[2023-03-15 08:55:06,628] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,628] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,628] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaf47280-f997-4d5d-b4f6-8a492d5b7efe/dqc_reference
[2023-03-15 08:55:08,346] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,347] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,347] [INFO] Running command: cat /var/lib/cwl/stgd468d409-dbbf-4bb2-b6f0-cde11722e1bf/OceanDNA-b29538.fa | prodigal -d OceanDNA-b29538/cds.fna -a OceanDNA-b29538/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:22,460] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:22,461] [INFO] Task started: HMMsearch
[2023-03-15 08:55:22,461] [INFO] Running command: hmmsearch --tblout OceanDNA-b29538/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaf47280-f997-4d5d-b4f6-8a492d5b7efe/dqc_reference/reference_markers.hmm OceanDNA-b29538/protein.faa > /dev/null
[2023-03-15 08:55:22,697] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:22,697] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd468d409-dbbf-4bb2-b6f0-cde11722e1bf/OceanDNA-b29538.fa]
[2023-03-15 08:55:22,719] [INFO] Query marker FASTA was written to OceanDNA-b29538/markers.fasta
[2023-03-15 08:55:22,719] [INFO] Task started: Blastn
[2023-03-15 08:55:22,719] [INFO] Running command: blastn -query OceanDNA-b29538/markers.fasta -db /var/lib/cwl/stgeaf47280-f997-4d5d-b4f6-8a492d5b7efe/dqc_reference/reference_markers.fasta -out OceanDNA-b29538/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:23,412] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:23,413] [INFO] Selected 30 target genomes.
[2023-03-15 08:55:23,414] [INFO] Target genome list was writen to OceanDNA-b29538/target_genomes.txt
[2023-03-15 08:55:23,428] [INFO] Task started: fastANI
[2023-03-15 08:55:23,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgd468d409-dbbf-4bb2-b6f0-cde11722e1bf/OceanDNA-b29538.fa --refList OceanDNA-b29538/target_genomes.txt --output OceanDNA-b29538/fastani_result.tsv --threads 1
[2023-03-15 08:55:43,945] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:43,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaf47280-f997-4d5d-b4f6-8a492d5b7efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:43,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaf47280-f997-4d5d-b4f6-8a492d5b7efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:43,961] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:43,961] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:55:43,961] [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
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	78.4803	275	640	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	78.4731	293	640	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	78.4706	293	640	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	78.4602	288	640	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	78.3234	303	640	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	76.877	107	640	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.7328	111	640	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	76.7134	127	640	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.6002	84	640	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	76.5922	120	640	95	below_threshold
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	76.5697	91	640	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.5518	132	640	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.477	122	640	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.3825	108	640	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	76.3379	112	640	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.3186	61	640	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	76.2909	85	640	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	76.2723	105	640	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	76.2688	107	640	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	76.2657	93	640	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	76.2608	97	640	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.171	81	640	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	76.1476	91	640	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.0732	79	640	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	75.997	60	640	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	75.973	79	640	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	75.9429	75	640	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	75.8138	55	640	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	75.766	55	640	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:55:43,962] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29538/tc_result.tsv
[2023-03-15 08:55:43,962] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:43,962] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:43,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaf47280-f997-4d5d-b4f6-8a492d5b7efe/dqc_reference/checkm_data
[2023-03-15 08:55:43,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:43,969] [INFO] Task started: CheckM
[2023-03-15 08:55:43,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29538/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29538/checkm_input OceanDNA-b29538/checkm_result
[2023-03-15 08:56:21,883] [INFO] Task succeeded: CheckM
[2023-03-15 08:56:21,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:56:21,886] [INFO] ===== Completeness check finished =====
[2023-03-15 08:56:21,886] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:56:21,886] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29538/markers.fasta)
[2023-03-15 08:56:21,886] [INFO] Task started: Blastn
[2023-03-15 08:56:21,886] [INFO] Running command: blastn -query OceanDNA-b29538/markers.fasta -db /var/lib/cwl/stgeaf47280-f997-4d5d-b4f6-8a492d5b7efe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29538/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:56:23,112] [INFO] Task succeeded: Blastn
[2023-03-15 08:56:23,113] [INFO] Selected 29 target genomes.
[2023-03-15 08:56:23,113] [INFO] Target genome list was writen to OceanDNA-b29538/target_genomes_gtdb.txt
[2023-03-15 08:56:23,156] [INFO] Task started: fastANI
[2023-03-15 08:56:23,157] [INFO] Running command: fastANI --query /var/lib/cwl/stgd468d409-dbbf-4bb2-b6f0-cde11722e1bf/OceanDNA-b29538.fa --refList OceanDNA-b29538/target_genomes_gtdb.txt --output OceanDNA-b29538/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:56:42,748] [INFO] Task succeeded: fastANI
[2023-03-15 08:56:42,763] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:56:42,763] [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_002115725.1	s__Marivita cryptomonadis	78.4713	275	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	99.81	99.78	0.91	0.91	31	-
GCF_002115805.1	s__Marivita geojedonensis	78.4608	294	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900129875.1	s__Marivita hallyeonensis	78.4602	288	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643905.1	s__Marivita sp017643905	78.4602	259	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637725.1	s__Marivita lacus	78.3234	303	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003149565.1	s__Marivita sp003149565	78.0558	234	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313245.1	s__Primorskyibacter marinus	76.877	107	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	76.8124	154	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	76.7328	111	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	76.6446	127	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	76.6031	125	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCF_014651375.1	s__Tateyamaria omphalii	76.5697	91	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	76.5367	133	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_009363655.1	s__Roseovarius sp009363655	76.4965	91	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_009857745.1	s__Thalassobius mangrovi	76.477	122	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	76.4657	86	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860705.1	s__Salipiger sp018860705	76.3859	108	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	76.3825	108	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018200035.1	s__Sulfitobacter sp018200035	76.381	103	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188035.1	s__Puniceibacterium sediminis	76.3419	113	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644665.1	s__Roseobacter sp015644665	76.287	98	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	76.2723	105	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900172265.1	s__Roseivivax jejudonensis	76.2657	93	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115815.1	s__Roseivivax halotolerans	76.2608	97	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.75	97.75	0.88	0.88	2	-
GCF_900114415.1	s__Shimia haliotis	76.171	81	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	76.0291	86	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	75.9174	83	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-15 08:56:42,763] [INFO] GTDB search result was written to OceanDNA-b29538/result_gtdb.tsv
[2023-03-15 08:56:42,763] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:56:42,766] [INFO] DFAST_QC result json was written to OceanDNA-b29538/dqc_result.json
[2023-03-15 08:56:42,766] [INFO] DFAST_QC completed!
[2023-03-15 08:56:42,766] [INFO] Total running time: 0h1m36s