2399	93	811	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.2368	63	811	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.1496	51	811	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.0972	62	811	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.0696	63	811	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	75.9614	59	811	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	75.9614	59	811	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_900102795.1	1156985	1156985	type	True	75.9042	60	811	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	75.6825	52	811	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:16,766] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28032/tc_result.tsv
[2023-03-15 21:02:16,766] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:16,766] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:16,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf029620f-88e6-401d-9b19-edc6eaa87a26/dqc_reference/checkm_data
[2023-03-15 21:02:16,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:16,771] [INFO] Task started: CheckM
[2023-03-15 21:02:16,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28032/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28032/checkm_input OceanDNA-b28032/checkm_result
[2023-03-15 21:02:58,253] [INFO] Task succeeded: CheckM
[2023-03-15 21:02:58,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:02:58,256] [INFO] ===== Completeness check finished =====
[2023-03-15 21:02:58,256] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:02:58,256] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28032/markers.fasta)
[2023-03-15 21:02:58,256] [INFO] Task started: Blastn
[2023-03-15 21:02:58,256] [INFO] Running command: blastn -query OceanDNA-b28032/markers.fasta -db /var/lib/cwl/stgf029620f-88e6-401d-9b19-edc6eaa87a26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28032/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:59,393] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:59,394] [INFO] Selected 14 target genomes.
[2023-03-15 21:02:59,394] [INFO] Target genome list was writen to OceanDNA-b28032/target_genomes_gtdb.txt
[2023-03-15 21:02:59,599] [INFO] Task started: fastANI
[2023-03-15 21:02:59,599] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6a26832-3787-43ce-a765-f71df5592847/OceanDNA-b28032.fa --refList OceanDNA-b28032/target_genomes_gtdb.txt --output OceanDNA-b28032/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:08,002] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:08,011] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:03:08,011] [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_905182105.1	s__Ascidiaceihabitans sp905182105	99.6422	754	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002478745.1	s__Ascidiaceihabitans sp002478745	89.7423	633	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.75	99.75	0.89	0.89	2	-
GCA_018647275.1	s__Ascidiaceihabitans sp018647275	88.9949	386	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182355.1	s__Ascidiaceihabitans sp905182355	79.0408	361	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302465.1	s__Ascidiaceihabitans donghaensis	77.3822	191	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	77.0806	132	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900116285.1	s__Sulfitobacter marinus	76.9868	107	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	76.9534	110	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.8178	97	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	76.6349	85	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	76.6314	95	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_900112755.1	s__Sulfitobacter brevis	76.3143	92	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285415.1	s__Actibacterium pelagium	76.245	63	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007995245.1	s__Tateyamaria sp007995245	76.0448	68	811	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:08,011] [INFO] GTDB search result was written to OceanDNA-b28032/result_gtdb.tsv
[2023-03-15 21:03:08,011] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:08,013] [INFO] DFAST_QC result json was written to OceanDNA-b28032/dqc_result.json
[2023-03-15 21:03:08,014] [INFO] DFAST_QC completed!
[2023-03-15 21:03:08,014] [INFO] Total running time: 0h1m24s