[2023-03-16 17:04:01,088] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:04:01,088] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:04:01,088] [INFO] DQC Reference Directory: /var/lib/cwl/stg128ea307-e04f-43a6-bf4b-9686c0755d7e/dqc_reference
[2023-03-16 17:04:02,314] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:04:02,315] [INFO] Task started: Prodigal
[2023-03-16 17:04:02,315] [INFO] Running command: cat /var/lib/cwl/stg6f250a43-7f33-4be3-8265-9ef643fd5c06/OceanDNA-b20975.fa | prodigal -d OceanDNA-b20975/cds.fna -a OceanDNA-b20975/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:04:26,980] [INFO] Task succeeded: Prodigal
[2023-03-16 17:04:26,981] [INFO] Task started: HMMsearch
[2023-03-16 17:04:26,981] [INFO] Running command: hmmsearch --tblout OceanDNA-b20975/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg128ea307-e04f-43a6-bf4b-9686c0755d7e/dqc_reference/reference_markers.hmm OceanDNA-b20975/protein.faa > /dev/null
[2023-03-16 17:04:27,208] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:04:27,208] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6f250a43-7f33-4be3-8265-9ef643fd5c06/OceanDNA-b20975.fa]
[2023-03-16 17:04:27,247] [INFO] Query marker FASTA was written to OceanDNA-b20975/markers.fasta
[2023-03-16 17:04:27,248] [INFO] Task started: Blastn
[2023-03-16 17:04:27,248] [INFO] Running command: blastn -query OceanDNA-b20975/markers.fasta -db /var/lib/cwl/stg128ea307-e04f-43a6-bf4b-9686c0755d7e/dqc_reference/reference_markers.fasta -out OceanDNA-b20975/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:04:27,820] [INFO] Task succeeded: Blastn
[2023-03-16 17:04:27,820] [INFO] Selected 19 target genomes.
[2023-03-16 17:04:27,821] [INFO] Target genome list was writen to OceanDNA-b20975/target_genomes.txt
[2023-03-16 17:04:27,894] [INFO] Task started: fastANI
[2023-03-16 17:04:27,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f250a43-7f33-4be3-8265-9ef643fd5c06/OceanDNA-b20975.fa --refList OceanDNA-b20975/target_genomes.txt --output OceanDNA-b20975/fastani_result.tsv --threads 1
[2023-03-16 17:04:53,922] [INFO] Task succeeded: fastANI
[2023-03-16 17:04:53,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg128ea307-e04f-43a6-bf4b-9686c0755d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:04:53,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg128ea307-e04f-43a6-bf4b-9686c0755d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:04:53,935] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:04:53,936] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:04:53,936] [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
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	74.9954	72	1311	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	74.895	120	1311	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	74.8793	137	1311	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	74.8657	198	1311	95	below_threshold
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	74.8643	203	1311	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	74.8594	72	1311	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	74.851	73	1311	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	74.8267	187	1311	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	74.8175	170	1311	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	74.817	206	1311	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.8136	172	1311	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	74.7648	133	1311	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	74.7645	223	1311	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	74.7543	171	1311	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	74.7424	168	1311	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.7331	194	1311	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	74.7295	115	1311	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	74.7278	118	1311	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	74.6592	132	1311	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:04:53,936] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20975/tc_result.tsv
[2023-03-16 17:04:53,936] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:04:53,936] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:04:53,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg128ea307-e04f-43a6-bf4b-9686c0755d7e/dqc_reference/checkm_data
[2023-03-16 17:04:53,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:04:53,960] [INFO] Task started: CheckM
[2023-03-16 17:04:53,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20975/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20975/checkm_input OceanDNA-b20975/checkm_result
[2023-03-16 17:06:07,916] [INFO] Task succeeded: CheckM
[2023-03-16 17:06:07,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:06:07,921] [INFO] ===== Completeness check finished =====
[2023-03-16 17:06:07,921] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:06:07,921] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20975/markers.fasta)
[2023-03-16 17:06:07,923] [INFO] Task started: Blastn
[2023-03-16 17:06:07,923] [INFO] Running command: blastn -query OceanDNA-b20975/markers.fasta -db /var/lib/cwl/stg128ea307-e04f-43a6-bf4b-9686c0755d7e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20975/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:06:08,790] [INFO] Task succeeded: Blastn
[2023-03-16 17:06:08,791] [INFO] Selected 24 target genomes.
[2023-03-16 17:06:08,791] [INFO] Target genome list was writen to OceanDNA-b20975/target_genomes_gtdb.txt
[2023-03-16 17:06:08,864] [INFO] Task started: fastANI
[2023-03-16 17:06:08,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f250a43-7f33-4be3-8265-9ef643fd5c06/OceanDNA-b20975.fa --refList OceanDNA-b20975/target_genomes_gtdb.txt --output OceanDNA-b20975/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:06:28,480] [INFO] Task succeeded: fastANI
[2023-03-16 17:06:28,490] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:06:28,491] [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_002724675.1	s__GCA-2724675 sp002724675	75.6609	90	1311	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA9615;f__UBA9615;g__GCA-2724675	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875315.1	s__SXON01 sp016875315	75.5632	149	1311	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152105.1	s__UBA2385 sp013152105	75.1796	85	1311	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__UBA2385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279065.1	s__Dyella_A sp002279065	75.1298	66	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018401435.1	s__M30B51 sp018401435	75.1093	249	1311	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__M30B51	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039565.1	s__Aeromicrobium terrae	74.9881	73	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361935.1	s__JABFXC01 sp013361935	74.9689	62	1311	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	99.88	99.88	0.94	0.92	3	-
GCF_006494815.1	s__Nocardioides sambongensis	74.8961	120	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	74.8827	136	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_003611735.1	s__Corallococcus sicarius	74.8308	186	1311	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014930455.1	s__Corallococcus sp014930455	74.815	206	1311	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611635.1	s__Corallococcus terminator	74.8075	175	1311	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	74.7912	83	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007845675.1	s__Lentzea sp007845675	74.7651	134	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270575.1	s__Streptomyces decoyicus	74.7401	170	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_003612115.1	s__Corallococcus sp003612115	74.7368	199	1311	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.04	99.04	0.92	0.92	2	-
GCF_013425525.1	s__Luteimonas sp013425525	74.7311	115	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873655.1	s__Aeromicrobium sp014873655	74.7216	74	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297645.1	s__Dokdonella_A sp002297645	74.5783	61	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-16 17:06:28,491] [INFO] GTDB search result was written to OceanDNA-b20975/result_gtdb.tsv
[2023-03-16 17:06:28,491] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:06:28,493] [INFO] DFAST_QC result json was written to OceanDNA-b20975/dqc_result.json
[2023-03-16 17:06:28,493] [INFO] DFAST_QC completed!
[2023-03-16 17:06:28,493] [INFO] Total running time: 0h2m27s