[2023-03-15 05:53:02,371] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:53:02,371] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:53:02,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bbda3a7-ba2c-4627-ae70-b1947d7c05f8/dqc_reference
[2023-03-15 05:53:03,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:53:03,552] [INFO] Task started: Prodigal
[2023-03-15 05:53:03,552] [INFO] Running command: cat /var/lib/cwl/stgaa629a76-6426-4eea-97d3-0e5e6faf5508/OceanDNA-b30710.fa | prodigal -d OceanDNA-b30710/cds.fna -a OceanDNA-b30710/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:53:24,520] [INFO] Task succeeded: Prodigal
[2023-03-15 05:53:24,521] [INFO] Task started: HMMsearch
[2023-03-15 05:53:24,521] [INFO] Running command: hmmsearch --tblout OceanDNA-b30710/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bbda3a7-ba2c-4627-ae70-b1947d7c05f8/dqc_reference/reference_markers.hmm OceanDNA-b30710/protein.faa > /dev/null
[2023-03-15 05:53:24,731] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:53:24,732] [INFO] Found 6/6 markers.
[2023-03-15 05:53:24,761] [INFO] Query marker FASTA was written to OceanDNA-b30710/markers.fasta
[2023-03-15 05:53:24,762] [INFO] Task started: Blastn
[2023-03-15 05:53:24,762] [INFO] Running command: blastn -query OceanDNA-b30710/markers.fasta -db /var/lib/cwl/stg6bbda3a7-ba2c-4627-ae70-b1947d7c05f8/dqc_reference/reference_markers.fasta -out OceanDNA-b30710/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:53:25,439] [INFO] Task succeeded: Blastn
[2023-03-15 05:53:25,444] [INFO] Selected 25 target genomes.
[2023-03-15 05:53:25,444] [INFO] Target genome list was writen to OceanDNA-b30710/target_genomes.txt
[2023-03-15 05:53:25,460] [INFO] Task started: fastANI
[2023-03-15 05:53:25,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa629a76-6426-4eea-97d3-0e5e6faf5508/OceanDNA-b30710.fa --refList OceanDNA-b30710/target_genomes.txt --output OceanDNA-b30710/fastani_result.tsv --threads 1
[2023-03-15 05:53:41,830] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:41,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bbda3a7-ba2c-4627-ae70-b1947d7c05f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:53:41,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bbda3a7-ba2c-4627-ae70-b1947d7c05f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:53:41,845] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:53:41,845] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:53:41,845] [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
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.3531	289	1067	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.2777	279	1067	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.2445	289	1067	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	77.2403	271	1067	95	below_threshold
Cypionkella psychrotolerans	strain=PAMC 27389	GCA_001294535.1	1678131	1678131	type	True	77.225	285	1067	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.2249	232	1067	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	77.178	239	1067	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.1064	277	1067	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	77.1004	242	1067	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	77.0914	266	1067	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	77.018	263	1067	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	76.9828	225	1067	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	76.9659	217	1067	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	76.9635	209	1067	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.9232	244	1067	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.9231	244	1067	95	below_threshold
Pseudorhodobacter ferrugineus	strain=DSM 5888	GCA_000420745.1	77008	77008	type	True	76.8782	184	1067	95	below_threshold
Gemmobacter tilapiae	strain=KCTC 23310	GCA_014652215.1	875041	875041	type	True	76.7789	211	1067	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	76.6576	228	1067	95	below_threshold
Pseudorhodobacter wandonensis	strain=KCTC 23672	GCA_001202035.1	1120568	1120568	type	True	76.4408	176	1067	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	76.0348	96	1067	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	75.8953	113	1067	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	75.7574	71	1067	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	75.6238	78	1067	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	75.5286	78	1067	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:53:41,847] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30710/tc_result.tsv
[2023-03-15 05:53:41,848] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:53:41,849] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:53:41,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bbda3a7-ba2c-4627-ae70-b1947d7c05f8/dqc_reference/checkm_data
[2023-03-15 05:53:41,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:53:41,857] [INFO] Task started: CheckM
[2023-03-15 05:53:41,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30710/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30710/checkm_input OceanDNA-b30710/checkm_result
[2023-03-15 05:54:34,263] [INFO] Task succeeded: CheckM
[2023-03-15 05:54:34,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:54:34,292] [INFO] ===== Completeness check finished =====
[2023-03-15 05:54:34,292] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:54:34,292] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30710/markers.fasta)
[2023-03-15 05:54:34,294] [INFO] Task started: Blastn
[2023-03-15 05:54:34,294] [INFO] Running command: blastn -query OceanDNA-b30710/markers.fasta -db /var/lib/cwl/stg6bbda3a7-ba2c-4627-ae70-b1947d7c05f8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30710/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:54:35,308] [INFO] Task succeeded: Blastn
[2023-03-15 05:54:35,310] [INFO] Selected 26 target genomes.
[2023-03-15 05:54:35,310] [INFO] Target genome list was writen to OceanDNA-b30710/target_genomes_gtdb.txt
[2023-03-15 05:54:35,332] [INFO] Task started: fastANI
[2023-03-15 05:54:35,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa629a76-6426-4eea-97d3-0e5e6faf5508/OceanDNA-b30710.fa --refList OceanDNA-b30710/target_genomes_gtdb.txt --output OceanDNA-b30710/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:54:51,749] [INFO] Task succeeded: fastANI
[2023-03-15 05:54:51,763] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:54:51,764] [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_903930735.1	s__CAIYZT01 sp903930735	79.2999	472	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAIYZT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001828855.1	s__Cypionkella sp001828855	77.8148	343	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	99.95	99.91	0.99	0.97	3	-
GCA_009773375.1	s__Cypionkella sp009773375	77.7484	331	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328815.1	s__UBA1943 sp013328815	77.6639	364	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	97.27	97.27	0.97	0.97	2	-
GCF_003991405.1	s__Pseudorhodobacter sp003991405	77.5731	232	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011008935.1	s__KMS-5 sp011008935	77.5449	324	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765795.1	s__UBA1943 sp016765795	77.3461	310	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	77.3224	237	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936395.1	s__ETT8 sp016936395	77.3157	247	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869835.1	s__KMS-5 sp016869835	77.3131	288	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243445.1	s__Gemmobacter_B straminiformis	77.2506	270	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010915705.1	s__ETT8 sp010915705	77.2371	231	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443995.1	s__ETT8 sp003443995	77.2255	291	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294535.1	s__Cypionkella psychrotolerans	77.2059	287	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845215.1	s__CYK-10 sp903845215	77.1982	223	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CYK-10	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011059185.1	s__Gemmobacter_B sp011059185	77.1208	270	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704435.1	s__JAAKGP01 sp016704435	77.0365	277	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	99.06	99.06	0.93	0.93	2	-
GCA_013298485.1	s__JAAFHS01 sp013298485	77.0341	155	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAFHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794355.1	s__ETT8 sp002794355	76.9969	249	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018063485.1	s__Cypionkella sp018063485	76.9645	171	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	76.9142	245	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000420745.1	s__Pseudorhodobacter ferrugineus	76.8957	185	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003509785.1	s__Gemmobacter sp003509785	76.8201	205	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	99.39	99.26	0.82	0.79	4	-
GCA_013297695.1	s__Rhodobacter_F sp013297695	76.6292	181	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	75.8953	113	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_003148765.1	s__Silicimonas algicola	75.5286	78	1067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 05:54:51,766] [INFO] GTDB search result was written to OceanDNA-b30710/result_gtdb.tsv
[2023-03-15 05:54:51,770] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:54:51,776] [INFO] DFAST_QC result json was written to OceanDNA-b30710/dqc_result.json
[2023-03-15 05:54:51,776] [INFO] DFAST_QC completed!
[2023-03-15 05:54:51,776] [INFO] Total running time: 0h1m49s