[2023-03-17 15:42:57,774] [INFO] DFAST_QC pipeline started.
[2023-03-17 15:42:57,775] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 15:42:57,775] [INFO] DQC Reference Directory: /var/lib/cwl/stg31abfe71-c1ac-4cca-94cb-4a933b14d5a4/dqc_reference
[2023-03-17 15:42:58,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 15:42:58,896] [INFO] Task started: Prodigal
[2023-03-17 15:42:58,896] [INFO] Running command: cat /var/lib/cwl/stgf2d4eb75-af6b-4811-833a-c021575827fd/OceanDNA-b22813.fa | prodigal -d OceanDNA-b22813/cds.fna -a OceanDNA-b22813/protein.faa -g 11 -q > /dev/null
[2023-03-17 15:43:31,456] [INFO] Task succeeded: Prodigal
[2023-03-17 15:43:31,456] [INFO] Task started: HMMsearch
[2023-03-17 15:43:31,456] [INFO] Running command: hmmsearch --tblout OceanDNA-b22813/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31abfe71-c1ac-4cca-94cb-4a933b14d5a4/dqc_reference/reference_markers.hmm OceanDNA-b22813/protein.faa > /dev/null
[2023-03-17 15:43:31,688] [INFO] Task succeeded: HMMsearch
[2023-03-17 15:43:31,688] [INFO] Found 6/6 markers.
[2023-03-17 15:43:31,715] [INFO] Query marker FASTA was written to OceanDNA-b22813/markers.fasta
[2023-03-17 15:43:31,715] [INFO] Task started: Blastn
[2023-03-17 15:43:31,715] [INFO] Running command: blastn -query OceanDNA-b22813/markers.fasta -db /var/lib/cwl/stg31abfe71-c1ac-4cca-94cb-4a933b14d5a4/dqc_reference/reference_markers.fasta -out OceanDNA-b22813/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:43:32,355] [INFO] Task succeeded: Blastn
[2023-03-17 15:43:32,356] [INFO] Selected 31 target genomes.
[2023-03-17 15:43:32,356] [INFO] Target genome list was writen to OceanDNA-b22813/target_genomes.txt
[2023-03-17 15:43:32,378] [INFO] Task started: fastANI
[2023-03-17 15:43:32,378] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2d4eb75-af6b-4811-833a-c021575827fd/OceanDNA-b22813.fa --refList OceanDNA-b22813/target_genomes.txt --output OceanDNA-b22813/fastani_result.tsv --threads 1
[2023-03-17 15:44:07,755] [INFO] Task succeeded: fastANI
[2023-03-17 15:44:07,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31abfe71-c1ac-4cca-94cb-4a933b14d5a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 15:44:07,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31abfe71-c1ac-4cca-94cb-4a933b14d5a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 15:44:07,770] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 15:44:07,770] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 15:44:07,771] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	76.0364	175	1349	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.8901	193	1349	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.7786	215	1349	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.7646	145	1349	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.7524	129	1349	95	below_threshold
Alienimonas californiensis	strain=CA12	GCA_007743815.1	2527989	2527989	type	True	75.7447	239	1349	95	below_threshold
Alienimonas chondri	strain=LzC2	GCA_013036045.1	2681879	2681879	type	True	75.561	175	1349	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.5116	158	1349	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	75.2571	184	1349	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.2431	253	1349	95	below_threshold
Tautonia marina	strain=JC650	GCA_009177065.1	2653855	2653855	type	True	75.1678	99	1349	95	below_threshold
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	75.1072	59	1349	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	74.9857	166	1349	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_008065095.1	114	114	type	True	74.985	166	1349	95	below_threshold
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	74.9753	149	1349	95	below_threshold
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	74.9712	165	1349	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	74.8892	118	1349	95	below_threshold
Microbacterium indicum	strain=DSM 19969	GCA_000422385.1	358100	358100	type	True	74.8744	93	1349	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	74.792	116	1349	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	74.7862	165	1349	95	below_threshold
Microbacterium halotolerans	strain=YIM 70130	GCA_003569805.1	246613	246613	type	True	74.7846	56	1349	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	74.7805	169	1349	95	below_threshold
Cryptosporangium arvum	strain=DSM 44712	GCA_000585375.1	80871	80871	type	True	74.7643	202	1349	95	below_threshold
Nocardioides silvaticus	strain=CCTCC AB 2018079	GCA_003160695.1	2201891	2201891	type	True	74.7487	140	1349	95	below_threshold
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	74.7189	190	1349	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	74.7172	152	1349	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 15:44:07,771] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22813/tc_result.tsv
[2023-03-17 15:44:07,772] [INFO] ===== Taxonomy check completed =====
[2023-03-17 15:44:07,772] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 15:44:07,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31abfe71-c1ac-4cca-94cb-4a933b14d5a4/dqc_reference/checkm_data
[2023-03-17 15:44:07,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 15:44:07,787] [INFO] Task started: CheckM
[2023-03-17 15:44:07,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22813/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22813/checkm_input OceanDNA-b22813/checkm_result
[2023-03-17 15:45:16,887] [INFO] Task succeeded: CheckM
[2023-03-17 15:45:16,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.26%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 15:45:16,891] [INFO] ===== Completeness check finished =====
[2023-03-17 15:45:16,892] [INFO] ===== Start GTDB Search =====
[2023-03-17 15:45:16,892] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22813/markers.fasta)
[2023-03-17 15:45:16,894] [INFO] Task started: Blastn
[2023-03-17 15:45:16,895] [INFO] Running command: blastn -query OceanDNA-b22813/markers.fasta -db /var/lib/cwl/stg31abfe71-c1ac-4cca-94cb-4a933b14d5a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22813/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:45:18,808] [INFO] Task succeeded: Blastn
[2023-03-17 15:45:18,809] [INFO] Selected 32 target genomes.
[2023-03-17 15:45:18,809] [INFO] Target genome list was writen to OceanDNA-b22813/target_genomes_gtdb.txt
[2023-03-17 15:45:18,981] [INFO] Task started: fastANI
[2023-03-17 15:45:18,981] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2d4eb75-af6b-4811-833a-c021575827fd/OceanDNA-b22813.fa --refList OceanDNA-b22813/target_genomes_gtdb.txt --output OceanDNA-b22813/fastani_result_gtdb.tsv --threads 1
[2023-03-17 15:45:53,152] [INFO] Task succeeded: fastANI
[2023-03-17 15:45:53,167] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 15:45:53,167] [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_007747795.1	s__Maioricimonas rarisocia	76.0367	175	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	75.9053	191	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859945.1	s__Pseudobythopirellula maris	75.7821	143	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007743815.1	s__Alienimonas californiensis	75.767	233	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Alienimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	75.7646	216	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007745175.1	s__Caulifigura coniformis	75.7531	129	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Caulifigura	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671185.1	s__QWPN01 sp003671185	75.696	78	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.6332	115	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745835.1	s__Botrimarina sp007745835	75.6074	154	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013036045.1	s__Alienimonas chondri	75.6024	168	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Alienimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.547	150	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822855.1	s__Planctopirus sp013822855	75.5243	70	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctopirus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007750855.1	s__Pirellulimonas nuda	75.495	156	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pirellulimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872645.1	s__SXKJ01 sp016872645	75.4818	60	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003389325.1	s__LB-PLM-3 sp003389325	75.4168	94	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__LB-PLM-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002405515.1	s__UBA4655 sp002405515	75.3878	119	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA4655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926295.1	s__RGVT01 sp009926295	75.2739	95	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831155.1	s__QWPN01 sp903831155	75.1733	135	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747215.1	s__Urbifossiella limnaea	75.1529	251	1349	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583645.1	s__Rhodovibrio sodomensis	74.8958	116	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009836625.1	s__WTGL01 sp009836625	74.8837	84	1349	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.03	98.03	0.95	0.91	5	-
GCA_009837085.1	s__WTGL01 sp009837085	74.8812	77	1349	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.78	99.78	0.96	0.95	3	-
GCA_012960515.1	s__Rubricoccus sp012960515	74.8713	56	1349	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004605.1	s__Pseudokineococcus marinus	74.7978	114	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001995175.1	s__Rathayibacter sp001995175	74.7928	113	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009845425.1	s__WTGL01 sp009845425	74.7669	68	1349	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.99	99.99	0.99	0.99	3	-
GCF_013205055.1	s__Rathayibacter sp013205055	74.7213	149	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000799385.1	s__Microbacterium sp000799385	74.6834	87	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 15:45:53,168] [INFO] GTDB search result was written to OceanDNA-b22813/result_gtdb.tsv
[2023-03-17 15:45:53,168] [INFO] ===== GTDB Search completed =====
[2023-03-17 15:45:53,171] [INFO] DFAST_QC result json was written to OceanDNA-b22813/dqc_result.json
[2023-03-17 15:45:53,171] [INFO] DFAST_QC completed!
[2023-03-17 15:45:53,171] [INFO] Total running time: 0h2m55s