[2024-01-24 10:57:38,559] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,563] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ae62715-3481-4a05-b32e-cb020a250b83/dqc_reference
[2024-01-24 10:57:39,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,974] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,974] [INFO] Running command: gunzip -c /var/lib/cwl/stg64afc87f-1a97-4807-a708-5d15b1a9e5de/GCF_018499875.1_ASM1849987v1_genomic.fna.gz | prodigal -d GCF_018499875.1_ASM1849987v1_genomic.fna/cds.fna -a GCF_018499875.1_ASM1849987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:12,198] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:12,198] [INFO] Task started: HMMsearch
[2024-01-24 10:58:12,199] [INFO] Running command: hmmsearch --tblout GCF_018499875.1_ASM1849987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ae62715-3481-4a05-b32e-cb020a250b83/dqc_reference/reference_markers.hmm GCF_018499875.1_ASM1849987v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:12,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:12,579] [INFO] Found 6/6 markers.
[2024-01-24 10:58:12,642] [INFO] Query marker FASTA was written to GCF_018499875.1_ASM1849987v1_genomic.fna/markers.fasta
[2024-01-24 10:58:12,643] [INFO] Task started: Blastn
[2024-01-24 10:58:12,643] [INFO] Running command: blastn -query GCF_018499875.1_ASM1849987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ae62715-3481-4a05-b32e-cb020a250b83/dqc_reference/reference_markers.fasta -out GCF_018499875.1_ASM1849987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:13,929] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:13,933] [INFO] Selected 19 target genomes.
[2024-01-24 10:58:13,933] [INFO] Target genome list was writen to GCF_018499875.1_ASM1849987v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:13,965] [INFO] Task started: fastANI
[2024-01-24 10:58:13,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg64afc87f-1a97-4807-a708-5d15b1a9e5de/GCF_018499875.1_ASM1849987v1_genomic.fna.gz --refList GCF_018499875.1_ASM1849987v1_genomic.fna/target_genomes.txt --output GCF_018499875.1_ASM1849987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:39,996] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:39,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ae62715-3481-4a05-b32e-cb020a250b83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:39,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ae62715-3481-4a05-b32e-cb020a250b83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:40,017] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:40,017] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:40,018] [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 corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	100.0	2707	2708	95	conclusive
Kineosporia mesophila	strain=JCM 16902	GCA_021129235.1	566012	566012	type	True	84.0938	1691	2708	95	below_threshold
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	83.8839	1630	2708	95	below_threshold
Kineococcus xinjiangensis	strain=DSM 22857	GCA_002934625.1	512762	512762	type	True	76.9152	493	2708	95	below_threshold
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	76.9024	532	2708	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	76.6475	514	2708	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.6029	401	2708	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	76.5634	410	2708	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	76.4417	410	2708	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	76.4064	394	2708	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	76.3977	390	2708	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	76.3017	634	2708	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	76.2945	570	2708	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	76.149	693	2708	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	76.135	692	2708	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	76.09	708	2708	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	76.0855	656	2708	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	76.0728	711	2708	95	below_threshold
Streptomyces fuscichromogenes	strain=CGMCC 4.7110	GCA_014645815.1	1324013	1324013	type	True	76.0203	679	2708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:40,022] [INFO] DFAST Taxonomy check result was written to GCF_018499875.1_ASM1849987v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:40,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:40,023] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:40,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ae62715-3481-4a05-b32e-cb020a250b83/dqc_reference/checkm_data
[2024-01-24 10:58:40,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:40,102] [INFO] Task started: CheckM
[2024-01-24 10:58:40,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018499875.1_ASM1849987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018499875.1_ASM1849987v1_genomic.fna/checkm_input GCF_018499875.1_ASM1849987v1_genomic.fna/checkm_result
[2024-01-24 11:00:39,819] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:39,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:39,845] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:39,845] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:39,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018499875.1_ASM1849987v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:39,846] [INFO] Task started: Blastn
[2024-01-24 11:00:39,846] [INFO] Running command: blastn -query GCF_018499875.1_ASM1849987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ae62715-3481-4a05-b32e-cb020a250b83/dqc_reference/reference_markers_gtdb.fasta -out GCF_018499875.1_ASM1849987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:41,778] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:41,782] [INFO] Selected 24 target genomes.
[2024-01-24 11:00:41,782] [INFO] Target genome list was writen to GCF_018499875.1_ASM1849987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:41,817] [INFO] Task started: fastANI
[2024-01-24 11:00:41,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg64afc87f-1a97-4807-a708-5d15b1a9e5de/GCF_018499875.1_ASM1849987v1_genomic.fna.gz --refList GCF_018499875.1_ASM1849987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018499875.1_ASM1849987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:01:07,452] [INFO] Task succeeded: fastANI
[2024-01-24 11:01:07,483] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:01:07,483] [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_018499875.1	s__Kineosporia sp018499875	100.0	2707	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000719025.1	s__Kineosporia aurantiaca	83.4834	1586	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	77.4418	456	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCA_016794595.1	s__JADJPO01 sp016794595	77.2927	550	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JADJPO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713225.1	s__JADJPO01 sp016713225	77.2006	561	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JADJPO01	95.0	99.38	99.28	0.94	0.94	3	-
GCF_002198675.1	s__R-H-3 sp002198675	77.1536	704	2708	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_014377795.1	s__JACMOY01 sp014377795	77.0609	286	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Angustibacteraceae;g__JACMOY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198655.1	s__R-H-3 sp002198655	77.0005	691	2708	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	76.9905	566	2708	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	76.8663	503	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396125.1	s__Cellulomonas denverensis	76.8639	540	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCA_012719445.1	s__JAAYAH01 sp012719445	76.7934	481	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JAAYAH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409475.1	s__Cellulomonas hominis_B	76.7697	494	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139485.1	s__Phycicoccus sp018139485	76.7609	379	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025965.2	s__Phycicoccus flavus	76.4802	466	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188025.1	s__Blastococcus sp900188025	76.4649	456	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519295.1	s__Cellulosimicrobium funkei	76.4117	386	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	76.3837	362	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	76.379	393	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	-
GCF_900102745.1	s__Geodermatophilus telluris	76.3131	631	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188375.1	s__Geodermatophilus pulveris	76.2929	571	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863195.1	s__Planobispora takensis	76.1531	688	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	76.1434	697	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_000424845.1	s__Streptomyces sp000424845	76.1393	422	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:01:07,485] [INFO] GTDB search result was written to GCF_018499875.1_ASM1849987v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:01:07,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:01:07,490] [INFO] DFAST_QC result json was written to GCF_018499875.1_ASM1849987v1_genomic.fna/dqc_result.json
[2024-01-24 11:01:07,490] [INFO] DFAST_QC completed!
[2024-01-24 11:01:07,490] [INFO] Total running time: 0h3m29s