[2024-01-24 15:02:03,500] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:03,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:03,502] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a9d485c-0d5c-4ae3-81f7-e2568c34635a/dqc_reference
[2024-01-24 15:02:06,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:06,126] [INFO] Task started: Prodigal
[2024-01-24 15:02:06,126] [INFO] Running command: gunzip -c /var/lib/cwl/stgcac16937-b56a-4aae-b9f5-da3c7d8aea64/GCF_004324765.1_ASM432476v1_genomic.fna.gz | prodigal -d GCF_004324765.1_ASM432476v1_genomic.fna/cds.fna -a GCF_004324765.1_ASM432476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:14,342] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:14,343] [INFO] Task started: HMMsearch
[2024-01-24 15:02:14,343] [INFO] Running command: hmmsearch --tblout GCF_004324765.1_ASM432476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a9d485c-0d5c-4ae3-81f7-e2568c34635a/dqc_reference/reference_markers.hmm GCF_004324765.1_ASM432476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:14,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:14,583] [INFO] Found 6/6 markers.
[2024-01-24 15:02:14,609] [INFO] Query marker FASTA was written to GCF_004324765.1_ASM432476v1_genomic.fna/markers.fasta
[2024-01-24 15:02:14,610] [INFO] Task started: Blastn
[2024-01-24 15:02:14,610] [INFO] Running command: blastn -query GCF_004324765.1_ASM432476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a9d485c-0d5c-4ae3-81f7-e2568c34635a/dqc_reference/reference_markers.fasta -out GCF_004324765.1_ASM432476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:15,966] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:15,970] [INFO] Selected 15 target genomes.
[2024-01-24 15:02:15,971] [INFO] Target genome list was writen to GCF_004324765.1_ASM432476v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:16,056] [INFO] Task started: fastANI
[2024-01-24 15:02:16,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgcac16937-b56a-4aae-b9f5-da3c7d8aea64/GCF_004324765.1_ASM432476v1_genomic.fna.gz --refList GCF_004324765.1_ASM432476v1_genomic.fna/target_genomes.txt --output GCF_004324765.1_ASM432476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:27,013] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:27,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a9d485c-0d5c-4ae3-81f7-e2568c34635a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:27,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a9d485c-0d5c-4ae3-81f7-e2568c34635a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:27,029] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:27,030] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:27,030] [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
Propioniciclava tarda	strain=DSM 22130	GCA_004324765.1	433330	433330	type	True	100.0	969	971	95	conclusive
Propioniciclava tarda	strain=DSM 22130	GCA_900182665.1	433330	433330	type	True	99.9969	953	971	95	conclusive
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	78.9078	427	971	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	78.8444	394	971	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	78.5294	349	971	95	below_threshold
Propionicimonas paludicola	strain=DSM 15597	GCA_002563675.1	185243	185243	type	True	78.4355	244	971	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	77.6779	221	971	95	below_threshold
Raineyella fluvialis	strain=CBA3103	GCA_009646095.1	2662261	2662261	type	True	77.609	194	971	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.4618	252	971	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.4574	227	971	95	below_threshold
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	77.1708	207	971	95	below_threshold
Arachnia propionica	strain=NBRC 14587	GCA_001592325.1	1750	1750	type	True	77.1337	140	971	95	below_threshold
Arachnia propionica	strain=NCTC12967	GCA_900637725.1	1750	1750	type	True	77.0813	142	971	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	76.9892	210	971	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	76.0971	240	971	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:27,031] [INFO] DFAST Taxonomy check result was written to GCF_004324765.1_ASM432476v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:27,032] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:27,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:27,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a9d485c-0d5c-4ae3-81f7-e2568c34635a/dqc_reference/checkm_data
[2024-01-24 15:02:27,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:27,064] [INFO] Task started: CheckM
[2024-01-24 15:02:27,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004324765.1_ASM432476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004324765.1_ASM432476v1_genomic.fna/checkm_input GCF_004324765.1_ASM432476v1_genomic.fna/checkm_result
[2024-01-24 15:02:57,665] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:57,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:57,692] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:57,692] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:57,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004324765.1_ASM432476v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:57,693] [INFO] Task started: Blastn
[2024-01-24 15:02:57,693] [INFO] Running command: blastn -query GCF_004324765.1_ASM432476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a9d485c-0d5c-4ae3-81f7-e2568c34635a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004324765.1_ASM432476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:59,743] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:59,746] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:59,747] [INFO] Target genome list was writen to GCF_004324765.1_ASM432476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:59,762] [INFO] Task started: fastANI
[2024-01-24 15:02:59,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgcac16937-b56a-4aae-b9f5-da3c7d8aea64/GCF_004324765.1_ASM432476v1_genomic.fna.gz --refList GCF_004324765.1_ASM432476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004324765.1_ASM432476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:10,927] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:10,942] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:10,942] [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_900182665.1	s__Propioniciclava tarda	99.9969	953	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propioniciclava	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_012517965.1	s__Propioniciclava sp012517965	80.53	504	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propioniciclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826085.1	s__Nigerium massiliense	79.2854	349	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Nigerium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017569205.1	s__Brevilactibacter sp014164685	79.2411	400	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	99.00	98.00	0.92	0.83	3	-
GCA_012838755.1	s__Brevilactibacter sp012838755	79.1112	337	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011393335.1	s__Brevilactibacter coleopterorum	78.8919	428	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004324755.1	s__Brevilactibacter sinopodophylli	78.8443	394	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711325.1	s__Brevilactibacter sp016711325	78.5678	334	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014858005.1	s__Brevilactibacter sp014858005	78.5454	347	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563675.1	s__Propionicimonas paludicola	78.4518	243	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716635.1	s__JADJVZ01 sp016716635	78.3686	247	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__JADJVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603275.1	s__Propionicimonas sp001603275	78.1946	233	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306015.1	s__Propionicimonas sp017306015	78.0987	305	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055925.1	s__Micropruina sp018055925	77.935	261	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408305.1	s__Naumannella cuiyingiana	77.1335	210	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Naumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015142735.1	s__Oerskovia sp015142735	76.5773	168	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	76.1505	175	971	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:10,944] [INFO] GTDB search result was written to GCF_004324765.1_ASM432476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:10,945] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:10,949] [INFO] DFAST_QC result json was written to GCF_004324765.1_ASM432476v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:10,949] [INFO] DFAST_QC completed!
[2024-01-24 15:03:10,949] [INFO] Total running time: 0h1m7s