[2023-03-18 22:14:42,684] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:14:42,685] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:14:42,685] [INFO] DQC Reference Directory: /var/lib/cwl/stg46ff104f-8b4c-4349-b19b-872c2f88e0dc/dqc_reference
[2023-03-18 22:14:43,782] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:14:43,783] [INFO] Task started: Prodigal
[2023-03-18 22:14:43,783] [INFO] Running command: cat /var/lib/cwl/stg9c0b13cc-260c-4a8f-b471-4e7e8988f8c0/OceanDNA-b22991.fa | prodigal -d OceanDNA-b22991/cds.fna -a OceanDNA-b22991/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:15:04,672] [INFO] Task succeeded: Prodigal
[2023-03-18 22:15:04,672] [INFO] Task started: HMMsearch
[2023-03-18 22:15:04,672] [INFO] Running command: hmmsearch --tblout OceanDNA-b22991/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46ff104f-8b4c-4349-b19b-872c2f88e0dc/dqc_reference/reference_markers.hmm OceanDNA-b22991/protein.faa > /dev/null
[2023-03-18 22:15:04,890] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:15:04,890] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9c0b13cc-260c-4a8f-b471-4e7e8988f8c0/OceanDNA-b22991.fa]
[2023-03-18 22:15:04,926] [INFO] Query marker FASTA was written to OceanDNA-b22991/markers.fasta
[2023-03-18 22:15:04,927] [INFO] Task started: Blastn
[2023-03-18 22:15:04,927] [INFO] Running command: blastn -query OceanDNA-b22991/markers.fasta -db /var/lib/cwl/stg46ff104f-8b4c-4349-b19b-872c2f88e0dc/dqc_reference/reference_markers.fasta -out OceanDNA-b22991/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:15:05,421] [INFO] Task succeeded: Blastn
[2023-03-18 22:15:05,423] [INFO] Selected 21 target genomes.
[2023-03-18 22:15:05,424] [INFO] Target genome list was writen to OceanDNA-b22991/target_genomes.txt
[2023-03-18 22:15:05,438] [INFO] Task started: fastANI
[2023-03-18 22:15:05,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c0b13cc-260c-4a8f-b471-4e7e8988f8c0/OceanDNA-b22991.fa --refList OceanDNA-b22991/target_genomes.txt --output OceanDNA-b22991/fastani_result.tsv --threads 1
[2023-03-18 22:15:24,178] [INFO] Task succeeded: fastANI
[2023-03-18 22:15:24,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46ff104f-8b4c-4349-b19b-872c2f88e0dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:15:24,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46ff104f-8b4c-4349-b19b-872c2f88e0dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:15:24,190] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:15:24,190] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:15:24,190] [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
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	74.879	60	1114	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8562	184	1114	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	74.8486	62	1114	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.8171	265	1114	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	74.809	116	1114	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	74.8077	64	1114	95	below_threshold
Usitatibacter rugosus	strain=0125_3	GCA_013003965.1	2732067	2732067	type	True	74.8052	79	1114	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.7864	242	1114	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	74.7723	154	1114	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	74.7366	240	1114	95	below_threshold
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	74.723	237	1114	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	74.7227	130	1114	95	below_threshold
Gordonia araii	strain=IFM 10211	GCA_013004535.1	263909	263909	type	True	74.6706	50	1114	95	below_threshold
Halegenticoccus tardaugens	strain=SYSU A00711	GCA_004116405.1	2071624	2071624	type	True	74.6664	69	1114	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	74.6572	117	1114	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	74.6491	154	1114	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	74.6417	236	1114	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:15:24,192] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22991/tc_result.tsv
[2023-03-18 22:15:24,195] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:15:24,195] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:15:24,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46ff104f-8b4c-4349-b19b-872c2f88e0dc/dqc_reference/checkm_data
[2023-03-18 22:15:24,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:15:24,836] [INFO] Task started: CheckM
[2023-03-18 22:15:24,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22991/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22991/checkm_input OceanDNA-b22991/checkm_result
[2023-03-18 22:16:16,877] [INFO] Task succeeded: CheckM
[2023-03-18 22:16:16,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:16:16,940] [INFO] ===== Completeness check finished =====
[2023-03-18 22:16:16,940] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:16:16,940] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22991/markers.fasta)
[2023-03-18 22:16:16,942] [INFO] Task started: Blastn
[2023-03-18 22:16:16,942] [INFO] Running command: blastn -query OceanDNA-b22991/markers.fasta -db /var/lib/cwl/stg46ff104f-8b4c-4349-b19b-872c2f88e0dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22991/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:16:17,666] [INFO] Task succeeded: Blastn
[2023-03-18 22:16:17,669] [INFO] Selected 18 target genomes.
[2023-03-18 22:16:17,669] [INFO] Target genome list was writen to OceanDNA-b22991/target_genomes_gtdb.txt
[2023-03-18 22:16:17,684] [INFO] Task started: fastANI
[2023-03-18 22:16:17,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c0b13cc-260c-4a8f-b471-4e7e8988f8c0/OceanDNA-b22991.fa --refList OceanDNA-b22991/target_genomes_gtdb.txt --output OceanDNA-b22991/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:16:31,523] [INFO] Task succeeded: fastANI
[2023-03-18 22:16:31,530] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:16:31,531] [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_003644265.1	s__B15-G4 sp003644265	77.7102	356	1114	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__B15-G4;g__B15-G4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892045.1	s__F1-120-MAGs118 sp903892045	75.3348	152	1114	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.41	99.41	0.87	0.87	3	-
GCA_011525785.1	s__WYBT01 sp011525785	75.1949	179	1114	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795285.1	s__SIAN01 sp016795285	75.1138	238	1114	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__SIAN01;g__SIAN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	75.0674	180	1114	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795345.1	s__JAEUHO01 sp016795345	74.9753	236	1114	d__Bacteria;p__Planctomycetota;c__PLA2;o__PLA2;f__JAEUHO01;g__JAEUHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693765.1	s__RECZ01 sp007693765	74.951	95	1114	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514895.1	s__JAAYZK01 sp012514895	74.9289	126	1114	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__SM23-33;f__FEN-1343;g__JAAYZK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	74.8408	63	1114	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709445.1	s__PNC22 sp016709445	74.828	71	1114	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649845.1	s__Polyangium spumosum	74.7342	242	1114	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693785.1	s__RECY01 sp007693785	74.6662	52	1114	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:16:31,532] [INFO] GTDB search result was written to OceanDNA-b22991/result_gtdb.tsv
[2023-03-18 22:16:31,534] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:16:31,538] [INFO] DFAST_QC result json was written to OceanDNA-b22991/dqc_result.json
[2023-03-18 22:16:31,539] [INFO] DFAST_QC completed!
[2023-03-18 22:16:31,539] [INFO] Total running time: 0h1m49s