[2024-01-24 14:55:26,664] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:26,666] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:26,667] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcd1194f-fe98-4214-b206-610e18a75b71/dqc_reference
[2024-01-24 14:55:27,992] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:27,993] [INFO] Task started: Prodigal
[2024-01-24 14:55:27,994] [INFO] Running command: gunzip -c /var/lib/cwl/stg36811b15-6c35-4bb4-b32d-d8a5c6934bfa/GCF_002250705.1_ASM225070v1_genomic.fna.gz | prodigal -d GCF_002250705.1_ASM225070v1_genomic.fna/cds.fna -a GCF_002250705.1_ASM225070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:41,023] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:41,024] [INFO] Task started: HMMsearch
[2024-01-24 14:55:41,024] [INFO] Running command: hmmsearch --tblout GCF_002250705.1_ASM225070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcd1194f-fe98-4214-b206-610e18a75b71/dqc_reference/reference_markers.hmm GCF_002250705.1_ASM225070v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:41,290] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:41,292] [INFO] Found 6/6 markers.
[2024-01-24 14:55:41,336] [INFO] Query marker FASTA was written to GCF_002250705.1_ASM225070v1_genomic.fna/markers.fasta
[2024-01-24 14:55:41,337] [INFO] Task started: Blastn
[2024-01-24 14:55:41,337] [INFO] Running command: blastn -query GCF_002250705.1_ASM225070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcd1194f-fe98-4214-b206-610e18a75b71/dqc_reference/reference_markers.fasta -out GCF_002250705.1_ASM225070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:42,511] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:42,517] [INFO] Selected 19 target genomes.
[2024-01-24 14:55:42,517] [INFO] Target genome list was writen to GCF_002250705.1_ASM225070v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:42,525] [INFO] Task started: fastANI
[2024-01-24 14:55:42,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg36811b15-6c35-4bb4-b32d-d8a5c6934bfa/GCF_002250705.1_ASM225070v1_genomic.fna.gz --refList GCF_002250705.1_ASM225070v1_genomic.fna/target_genomes.txt --output GCF_002250705.1_ASM225070v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:00,047] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:00,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcd1194f-fe98-4214-b206-610e18a75b71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:00,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcd1194f-fe98-4214-b206-610e18a75b71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:00,064] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:00,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:00,064] [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
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	100.0	1459	1460	95	conclusive
Enemella dayhoffiae	strain=NML 130396	GCA_002250625.1	2016507	2016507	type	True	82.8555	855	1460	95	below_threshold
Granulicoccus phenolivorans	strain=DSM 17626	GCA_000423085.1	266854	266854	type	True	78.8211	471	1460	95	below_threshold
Granulicoccus phenolivorans	strain=NBRC 107789	GCA_001552335.1	266854	266854	type	True	78.8134	458	1460	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	78.6708	424	1460	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	78.649	489	1460	95	below_threshold
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	78.5349	306	1460	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	78.3292	447	1460	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	78.2979	470	1460	95	below_threshold
Parenemella sanctibonifatiensis	strain=NML 150081	GCA_002250565.1	2016505	2016505	type	True	77.8855	311	1460	95	below_threshold
Raineyella fluvialis	strain=CBA3103	GCA_009646095.1	2662261	2662261	type	True	77.5922	307	1460	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	77.4778	391	1460	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	77.3533	301	1460	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.3227	371	1460	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	77.17	327	1460	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	76.9142	371	1460	95	below_threshold
Modestobacter excelsi	strain=1G6	GCA_005930495.1	2213161	2213161	type	True	76.3196	337	1460	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	76.2429	439	1460	95	below_threshold
Arthrobacter zhaoguopingii	strain=J391	GCA_009828595.1	2681491	2681491	type	True	76.1796	146	1460	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:00,067] [INFO] DFAST Taxonomy check result was written to GCF_002250705.1_ASM225070v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:00,067] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:00,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:00,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcd1194f-fe98-4214-b206-610e18a75b71/dqc_reference/checkm_data
[2024-01-24 14:56:00,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:00,112] [INFO] Task started: CheckM
[2024-01-24 14:56:00,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002250705.1_ASM225070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002250705.1_ASM225070v1_genomic.fna/checkm_input GCF_002250705.1_ASM225070v1_genomic.fna/checkm_result
[2024-01-24 14:57:09,793] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:09,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:09,813] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:09,813] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:09,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002250705.1_ASM225070v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:09,814] [INFO] Task started: Blastn
[2024-01-24 14:57:09,814] [INFO] Running command: blastn -query GCF_002250705.1_ASM225070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcd1194f-fe98-4214-b206-610e18a75b71/dqc_reference/reference_markers_gtdb.fasta -out GCF_002250705.1_ASM225070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:11,549] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:11,552] [INFO] Selected 13 target genomes.
[2024-01-24 14:57:11,552] [INFO] Target genome list was writen to GCF_002250705.1_ASM225070v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:11,563] [INFO] Task started: fastANI
[2024-01-24 14:57:11,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg36811b15-6c35-4bb4-b32d-d8a5c6934bfa/GCF_002250705.1_ASM225070v1_genomic.fna.gz --refList GCF_002250705.1_ASM225070v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002250705.1_ASM225070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:21,993] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:22,004] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:22,004] [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_004362375.1	s__Enemella evansiae	98.3352	1386	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.12	97.98	0.94	0.92	8	conclusive
GCA_002250625.1	s__Enemella sp002250625	82.8632	854	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.13	98.13	0.89	0.89	2	-
GCF_000423085.1	s__Granulicoccus phenolivorans	78.83	470	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Granulicoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003344635.1	s__Desertihabitans aurantiacus	78.6408	427	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_013408305.1	s__Naumannella cuiyingiana	78.5442	467	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Naumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101785.1	s__Auraticoccus monumenti	78.2856	452	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009742705.1	s__Auraticoccus cholistanensis	78.2726	473	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012839035.1	s__Enemella sp012839035	78.1597	323	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002250475.1	s__NML-160184 sp002250475	78.0326	301	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__NML-160184	95.0	97.56	97.56	0.90	0.90	2	-
GCF_017876495.1	s__Friedmanniella capsulata	77.8776	445	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055925.1	s__Micropruina sp018055925	77.761	299	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002843035.1	s__Propionicimonas sp002843035	77.7128	289	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110855.1	s__Friedmanniella flava	77.5002	388	1460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:22,006] [INFO] GTDB search result was written to GCF_002250705.1_ASM225070v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:22,007] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:22,011] [INFO] DFAST_QC result json was written to GCF_002250705.1_ASM225070v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:22,011] [INFO] DFAST_QC completed!
[2024-01-24 14:57:22,011] [INFO] Total running time: 0h1m55s