[2024-01-24 13:12:56,107] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:56,109] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:56,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg6daa15ce-2676-4a20-9e66-68931a66a0d2/dqc_reference
[2024-01-24 13:12:57,455] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,456] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,456] [INFO] Running command: gunzip -c /var/lib/cwl/stg42eecad4-4c23-498c-b86f-4bb905d27957/GCF_013085345.1_ASM1308534v1_genomic.fna.gz | prodigal -d GCF_013085345.1_ASM1308534v1_genomic.fna/cds.fna -a GCF_013085345.1_ASM1308534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:06,306] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:06,307] [INFO] Task started: HMMsearch
[2024-01-24 13:13:06,307] [INFO] Running command: hmmsearch --tblout GCF_013085345.1_ASM1308534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6daa15ce-2676-4a20-9e66-68931a66a0d2/dqc_reference/reference_markers.hmm GCF_013085345.1_ASM1308534v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:06,596] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:06,597] [INFO] Found 6/6 markers.
[2024-01-24 13:13:06,626] [INFO] Query marker FASTA was written to GCF_013085345.1_ASM1308534v1_genomic.fna/markers.fasta
[2024-01-24 13:13:06,626] [INFO] Task started: Blastn
[2024-01-24 13:13:06,626] [INFO] Running command: blastn -query GCF_013085345.1_ASM1308534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6daa15ce-2676-4a20-9e66-68931a66a0d2/dqc_reference/reference_markers.fasta -out GCF_013085345.1_ASM1308534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:08,037] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:08,040] [INFO] Selected 17 target genomes.
[2024-01-24 13:13:08,040] [INFO] Target genome list was writen to GCF_013085345.1_ASM1308534v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:08,047] [INFO] Task started: fastANI
[2024-01-24 13:13:08,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg42eecad4-4c23-498c-b86f-4bb905d27957/GCF_013085345.1_ASM1308534v1_genomic.fna.gz --refList GCF_013085345.1_ASM1308534v1_genomic.fna/target_genomes.txt --output GCF_013085345.1_ASM1308534v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:22,887] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:22,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6daa15ce-2676-4a20-9e66-68931a66a0d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:22,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6daa15ce-2676-4a20-9e66-68931a66a0d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:22,901] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:22,901] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:22,901] [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
Isoptericola sediminis	strain=JC619	GCA_013085345.1	2733572	2733572	type	True	100.0	1063	1067	95	conclusive
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	84.3504	818	1067	95	below_threshold
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	82.5633	765	1067	95	below_threshold
Isoptericola dokdonensis	strain=DS-3	GCA_001636295.1	372663	372663	type	True	82.4023	743	1067	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	79.8323	557	1067	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	79.6711	613	1067	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	79.4574	566	1067	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.4389	571	1067	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	79.3734	498	1067	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.2758	494	1067	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	79.1826	495	1067	95	below_threshold
Myceligenerans indicum	strain=I2	GCA_016742955.1	2593663	2593663	type	True	79.1724	513	1067	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	79.1435	561	1067	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.0173	511	1067	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.998	501	1067	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.7808	457	1067	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	78.7056	441	1067	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:22,903] [INFO] DFAST Taxonomy check result was written to GCF_013085345.1_ASM1308534v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:22,904] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:22,904] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:22,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6daa15ce-2676-4a20-9e66-68931a66a0d2/dqc_reference/checkm_data
[2024-01-24 13:13:22,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:22,938] [INFO] Task started: CheckM
[2024-01-24 13:13:22,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013085345.1_ASM1308534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013085345.1_ASM1308534v1_genomic.fna/checkm_input GCF_013085345.1_ASM1308534v1_genomic.fna/checkm_result
[2024-01-24 13:14:11,130] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:11,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:11,162] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:11,163] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:11,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013085345.1_ASM1308534v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:11,163] [INFO] Task started: Blastn
[2024-01-24 13:14:11,164] [INFO] Running command: blastn -query GCF_013085345.1_ASM1308534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6daa15ce-2676-4a20-9e66-68931a66a0d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_013085345.1_ASM1308534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:13,321] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:13,325] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:13,325] [INFO] Target genome list was writen to GCF_013085345.1_ASM1308534v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:13,340] [INFO] Task started: fastANI
[2024-01-24 13:14:13,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg42eecad4-4c23-498c-b86f-4bb905d27957/GCF_013085345.1_ASM1308534v1_genomic.fna.gz --refList GCF_013085345.1_ASM1308534v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013085345.1_ASM1308534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:24,684] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:24,699] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:24,699] [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_013085345.1	s__Isoptericola sediminis	100.0	1063	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013149805.1	s__Isoptericola chiayiensis	84.3629	817	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003075.1	s__Isoptericola halotolerans_A	82.8341	729	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002563715.1	s__Isoptericola jiangsuensis	82.5666	765	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636295.1	s__Isoptericola dokdonensis	82.3891	744	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149785.1	s__Isoptericola halotolerans	82.3365	740	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011634835.1	s__Isoptericola sp011634835	81.6197	691	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215105.1	s__Isoptericola variabilis_A	81.5945	666	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_000718325.1	s__Oerskovia turbata	79.4102	492	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.78	99.34	0.96	0.90	4	-
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	79.3261	573	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	-
GCF_001692445.1	s__Oerskovia enterophila	79.167	497	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	98.35	97.89	0.90	0.89	4	-
GCF_012396155.1	s__Cellulomonas septica	79.1273	322	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798015.1	s__Luteimicrobium subarcticum	78.8162	465	1067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:24,701] [INFO] GTDB search result was written to GCF_013085345.1_ASM1308534v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:24,701] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:24,705] [INFO] DFAST_QC result json was written to GCF_013085345.1_ASM1308534v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:24,705] [INFO] DFAST_QC completed!
[2024-01-24 13:14:24,705] [INFO] Total running time: 0h1m29s