[2023-03-15 10:21:46,236] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:46,236] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:46,236] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc906ef9-110f-4352-a515-44df68ca7586/dqc_reference
[2023-03-15 10:21:47,931] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:47,934] [INFO] Task started: Prodigal
[2023-03-15 10:21:47,934] [INFO] Running command: cat /var/lib/cwl/stg05f26823-79a6-41c0-8f81-e65d71bcd9d7/OceanDNA-b29551.fa | prodigal -d OceanDNA-b29551/cds.fna -a OceanDNA-b29551/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:21:59,956] [INFO] Task succeeded: Prodigal
[2023-03-15 10:21:59,957] [INFO] Task started: HMMsearch
[2023-03-15 10:21:59,957] [INFO] Running command: hmmsearch --tblout OceanDNA-b29551/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc906ef9-110f-4352-a515-44df68ca7586/dqc_reference/reference_markers.hmm OceanDNA-b29551/protein.faa > /dev/null
[2023-03-15 10:22:00,273] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:22:00,273] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg05f26823-79a6-41c0-8f81-e65d71bcd9d7/OceanDNA-b29551.fa]
[2023-03-15 10:22:00,294] [INFO] Query marker FASTA was written to OceanDNA-b29551/markers.fasta
[2023-03-15 10:22:00,294] [INFO] Task started: Blastn
[2023-03-15 10:22:00,294] [INFO] Running command: blastn -query OceanDNA-b29551/markers.fasta -db /var/lib/cwl/stgfc906ef9-110f-4352-a515-44df68ca7586/dqc_reference/reference_markers.fasta -out OceanDNA-b29551/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:01,113] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:01,114] [INFO] Selected 17 target genomes.
[2023-03-15 10:22:01,114] [INFO] Target genome list was writen to OceanDNA-b29551/target_genomes.txt
[2023-03-15 10:22:01,125] [INFO] Task started: fastANI
[2023-03-15 10:22:01,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg05f26823-79a6-41c0-8f81-e65d71bcd9d7/OceanDNA-b29551.fa --refList OceanDNA-b29551/target_genomes.txt --output OceanDNA-b29551/fastani_result.tsv --threads 1
[2023-03-15 10:22:13,976] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:13,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc906ef9-110f-4352-a515-44df68ca7586/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:22:13,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc906ef9-110f-4352-a515-44df68ca7586/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:22:13,987] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:22:13,987] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:22:13,987] [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	83.8412	505	590	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	83.6501	491	590	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	81.3141	443	590	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.6043	280	590	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.5023	274	590	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	78.3331	247	590	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.265	232	590	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2361	234	590	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	77.8337	198	590	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	77.8094	262	590	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.7808	203	590	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.7446	205	590	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.714	198	590	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	77.6127	221	590	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.4174	209	590	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3845	188	590	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.8278	119	590	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:22:13,987] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29551/tc_result.tsv
[2023-03-15 10:22:13,987] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:22:13,987] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:22:13,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc906ef9-110f-4352-a515-44df68ca7586/dqc_reference/checkm_data
[2023-03-15 10:22:13,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:22:13,993] [INFO] Task started: CheckM
[2023-03-15 10:22:13,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29551/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29551/checkm_input OceanDNA-b29551/checkm_result
[2023-03-15 10:22:47,469] [INFO] Task succeeded: CheckM
[2023-03-15 10:22:47,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.10%
Contamintation: 0.90%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 10:22:47,472] [INFO] ===== Completeness check finished =====
[2023-03-15 10:22:47,472] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:22:47,473] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29551/markers.fasta)
[2023-03-15 10:22:47,473] [INFO] Task started: Blastn
[2023-03-15 10:22:47,473] [INFO] Running command: blastn -query OceanDNA-b29551/markers.fasta -db /var/lib/cwl/stgfc906ef9-110f-4352-a515-44df68ca7586/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29551/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:48,937] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:48,938] [INFO] Selected 12 target genomes.
[2023-03-15 10:22:48,938] [INFO] Target genome list was writen to OceanDNA-b29551/target_genomes_gtdb.txt
[2023-03-15 10:22:49,382] [INFO] Task started: fastANI
[2023-03-15 10:22:49,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg05f26823-79a6-41c0-8f81-e65d71bcd9d7/OceanDNA-b29551.fa --refList OceanDNA-b29551/target_genomes_gtdb.txt --output OceanDNA-b29551/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:22:57,429] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:57,437] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:22:57,437] [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_004000255.1	s__Nioella ostreopsis	83.8115	506	590	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	83.6501	491	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001879715.1	s__Nioella nitratireducens	81.3289	442	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003428585.1	s__Nioella sp003428585	81.1542	420	590	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	80.6949	344	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155465.1	s__Alterinioella nitratireducens	80.5466	400	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	-
GCF_012395815.1	s__Roseicyclus sp012395815	79.2838	331	590	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	79.2038	292	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.6434	265	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000590925.1	s__Roseicyclus elongatus	78.6195	279	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	78.1818	172	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518925.1	s__Paracoccus sp000518925	77.4788	213	590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-15 10:22:57,437] [INFO] GTDB search result was written to OceanDNA-b29551/result_gtdb.tsv
[2023-03-15 10:22:57,437] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:22:57,439] [INFO] DFAST_QC result json was written to OceanDNA-b29551/dqc_result.json
[2023-03-15 10:22:57,439] [INFO] DFAST_QC completed!
[2023-03-15 10:22:57,439] [INFO] Total running time: 0h1m11s