[2023-03-18 21:34:09,332] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:34:09,332] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:34:09,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg072f77d4-a8b5-4bda-a648-f2880dacd3dd/dqc_reference
[2023-03-18 21:34:10,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:34:10,575] [INFO] Task started: Prodigal
[2023-03-18 21:34:10,575] [INFO] Running command: cat /var/lib/cwl/stg152bf5e6-36ec-4579-b49c-069121aaaccf/OceanDNA-b30479.fa | prodigal -d OceanDNA-b30479/cds.fna -a OceanDNA-b30479/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:34:33,536] [INFO] Task succeeded: Prodigal
[2023-03-18 21:34:33,537] [INFO] Task started: HMMsearch
[2023-03-18 21:34:33,537] [INFO] Running command: hmmsearch --tblout OceanDNA-b30479/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg072f77d4-a8b5-4bda-a648-f2880dacd3dd/dqc_reference/reference_markers.hmm OceanDNA-b30479/protein.faa > /dev/null
[2023-03-18 21:34:33,744] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:34:33,745] [INFO] Found 6/6 markers.
[2023-03-18 21:34:33,770] [INFO] Query marker FASTA was written to OceanDNA-b30479/markers.fasta
[2023-03-18 21:34:33,771] [INFO] Task started: Blastn
[2023-03-18 21:34:33,771] [INFO] Running command: blastn -query OceanDNA-b30479/markers.fasta -db /var/lib/cwl/stg072f77d4-a8b5-4bda-a648-f2880dacd3dd/dqc_reference/reference_markers.fasta -out OceanDNA-b30479/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:34:34,495] [INFO] Task succeeded: Blastn
[2023-03-18 21:34:34,497] [INFO] Selected 33 target genomes.
[2023-03-18 21:34:34,497] [INFO] Target genome list was writen to OceanDNA-b30479/target_genomes.txt
[2023-03-18 21:34:34,515] [INFO] Task started: fastANI
[2023-03-18 21:34:34,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg152bf5e6-36ec-4579-b49c-069121aaaccf/OceanDNA-b30479.fa --refList OceanDNA-b30479/target_genomes.txt --output OceanDNA-b30479/fastani_result.tsv --threads 1
[2023-03-18 21:34:57,525] [INFO] Task succeeded: fastANI
[2023-03-18 21:34:57,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg072f77d4-a8b5-4bda-a648-f2880dacd3dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:34:57,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg072f77d4-a8b5-4bda-a648-f2880dacd3dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:34:57,543] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:34:57,543] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:34:57,543] [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
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	78.9164	514	1165	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.1346	415	1165	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.1334	420	1165	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.0049	354	1165	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.9105	416	1165	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.8517	371	1165	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	77.8484	424	1165	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	77.8224	364	1165	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.7685	332	1165	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.7491	375	1165	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.749	370	1165	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.7389	375	1165	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.6214	397	1165	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	77.5288	305	1165	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.4991	308	1165	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	77.4343	317	1165	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.4221	347	1165	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.3108	280	1165	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.2647	297	1165	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.2252	316	1165	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.2129	300	1165	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	77.1251	255	1165	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.1223	252	1165	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.0685	243	1165	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.0523	232	1165	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.8585	282	1165	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	76.8585	247	1165	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.8372	172	1165	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.8043	205	1165	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.7956	177	1165	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.673	259	1165	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.2367	123	1165	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	75.99	123	1165	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:34:57,545] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30479/tc_result.tsv
[2023-03-18 21:34:57,547] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:34:57,547] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:34:57,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg072f77d4-a8b5-4bda-a648-f2880dacd3dd/dqc_reference/checkm_data
[2023-03-18 21:34:57,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:34:57,556] [INFO] Task started: CheckM
[2023-03-18 21:34:57,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30479/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30479/checkm_input OceanDNA-b30479/checkm_result
[2023-03-18 21:35:59,320] [INFO] Task succeeded: CheckM
[2023-03-18 21:35:59,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.76%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:35:59,342] [INFO] ===== Completeness check finished =====
[2023-03-18 21:35:59,342] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:35:59,343] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30479/markers.fasta)
[2023-03-18 21:35:59,343] [INFO] Task started: Blastn
[2023-03-18 21:35:59,343] [INFO] Running command: blastn -query OceanDNA-b30479/markers.fasta -db /var/lib/cwl/stg072f77d4-a8b5-4bda-a648-f2880dacd3dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30479/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:36:00,542] [INFO] Task succeeded: Blastn
[2023-03-18 21:36:00,544] [INFO] Selected 25 target genomes.
[2023-03-18 21:36:00,544] [INFO] Target genome list was writen to OceanDNA-b30479/target_genomes_gtdb.txt
[2023-03-18 21:36:00,661] [INFO] Task started: fastANI
[2023-03-18 21:36:00,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg152bf5e6-36ec-4579-b49c-069121aaaccf/OceanDNA-b30479.fa --refList OceanDNA-b30479/target_genomes_gtdb.txt --output OceanDNA-b30479/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:36:19,427] [INFO] Task succeeded: fastANI
[2023-03-18 21:36:19,441] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:36:19,442] [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_001969365.1	s__Tateyamaria omphalii_A	79.4878	627	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995245.1	s__Tateyamaria sp007995245	79.3468	601	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814025.1	s__Tateyamaria sp000814025	79.2909	611	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651375.1	s__Tateyamaria omphalii	78.9289	512	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	77.932	378	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.9105	416	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.8697	369	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811755.1	s__Roseobacter cerasinus	77.8229	364	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	77.8088	409	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	77.7782	331	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.76	368	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.7492	375	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009363555.1	s__Sulfitobacter sp009363555	77.705	362	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	77.6704	329	1165	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_013031405.1	s__Ruegeria sp013031405	77.6482	383	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.6059	399	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCA_003511785.1	s__UBA7951 sp003511785	77.5931	224	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	77.424	318	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	77.4172	357	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803475.1	s__Aliishimia ponticola	77.4134	348	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216475.1	s__GCA-004216475 sp004216475	77.3633	341	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-004216475	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302455.1	s__Ruegeria_E mediterranea	77.234	315	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	99.84	99.84	0.96	0.96	2	-
GCF_009649175.1	s__Rhodovulum strictum	77.0791	242	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	76.9567	182	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	76.8393	248	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:36:19,442] [INFO] GTDB search result was written to OceanDNA-b30479/result_gtdb.tsv
[2023-03-18 21:36:19,442] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:36:19,446] [INFO] DFAST_QC result json was written to OceanDNA-b30479/dqc_result.json
[2023-03-18 21:36:19,446] [INFO] DFAST_QC completed!
[2023-03-18 21:36:19,446] [INFO] Total running time: 0h2m10s