[2024-01-24 11:19:55,048] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:55,050] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:55,050] [INFO] DQC Reference Directory: /var/lib/cwl/stgac29b13d-586a-4fe4-98a5-4c81ba278566/dqc_reference
[2024-01-24 11:19:56,398] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,399] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,399] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9bd4898-72e9-4415-bab8-7c914398a584/GCF_003002815.1_ASM300281v1_genomic.fna.gz | prodigal -d GCF_003002815.1_ASM300281v1_genomic.fna/cds.fna -a GCF_003002815.1_ASM300281v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:36,065] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:36,066] [INFO] Task started: HMMsearch
[2024-01-24 11:20:36,066] [INFO] Running command: hmmsearch --tblout GCF_003002815.1_ASM300281v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac29b13d-586a-4fe4-98a5-4c81ba278566/dqc_reference/reference_markers.hmm GCF_003002815.1_ASM300281v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:36,496] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:36,498] [INFO] Found 6/6 markers.
[2024-01-24 11:20:36,582] [INFO] Query marker FASTA was written to GCF_003002815.1_ASM300281v1_genomic.fna/markers.fasta
[2024-01-24 11:20:36,583] [INFO] Task started: Blastn
[2024-01-24 11:20:36,583] [INFO] Running command: blastn -query GCF_003002815.1_ASM300281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac29b13d-586a-4fe4-98a5-4c81ba278566/dqc_reference/reference_markers.fasta -out GCF_003002815.1_ASM300281v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:38,052] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:38,057] [INFO] Selected 31 target genomes.
[2024-01-24 11:20:38,057] [INFO] Target genome list was writen to GCF_003002815.1_ASM300281v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:38,071] [INFO] Task started: fastANI
[2024-01-24 11:20:38,071] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9bd4898-72e9-4415-bab8-7c914398a584/GCF_003002815.1_ASM300281v1_genomic.fna.gz --refList GCF_003002815.1_ASM300281v1_genomic.fna/target_genomes.txt --output GCF_003002815.1_ASM300281v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:40,741] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:40,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac29b13d-586a-4fe4-98a5-4c81ba278566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:40,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac29b13d-586a-4fe4-98a5-4c81ba278566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:40,766] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:21:40,766] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:21:40,766] [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
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	81.5215	1527	3541	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	81.4239	1566	3541	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	81.1809	1718	3541	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	81.0804	1648	3541	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	81.0712	1631	3541	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	80.9954	1625	3541	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	80.8424	1813	3541	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	80.8	1788	3541	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	80.5279	1528	3541	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	80.3743	1407	3541	95	below_threshold
Lentzea xinjiangensis	strain=CGMCC 4.3525	GCA_900110955.1	402600	402600	type	True	80.3332	1509	3541	95	below_threshold
Lentzea fradiae	strain=CGMCC 4.3506	GCA_900100955.1	200378	200378	type	True	80.3081	1482	3541	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	80.3077	1597	3541	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	80.2055	1292	3541	95	below_threshold
Lentzea flava	strain=JCM 3296	GCA_014648475.1	103732	103732	type	True	80.1105	1461	3541	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	80.0785	1486	3541	95	below_threshold
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	80.0783	1572	3541	95	below_threshold
Lentzea albidocapillata	strain=NRRL B-24057	GCA_000719115.1	40571	40571	type	True	80.0418	1404	3541	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	80.0348	1460	3541	95	below_threshold
Lentzea indica	strain=PSKA42	GCA_012184385.1	2604800	2604800	type	True	80.0172	1334	3541	95	below_threshold
Lentzea flaviverrucosa	strain=DSM 44664	GCA_003350445.1	200379	200379	type	True	79.9915	1504	3541	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	79.9661	1500	3541	95	below_threshold
Lentzea waywayandensis	strain=DSM 44232	GCA_900115955.1	84724	84724	type	True	79.956	1558	3541	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	79.9226	1476	3541	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.3065	1100	3541	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	77.8944	1059	3541	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	76.1235	301	3541	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	75.8904	708	3541	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	75.8843	707	3541	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	75.7766	430	3541	95	below_threshold
Amnibacterium kyonggiense	strain=DSM 24782	GCA_004364555.1	595671	595671	type	True	75.5417	449	3541	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:40,768] [INFO] DFAST Taxonomy check result was written to GCF_003002815.1_ASM300281v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:40,768] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:40,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:40,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac29b13d-586a-4fe4-98a5-4c81ba278566/dqc_reference/checkm_data
[2024-01-24 11:21:40,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:40,865] [INFO] Task started: CheckM
[2024-01-24 11:21:40,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003002815.1_ASM300281v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003002815.1_ASM300281v1_genomic.fna/checkm_input GCF_003002815.1_ASM300281v1_genomic.fna/checkm_result
[2024-01-24 11:24:10,769] [INFO] Task succeeded: CheckM
[2024-01-24 11:24:10,771] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:24:10,802] [INFO] ===== Completeness check finished =====
[2024-01-24 11:24:10,802] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:24:10,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003002815.1_ASM300281v1_genomic.fna/markers.fasta)
[2024-01-24 11:24:10,803] [INFO] Task started: Blastn
[2024-01-24 11:24:10,803] [INFO] Running command: blastn -query GCF_003002815.1_ASM300281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac29b13d-586a-4fe4-98a5-4c81ba278566/dqc_reference/reference_markers_gtdb.fasta -out GCF_003002815.1_ASM300281v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:24:12,940] [INFO] Task succeeded: Blastn
[2024-01-24 11:24:12,945] [INFO] Selected 27 target genomes.
[2024-01-24 11:24:12,945] [INFO] Target genome list was writen to GCF_003002815.1_ASM300281v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:24:12,964] [INFO] Task started: fastANI
[2024-01-24 11:24:12,965] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9bd4898-72e9-4415-bab8-7c914398a584/GCF_003002815.1_ASM300281v1_genomic.fna.gz --refList GCF_003002815.1_ASM300281v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003002815.1_ASM300281v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:25:16,093] [INFO] Task succeeded: fastANI
[2024-01-24 11:25:16,116] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:25:16,116] [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_003002815.1	s__Umezawaea tangerina	100.0	3538	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Umezawaea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014648515.1	s__Actinosynnema coeruleofuscum	81.4634	1540	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCF_016464305.1	s__REN6 sp016464305	81.2798	1397	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	81.1788	1720	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_001280085.1	s__Actinosynnema sp001280085	81.0641	1720	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716745.1	s__Actinosynnema saharense	81.0459	1657	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769385.1	s__Actinosynnema deserti	81.0278	1642	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014735.1	s__Actinosynnema carneum	81.0103	1620	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_001984175.1	s__Actinosynnema sp001984175	80.8628	1602	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328705.1	s__Actinosynnema espanaense	80.8122	1602	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	80.8067	1824	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003634995.1	s__Actinosynnema variisporeum	80.7273	1616	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007845675.1	s__Lentzea sp007845675	80.572	1518	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279525.1	s__Lentzea sp001279525	80.325	1530	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110955.1	s__Lentzea xinjiangensis	80.3044	1512	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648475.1	s__Lentzea flava	80.0977	1465	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646255.1	s__Lentzea pudingi	80.0298	1461	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012184385.1	s__Lentzea indica	80.025	1331	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350445.1	s__Lentzea flaviverrucosa	79.9947	1501	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000955955.1	s__Lentzea aerocolonigenes_A	79.954	1367	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115955.1	s__Lentzea waywayandensis	79.9365	1563	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265345.1	s__Lentzea terrae	79.9115	1478	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	79.4325	1371	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114845.1	s__Nocardioides simplex	75.9021	698	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.16	97.49	0.97	0.92	4	-
GCF_014190775.1	s__Leifsonia aquatica	75.7609	435	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCA_001898805.1	s__Leifsonia sp001898805	75.6256	449	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364555.1	s__Amnibacterium kyonggiense	75.5449	447	3541	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Amnibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:25:16,120] [INFO] GTDB search result was written to GCF_003002815.1_ASM300281v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:25:16,126] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:25:16,136] [INFO] DFAST_QC result json was written to GCF_003002815.1_ASM300281v1_genomic.fna/dqc_result.json
[2024-01-24 11:25:16,136] [INFO] DFAST_QC completed!
[2024-01-24 11:25:16,136] [INFO] Total running time: 0h5m21s