[2024-01-24 11:51:24,447] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,453] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd50a213-e72f-423c-96fa-ab834384373f/dqc_reference
[2024-01-24 11:51:25,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,866] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,866] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfce0e25-6ccb-4d69-907d-607aba7dd053/GCF_013408685.1_ASM1340868v1_genomic.fna.gz | prodigal -d GCF_013408685.1_ASM1340868v1_genomic.fna/cds.fna -a GCF_013408685.1_ASM1340868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:35,667] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:35,668] [INFO] Task started: HMMsearch
[2024-01-24 11:51:35,668] [INFO] Running command: hmmsearch --tblout GCF_013408685.1_ASM1340868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd50a213-e72f-423c-96fa-ab834384373f/dqc_reference/reference_markers.hmm GCF_013408685.1_ASM1340868v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:35,956] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:35,957] [INFO] Found 6/6 markers.
[2024-01-24 11:51:35,994] [INFO] Query marker FASTA was written to GCF_013408685.1_ASM1340868v1_genomic.fna/markers.fasta
[2024-01-24 11:51:35,994] [INFO] Task started: Blastn
[2024-01-24 11:51:35,994] [INFO] Running command: blastn -query GCF_013408685.1_ASM1340868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd50a213-e72f-423c-96fa-ab834384373f/dqc_reference/reference_markers.fasta -out GCF_013408685.1_ASM1340868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:37,278] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:37,282] [INFO] Selected 26 target genomes.
[2024-01-24 11:51:37,282] [INFO] Target genome list was writen to GCF_013408685.1_ASM1340868v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:37,291] [INFO] Task started: fastANI
[2024-01-24 11:51:37,291] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfce0e25-6ccb-4d69-907d-607aba7dd053/GCF_013408685.1_ASM1340868v1_genomic.fna.gz --refList GCF_013408685.1_ASM1340868v1_genomic.fna/target_genomes.txt --output GCF_013408685.1_ASM1340868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:56,223] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:56,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd50a213-e72f-423c-96fa-ab834384373f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:56,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd50a213-e72f-423c-96fa-ab834384373f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:56,242] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:56,243] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:56,243] [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
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	80.806	553	1251	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	80.6694	477	1251	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	79.4888	513	1251	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	79.3739	529	1251	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.2945	562	1251	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	79.2245	488	1251	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	79.1949	479	1251	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	79.1911	541	1251	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.1392	490	1251	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	79.1354	554	1251	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	79.1001	579	1251	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	79.0914	537	1251	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.0022	539	1251	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.0022	495	1251	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.9773	505	1251	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	78.9553	536	1251	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.9119	495	1251	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.8516	489	1251	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	78.8459	490	1251	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	78.845	388	1251	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	78.8089	402	1251	95	below_threshold
Curtobacterium luteum	strain=DSM 20542	GCA_016907595.1	33881	33881	type	True	78.6908	466	1251	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	78.6412	409	1251	95	below_threshold
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	78.5957	459	1251	95	below_threshold
Curtobacterium luteum	strain=ATCC 15830	GCA_013359885.1	33881	33881	type	True	78.5585	449	1251	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	78.2502	454	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:56,245] [INFO] DFAST Taxonomy check result was written to GCF_013408685.1_ASM1340868v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:56,245] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:56,245] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:56,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd50a213-e72f-423c-96fa-ab834384373f/dqc_reference/checkm_data
[2024-01-24 11:51:56,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:56,284] [INFO] Task started: CheckM
[2024-01-24 11:51:56,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408685.1_ASM1340868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408685.1_ASM1340868v1_genomic.fna/checkm_input GCF_013408685.1_ASM1340868v1_genomic.fna/checkm_result
[2024-01-24 11:52:37,077] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:37,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:37,100] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:37,100] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:37,100] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408685.1_ASM1340868v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:37,101] [INFO] Task started: Blastn
[2024-01-24 11:52:37,101] [INFO] Running command: blastn -query GCF_013408685.1_ASM1340868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd50a213-e72f-423c-96fa-ab834384373f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408685.1_ASM1340868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:39,176] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:39,180] [INFO] Selected 11 target genomes.
[2024-01-24 11:52:39,180] [INFO] Target genome list was writen to GCF_013408685.1_ASM1340868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:39,186] [INFO] Task started: fastANI
[2024-01-24 11:52:39,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfce0e25-6ccb-4d69-907d-607aba7dd053/GCF_013408685.1_ASM1340868v1_genomic.fna.gz --refList GCF_013408685.1_ASM1340868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408685.1_ASM1340868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:48,553] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:48,569] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:48,570] [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_013408685.1	s__Schumannella luteola	100.0	1249	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006517435.1	s__Schumannella sp006517435	92.0279	1060	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517535.1	s__Schumannella sp006517535	87.7129	909	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627075.1	s__Protaetiibacter intestinalis	80.7847	555	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003852775.1	s__Protaetiibacter sp003852775	80.7403	506	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014483895.1	s__Protaetiibacter sp014483895	80.6659	562	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325245.1	s__Pseudolysinimonas sp002325245	80.6412	464	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	99.78	99.17	0.96	0.89	14	-
GCF_011751865.2	s__Protaetiibacter sp011751905	80.008	469	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	98.78	98.78	0.94	0.94	2	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	79.8844	554	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142065.1	s__Agromyces cerinus	79.1146	550	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384855.1	s__Agromyces sp003384855	79.0275	561	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:48,571] [INFO] GTDB search result was written to GCF_013408685.1_ASM1340868v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:48,572] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:48,576] [INFO] DFAST_QC result json was written to GCF_013408685.1_ASM1340868v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:48,576] [INFO] DFAST_QC completed!
[2024-01-24 11:52:48,576] [INFO] Total running time: 0h1m24s