[2023-03-18 01:06:53,683] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:06:53,683] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:06:53,683] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc40081b-5d8e-4aa2-8254-7dc113f1550b/dqc_reference
[2023-03-18 01:06:54,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:06:54,813] [INFO] Task started: Prodigal
[2023-03-18 01:06:54,813] [INFO] Running command: cat /var/lib/cwl/stgcfbee76d-5b66-436f-b7d6-d076c1d9a152/OceanDNA-b2920.fa | prodigal -d OceanDNA-b2920/cds.fna -a OceanDNA-b2920/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:07:10,359] [INFO] Task succeeded: Prodigal
[2023-03-18 01:07:10,359] [INFO] Task started: HMMsearch
[2023-03-18 01:07:10,359] [INFO] Running command: hmmsearch --tblout OceanDNA-b2920/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc40081b-5d8e-4aa2-8254-7dc113f1550b/dqc_reference/reference_markers.hmm OceanDNA-b2920/protein.faa > /dev/null
[2023-03-18 01:07:10,546] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:07:10,547] [INFO] Found 6/6 markers.
[2023-03-18 01:07:10,564] [INFO] Query marker FASTA was written to OceanDNA-b2920/markers.fasta
[2023-03-18 01:07:10,565] [INFO] Task started: Blastn
[2023-03-18 01:07:10,565] [INFO] Running command: blastn -query OceanDNA-b2920/markers.fasta -db /var/lib/cwl/stgdc40081b-5d8e-4aa2-8254-7dc113f1550b/dqc_reference/reference_markers.fasta -out OceanDNA-b2920/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:07:11,430] [INFO] Task succeeded: Blastn
[2023-03-18 01:07:11,431] [INFO] Selected 33 target genomes.
[2023-03-18 01:07:11,431] [INFO] Target genome list was writen to OceanDNA-b2920/target_genomes.txt
[2023-03-18 01:07:11,451] [INFO] Task started: fastANI
[2023-03-18 01:07:11,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfbee76d-5b66-436f-b7d6-d076c1d9a152/OceanDNA-b2920.fa --refList OceanDNA-b2920/target_genomes.txt --output OceanDNA-b2920/fastani_result.tsv --threads 1
[2023-03-18 01:07:35,432] [INFO] Task succeeded: fastANI
[2023-03-18 01:07:35,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc40081b-5d8e-4aa2-8254-7dc113f1550b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:07:35,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc40081b-5d8e-4aa2-8254-7dc113f1550b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:07:35,447] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:07:35,447] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:07:35,448] [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
Kineococcus radiotolerans	strain=SRS30216	GCA_000017305.1	131568	131568	type	True	76.1832	74	796	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	76.1726	51	796	95	below_threshold
Nocardioides insulae	strain=DSM 17944	GCA_000422825.1	394734	394734	type	True	76.1135	56	796	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	76.1109	74	796	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	76.0726	76	796	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	75.9977	70	796	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	75.9534	78	796	95	below_threshold
Kitasatospora phosalacinea	strain=NRRL B-16230	GCA_000716545.1	2065	2065	type	True	75.9421	73	796	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	75.9299	64	796	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	75.9279	76	796	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	75.8719	69	796	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	75.8712	72	796	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	75.845	78	796	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	75.8339	80	796	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	75.8339	80	796	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	75.8268	64	796	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	75.8247	86	796	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	75.8223	78	796	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	75.7336	58	796	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	75.6545	64	796	95	below_threshold
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	75.5776	67	796	95	below_threshold
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	75.5652	69	796	95	below_threshold
Micromonospora zamorensis	strain=DSM 45600	GCA_900090275.1	709883	709883	type	True	75.5422	65	796	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	75.5286	50	796	95	below_threshold
Thermasporomyces composti	strain=DSM 22891	GCA_003386795.1	696763	696763	type	True	75.5018	54	796	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	75.4656	59	796	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:07:35,448] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2920/tc_result.tsv
[2023-03-18 01:07:35,448] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:07:35,448] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:07:35,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc40081b-5d8e-4aa2-8254-7dc113f1550b/dqc_reference/checkm_data
[2023-03-18 01:07:35,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:07:35,554] [INFO] Task started: CheckM
[2023-03-18 01:07:35,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2920/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2920/checkm_input OceanDNA-b2920/checkm_result
[2023-03-18 01:08:19,050] [INFO] Task succeeded: CheckM
[2023-03-18 01:08:19,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:08:19,054] [INFO] ===== Completeness check finished =====
[2023-03-18 01:08:19,054] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:08:19,054] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2920/markers.fasta)
[2023-03-18 01:08:19,056] [INFO] Task started: Blastn
[2023-03-18 01:08:19,056] [INFO] Running command: blastn -query OceanDNA-b2920/markers.fasta -db /var/lib/cwl/stgdc40081b-5d8e-4aa2-8254-7dc113f1550b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2920/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:08:20,360] [INFO] Task succeeded: Blastn
[2023-03-18 01:08:20,364] [INFO] Selected 22 target genomes.
[2023-03-18 01:08:20,364] [INFO] Target genome list was writen to OceanDNA-b2920/target_genomes_gtdb.txt
[2023-03-18 01:08:20,387] [INFO] Task started: fastANI
[2023-03-18 01:08:20,388] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfbee76d-5b66-436f-b7d6-d076c1d9a152/OceanDNA-b2920.fa --refList OceanDNA-b2920/target_genomes_gtdb.txt --output OceanDNA-b2920/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:08:33,501] [INFO] Task succeeded: fastANI
[2023-03-18 01:08:33,512] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:08:33,513] [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_903954205.1	s__Mxb001 sp903954205	79.4258	271	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	98.46	98.20	0.79	0.70	14	-
GCA_016870425.1	s__Mxb001 sp016870425	78.9758	317	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004379115.1	s__Mxb001 sp004379115	78.1858	264	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870515.1	s__Mxb001 sp016870515	78.1207	253	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848435.1	s__Mxb001 sp903848435	78.0273	172	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	96.93	95.89	0.80	0.74	3	-
GCA_903909555.1	s__Mxb001 sp903909555	77.4455	242	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	99.15	99.05	0.83	0.81	4	-
GCA_903934925.1	s__UBA10649 sp903934925	77.09	96	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	99.42	99.35	0.85	0.83	4	-
GCA_903940375.1	s__UBA10649 sp903940375	76.6612	92	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	98.93	98.93	0.81	0.81	2	-
GCA_017856385.1	s__UBA10649 sp017856385	76.5725	111	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849335.1	s__UBA10649 sp017849335	76.4161	67	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348545.1	s__Jiangella ureilytica	76.1109	74	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191495.1	s__Nocardioides soli	76.0938	75	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_900105585.1	s__Nocardioides exalbidus	75.8567	65	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583405.1	s__Micromonospora radicis	75.7336	58	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969715.1	s__REEB473 sp018969715	75.6781	50	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__AcAMD-5;g__REEB473	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090275.1	s__Micromonospora zamorensis	75.5032	65	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.71	96.30	0.91	0.89	6	-
GCF_009707425.1	s__Micromonospora sp009707425	75.446	61	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001795.1	s__Actinomadura_B viridilutea	75.33	58	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:08:33,513] [INFO] GTDB search result was written to OceanDNA-b2920/result_gtdb.tsv
[2023-03-18 01:08:33,513] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:08:33,515] [INFO] DFAST_QC result json was written to OceanDNA-b2920/dqc_result.json
[2023-03-18 01:08:33,515] [INFO] DFAST_QC completed!
[2023-03-18 01:08:33,516] [INFO] Total running time: 0h1m40s