[2024-01-25 19:32:36,466] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:32:36,468] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:32:36,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg81b7cafe-445e-42c6-a87a-d2bd01edd5a0/dqc_reference
[2024-01-25 19:32:37,553] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:32:37,554] [INFO] Task started: Prodigal
[2024-01-25 19:32:37,554] [INFO] Running command: gunzip -c /var/lib/cwl/stge50f24b5-6144-4363-b286-c3a001bb7783/GCF_021129305.1_ASM2112930v1_genomic.fna.gz | prodigal -d GCF_021129305.1_ASM2112930v1_genomic.fna/cds.fna -a GCF_021129305.1_ASM2112930v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:07,553] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:07,554] [INFO] Task started: HMMsearch
[2024-01-25 19:33:07,554] [INFO] Running command: hmmsearch --tblout GCF_021129305.1_ASM2112930v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81b7cafe-445e-42c6-a87a-d2bd01edd5a0/dqc_reference/reference_markers.hmm GCF_021129305.1_ASM2112930v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:07,884] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:07,885] [INFO] Found 6/6 markers.
[2024-01-25 19:33:07,959] [INFO] Query marker FASTA was written to GCF_021129305.1_ASM2112930v1_genomic.fna/markers.fasta
[2024-01-25 19:33:07,960] [INFO] Task started: Blastn
[2024-01-25 19:33:07,960] [INFO] Running command: blastn -query GCF_021129305.1_ASM2112930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81b7cafe-445e-42c6-a87a-d2bd01edd5a0/dqc_reference/reference_markers.fasta -out GCF_021129305.1_ASM2112930v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:09,161] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:09,164] [INFO] Selected 19 target genomes.
[2024-01-25 19:33:09,164] [INFO] Target genome list was writen to GCF_021129305.1_ASM2112930v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:09,170] [INFO] Task started: fastANI
[2024-01-25 19:33:09,170] [INFO] Running command: fastANI --query /var/lib/cwl/stge50f24b5-6144-4363-b286-c3a001bb7783/GCF_021129305.1_ASM2112930v1_genomic.fna.gz --refList GCF_021129305.1_ASM2112930v1_genomic.fna/target_genomes.txt --output GCF_021129305.1_ASM2112930v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:28,947] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:28,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81b7cafe-445e-42c6-a87a-d2bd01edd5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:28,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81b7cafe-445e-42c6-a87a-d2bd01edd5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:28,959] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:33:28,959] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:33:28,959] [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
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	85.5554	1806	3094	95	below_threshold
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	83.3883	1685	3094	95	below_threshold
Kineosporia mesophila	strain=JCM 16902	GCA_021129235.1	566012	566012	type	True	82.9589	1561	3094	95	below_threshold
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	77.3324	510	3094	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	77.2559	428	3094	95	below_threshold
Kineococcus xinjiangensis	strain=DSM 22857	GCA_002934625.1	512762	512762	type	True	77.1964	452	3094	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	77.0715	464	3094	95	below_threshold
Kineococcus radiotolerans	strain=SRS30216	GCA_000017305.1	131568	131568	type	True	77.032	461	3094	95	below_threshold
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	76.835	321	3094	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	76.8107	336	3094	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	76.804	385	3094	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	76.6084	399	3094	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.5241	388	3094	95	below_threshold
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	76.4842	229	3094	95	below_threshold
Streptomyces spongiicola	strain=HNM0071	GCA_003122365.1	1690221	1690221	type	True	76.4708	416	3094	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	76.412	486	3094	95	below_threshold
Actinomadura harenae	strain=NEAU-Ht49	GCA_003696215.1	2483351	2483351	type	True	76.3102	530	3094	95	below_threshold
Labedella phragmitis	strain=11W25H-1	GCA_004078635.1	2498849	2498849	type	True	76.1219	157	3094	95	below_threshold
Pseudodesulfovibrio cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	74.7412	57	3094	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:28,962] [INFO] DFAST Taxonomy check result was written to GCF_021129305.1_ASM2112930v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:28,962] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:28,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:28,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81b7cafe-445e-42c6-a87a-d2bd01edd5a0/dqc_reference/checkm_data
[2024-01-25 19:33:28,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:29,045] [INFO] Task started: CheckM
[2024-01-25 19:33:29,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021129305.1_ASM2112930v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021129305.1_ASM2112930v1_genomic.fna/checkm_input GCF_021129305.1_ASM2112930v1_genomic.fna/checkm_result
[2024-01-25 19:35:04,385] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:04,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:04,405] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:04,405] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:04,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021129305.1_ASM2112930v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:04,406] [INFO] Task started: Blastn
[2024-01-25 19:35:04,406] [INFO] Running command: blastn -query GCF_021129305.1_ASM2112930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81b7cafe-445e-42c6-a87a-d2bd01edd5a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_021129305.1_ASM2112930v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:06,487] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:06,490] [INFO] Selected 24 target genomes.
[2024-01-25 19:35:06,490] [INFO] Target genome list was writen to GCF_021129305.1_ASM2112930v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:06,502] [INFO] Task started: fastANI
[2024-01-25 19:35:06,502] [INFO] Running command: fastANI --query /var/lib/cwl/stge50f24b5-6144-4363-b286-c3a001bb7783/GCF_021129305.1_ASM2112930v1_genomic.fna.gz --refList GCF_021129305.1_ASM2112930v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021129305.1_ASM2112930v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:30,373] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:30,386] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:35:30,387] [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_000719025.1	s__Kineosporia aurantiaca	83.4364	1597	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018499875.1	s__Kineosporia sp018499875	83.4043	1681	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713225.1	s__JADJPO01 sp016713225	77.472	501	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JADJPO01	95.0	99.38	99.28	0.94	0.94	3	-
GCF_900111375.1	s__Pedococcus cremeus	77.3401	423	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_012396125.1	s__Cellulomonas denverensis	77.3086	517	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900104525.1	s__Pedococcus dokdonensis	77.2332	373	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198655.1	s__R-H-3 sp002198655	77.2026	573	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213575.1	s__R-H-3 sp016213575	77.1957	468	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198675.1	s__R-H-3 sp002198675	77.1839	593	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934625.1	s__Kineococcus xinjiangensis	77.1744	457	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719445.1	s__JAAYAH01 sp012719445	77.1398	451	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JAAYAH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717165.1	s__JADKGA01 sp016717165	77.1209	263	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__JADKGA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906315.1	s__Kineococcus vitellinus	77.0671	465	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017305.1	s__Kineococcus radiotolerans	76.9958	466	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	98.46	98.46	0.90	0.90	2	-
GCF_003696205.1	s__Cellulomonas sp003696205	76.9229	422	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679345.1	s__Cellulomonas cellulans_A	76.8707	475	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	76.8082	336	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014084125.1	s__Streptacidiphilus sp014084125	76.5805	651	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716785.1	s__Thermopolyspora flexuosa	76.47	474	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermopolyspora	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003696215.1	s__Spirillospora harenae	76.2897	536	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004078635.1	s__Labedella phragmitis	76.1112	158	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013820915.1	s__JACDHR01 sp013820915	74.8217	75	3094	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__Longimicrobiaceae;g__JACDHR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:30,388] [INFO] GTDB search result was written to GCF_021129305.1_ASM2112930v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:30,388] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:30,392] [INFO] DFAST_QC result json was written to GCF_021129305.1_ASM2112930v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:30,392] [INFO] DFAST_QC completed!
[2024-01-25 19:35:30,392] [INFO] Total running time: 0h2m54s