[2023-06-19 09:16:53,183] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:16:53,186] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:16:53,186] [INFO] DQC Reference Directory: /var/lib/cwl/stgf07293f2-9181-4e5e-9c30-c1a20fd6c042/dqc_reference
[2023-06-19 09:16:55,392] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:16:55,393] [INFO] Task started: Prodigal
[2023-06-19 09:16:55,393] [INFO] Running command: gunzip -c /var/lib/cwl/stg47e05dd9-8137-4e5b-9e7f-8afd01d0f5c0/GCA_014338005.1_ASM1433800v1_genomic.fna.gz | prodigal -d GCA_014338005.1_ASM1433800v1_genomic.fna/cds.fna -a GCA_014338005.1_ASM1433800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:17:07,776] [INFO] Task succeeded: Prodigal
[2023-06-19 09:17:07,776] [INFO] Task started: HMMsearch
[2023-06-19 09:17:07,777] [INFO] Running command: hmmsearch --tblout GCA_014338005.1_ASM1433800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf07293f2-9181-4e5e-9c30-c1a20fd6c042/dqc_reference/reference_markers.hmm GCA_014338005.1_ASM1433800v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:17:08,101] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:17:08,102] [INFO] Found 6/6 markers.
[2023-06-19 09:17:08,156] [INFO] Query marker FASTA was written to GCA_014338005.1_ASM1433800v1_genomic.fna/markers.fasta
[2023-06-19 09:17:08,157] [INFO] Task started: Blastn
[2023-06-19 09:17:08,157] [INFO] Running command: blastn -query GCA_014338005.1_ASM1433800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf07293f2-9181-4e5e-9c30-c1a20fd6c042/dqc_reference/reference_markers.fasta -out GCA_014338005.1_ASM1433800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:17:08,761] [INFO] Task succeeded: Blastn
[2023-06-19 09:17:08,766] [INFO] Selected 28 target genomes.
[2023-06-19 09:17:08,766] [INFO] Target genome list was writen to GCA_014338005.1_ASM1433800v1_genomic.fna/target_genomes.txt
[2023-06-19 09:17:08,772] [INFO] Task started: fastANI
[2023-06-19 09:17:08,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg47e05dd9-8137-4e5b-9e7f-8afd01d0f5c0/GCA_014338005.1_ASM1433800v1_genomic.fna.gz --refList GCA_014338005.1_ASM1433800v1_genomic.fna/target_genomes.txt --output GCA_014338005.1_ASM1433800v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:17:32,572] [INFO] Task succeeded: fastANI
[2023-06-19 09:17:32,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf07293f2-9181-4e5e-9c30-c1a20fd6c042/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:17:32,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf07293f2-9181-4e5e-9c30-c1a20fd6c042/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:17:32,584] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:17:32,584] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 09:17:32,584] [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
Aggregatilinea lenta	strain=MO-CFX2	GCA_003569045.1	913108	913108	type	True	75.935	167	1501	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	74.8986	67	1501	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	74.7724	58	1501	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	74.7585	65	1501	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	74.73	62	1501	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	74.6876	69	1501	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	74.687	68	1501	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	74.6864	55	1501	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 09:17:32,586] [INFO] DFAST Taxonomy check result was written to GCA_014338005.1_ASM1433800v1_genomic.fna/tc_result.tsv
[2023-06-19 09:17:32,586] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:17:32,586] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:17:32,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf07293f2-9181-4e5e-9c30-c1a20fd6c042/dqc_reference/checkm_data
[2023-06-19 09:17:32,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:17:32,638] [INFO] Task started: CheckM
[2023-06-19 09:17:32,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014338005.1_ASM1433800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014338005.1_ASM1433800v1_genomic.fna/checkm_input GCA_014338005.1_ASM1433800v1_genomic.fna/checkm_result
[2023-06-19 09:18:11,879] [INFO] Task succeeded: CheckM
[2023-06-19 09:18:11,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:18:11,914] [INFO] ===== Completeness check finished =====
[2023-06-19 09:18:11,914] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:18:11,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014338005.1_ASM1433800v1_genomic.fna/markers.fasta)
[2023-06-19 09:18:11,915] [INFO] Task started: Blastn
[2023-06-19 09:18:11,915] [INFO] Running command: blastn -query GCA_014338005.1_ASM1433800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf07293f2-9181-4e5e-9c30-c1a20fd6c042/dqc_reference/reference_markers_gtdb.fasta -out GCA_014338005.1_ASM1433800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:18:12,798] [INFO] Task succeeded: Blastn
[2023-06-19 09:18:12,805] [INFO] Selected 18 target genomes.
[2023-06-19 09:18:12,805] [INFO] Target genome list was writen to GCA_014338005.1_ASM1433800v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:18:12,817] [INFO] Task started: fastANI
[2023-06-19 09:18:12,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg47e05dd9-8137-4e5b-9e7f-8afd01d0f5c0/GCA_014338005.1_ASM1433800v1_genomic.fna.gz --refList GCA_014338005.1_ASM1433800v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014338005.1_ASM1433800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:18:27,282] [INFO] Task succeeded: fastANI
[2023-06-19 09:18:27,302] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:18:27,302] [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_014338005.1	s__CFX2 sp014338005	100.0	1494	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	98.19	98.19	0.87	0.87	2	conclusive
GCA_013388735.1	s__CFX2 sp013388735	88.1958	1114	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223085.1	s__CFX2 sp016223085	79.3035	882	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903864435.1	s__CFX2 sp903864435	76.8359	304	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788625.1	s__CFX2 sp016788625	76.5874	355	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388745.1	s__JACAER01 sp013388745	76.3032	262	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__JACAER01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242205.1	s__ZC4RG36 sp003242205	76.1957	166	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__ZC4RG36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789005.1	s__OLB15 sp016789005	76.1449	196	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010092805.1	s__OLB15 sp010092805	76.0034	142	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303635.1	s__CFX2 sp017303635	75.9974	169	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788435.1	s__OLB15 sp016788435	75.8855	158	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056405.1	s__UBA2029 sp018056405	75.8339	104	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__UBA2029	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432315.1	s__LM3-B42 sp018432315	75.8254	210	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__LM3-B42	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124855.1	s__CFX2 sp016124855	75.5907	64	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016927535.1	s__JAFGMM01 sp016927535	75.4596	141	1501	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__JAFGMM01;g__JAFGMM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 09:18:27,304] [INFO] GTDB search result was written to GCA_014338005.1_ASM1433800v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:18:27,305] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:18:27,308] [INFO] DFAST_QC result json was written to GCA_014338005.1_ASM1433800v1_genomic.fna/dqc_result.json
[2023-06-19 09:18:27,309] [INFO] DFAST_QC completed!
[2023-06-19 09:18:27,309] [INFO] Total running time: 0h1m34s