[2023-03-18 04:37:59,267] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:37:59,267] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:37:59,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg9417b47c-ad93-4449-a382-11f92c7e9e96/dqc_reference
[2023-03-18 04:38:00,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:38:00,363] [INFO] Task started: Prodigal
[2023-03-18 04:38:00,363] [INFO] Running command: cat /var/lib/cwl/stg076b334d-b971-4c75-8f9e-df6a010b61e6/OceanDNA-b34301.fa | prodigal -d OceanDNA-b34301/cds.fna -a OceanDNA-b34301/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:38:06,933] [INFO] Task succeeded: Prodigal
[2023-03-18 04:38:06,933] [INFO] Task started: HMMsearch
[2023-03-18 04:38:06,933] [INFO] Running command: hmmsearch --tblout OceanDNA-b34301/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9417b47c-ad93-4449-a382-11f92c7e9e96/dqc_reference/reference_markers.hmm OceanDNA-b34301/protein.faa > /dev/null
[2023-03-18 04:38:07,097] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:38:07,097] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg076b334d-b971-4c75-8f9e-df6a010b61e6/OceanDNA-b34301.fa]
[2023-03-18 04:38:07,114] [INFO] Query marker FASTA was written to OceanDNA-b34301/markers.fasta
[2023-03-18 04:38:07,116] [INFO] Task started: Blastn
[2023-03-18 04:38:07,116] [INFO] Running command: blastn -query OceanDNA-b34301/markers.fasta -db /var/lib/cwl/stg9417b47c-ad93-4449-a382-11f92c7e9e96/dqc_reference/reference_markers.fasta -out OceanDNA-b34301/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:07,699] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:07,700] [INFO] Selected 18 target genomes.
[2023-03-18 04:38:07,700] [INFO] Target genome list was writen to OceanDNA-b34301/target_genomes.txt
[2023-03-18 04:38:07,716] [INFO] Task started: fastANI
[2023-03-18 04:38:07,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg076b334d-b971-4c75-8f9e-df6a010b61e6/OceanDNA-b34301.fa --refList OceanDNA-b34301/target_genomes.txt --output OceanDNA-b34301/fastani_result.tsv --threads 1
[2023-03-18 04:38:18,435] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:18,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9417b47c-ad93-4449-a382-11f92c7e9e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:38:18,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9417b47c-ad93-4449-a382-11f92c7e9e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:38:18,444] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 04:38:18,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 04:38:18,444] [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
Alishewanella aestuarii	strain=B11	GCA_000280055.1	453835	453835	type	True	95.2589	221	236	95	conclusive
Alishewanella jeotgali	strain=KCTC 22429	GCA_000245735.2	545533	545533	type	True	94.9333	213	236	95	below_threshold
Alishewanella agri	strain=BL06	GCA_000272005.1	553384	553384	type	True	88.7379	201	236	95	below_threshold
Alishewanella longhuensis	strain=CGMCC 1.7003	GCA_014653435.1	1091037	1091037	type	True	78.2835	101	236	95	below_threshold
Alishewanella tabrizica	strain=KCTC 23723	GCA_014652375.1	671278	671278	type	True	78.2267	69	236	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	77.5827	61	236	95	below_threshold
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	77.4786	67	236	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	77.3814	83	236	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	77.1561	59	236	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	76.988	66	236	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	76.8765	59	236	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	76.5032	50	236	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:38:18,444] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34301/tc_result.tsv
[2023-03-18 04:38:18,444] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:38:18,444] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:38:18,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9417b47c-ad93-4449-a382-11f92c7e9e96/dqc_reference/checkm_data
[2023-03-18 04:38:18,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:38:18,614] [INFO] Task started: CheckM
[2023-03-18 04:38:18,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34301/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34301/checkm_input OceanDNA-b34301/checkm_result
[2023-03-18 04:38:40,791] [INFO] Task succeeded: CheckM
[2023-03-18 04:38:40,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:38:40,793] [INFO] ===== Completeness check finished =====
[2023-03-18 04:38:40,793] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:38:40,793] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34301/markers.fasta)
[2023-03-18 04:38:40,795] [INFO] Task started: Blastn
[2023-03-18 04:38:40,795] [INFO] Running command: blastn -query OceanDNA-b34301/markers.fasta -db /var/lib/cwl/stg9417b47c-ad93-4449-a382-11f92c7e9e96/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34301/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:41,584] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:41,584] [INFO] Selected 17 target genomes.
[2023-03-18 04:38:41,585] [INFO] Target genome list was writen to OceanDNA-b34301/target_genomes_gtdb.txt
[2023-03-18 04:38:41,594] [INFO] Task started: fastANI
[2023-03-18 04:38:41,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg076b334d-b971-4c75-8f9e-df6a010b61e6/OceanDNA-b34301.fa --refList OceanDNA-b34301/target_genomes_gtdb.txt --output OceanDNA-b34301/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:38:52,045] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:52,054] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:38:52,055] [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_000280055.1	s__Alishewanella aestuarii	95.2589	221	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	96.26	96.26	0.87	0.87	2	-
GCF_000245735.1	s__Alishewanella jeotgali	94.9333	213	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	N/A	N/A	N/A	N/A	1	-
GCF_000272005.1	s__Alishewanella agri	88.7379	201	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	96.64	95.87	0.84	0.80	3	-
GCF_014653435.1	s__Alishewanella longhuensis	78.2835	101	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652375.1	s__Alishewanella tabrizica	78.2267	69	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402695.1	s__Arsukibacterium sp018402695	77.6804	71	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364615.1	s__Arsukibacterium sp002364615	77.5621	50	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_900215315.1	s__Arsukibacterium tuosuense	77.4786	67	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840125.1	s__Rheinheimera sp002840125	77.4736	67	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296695.1	s__Rheinheimera nanhaiensis	77.3814	83	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108485.1	s__Rheinheimera pacifica	77.1561	59	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004369005.1	s__Rheinheimera aquimaris	77.0313	54	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	98.51	97.48	0.94	0.92	4	-
GCF_011634895.1	s__Rheinheimera pleomorphica	76.988	66	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513785.1	s__Rheinheimera sp001513785	76.6963	61	236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:38:52,055] [INFO] GTDB search result was written to OceanDNA-b34301/result_gtdb.tsv
[2023-03-18 04:38:52,055] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:38:52,096] [INFO] DFAST_QC result json was written to OceanDNA-b34301/dqc_result.json
[2023-03-18 04:38:52,096] [INFO] DFAST_QC completed!
[2023-03-18 04:38:52,096] [INFO] Total running time: 0h0m53s