[2024-01-25 20:04:35,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:35,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:35,649] [INFO] DQC Reference Directory: /var/lib/cwl/stg12c0f348-eee4-4595-aaf8-e05243d53566/dqc_reference
[2024-01-25 20:04:36,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:36,812] [INFO] Task started: Prodigal
[2024-01-25 20:04:36,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bcb1d2c-f7e4-4ee7-8787-20f4d5d7d7ef/GCF_000515355.1_ASM51535v1_genomic.fna.gz | prodigal -d GCF_000515355.1_ASM51535v1_genomic.fna/cds.fna -a GCF_000515355.1_ASM51535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:50,462] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:50,462] [INFO] Task started: HMMsearch
[2024-01-25 20:04:50,462] [INFO] Running command: hmmsearch --tblout GCF_000515355.1_ASM51535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12c0f348-eee4-4595-aaf8-e05243d53566/dqc_reference/reference_markers.hmm GCF_000515355.1_ASM51535v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:50,763] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:50,764] [INFO] Found 6/6 markers.
[2024-01-25 20:04:50,811] [INFO] Query marker FASTA was written to GCF_000515355.1_ASM51535v1_genomic.fna/markers.fasta
[2024-01-25 20:04:50,811] [INFO] Task started: Blastn
[2024-01-25 20:04:50,811] [INFO] Running command: blastn -query GCF_000515355.1_ASM51535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12c0f348-eee4-4595-aaf8-e05243d53566/dqc_reference/reference_markers.fasta -out GCF_000515355.1_ASM51535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:52,046] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:52,049] [INFO] Selected 12 target genomes.
[2024-01-25 20:04:52,049] [INFO] Target genome list was writen to GCF_000515355.1_ASM51535v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:52,057] [INFO] Task started: fastANI
[2024-01-25 20:04:52,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bcb1d2c-f7e4-4ee7-8787-20f4d5d7d7ef/GCF_000515355.1_ASM51535v1_genomic.fna.gz --refList GCF_000515355.1_ASM51535v1_genomic.fna/target_genomes.txt --output GCF_000515355.1_ASM51535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:06,878] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:06,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12c0f348-eee4-4595-aaf8-e05243d53566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:06,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12c0f348-eee4-4595-aaf8-e05243d53566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:06,887] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:05:06,887] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:06,887] [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
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	99.9999	1813	1826	95	conclusive
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	89.6303	1416	1826	95	below_threshold
Promicromonospora soli	strain=CGMCC 4.7398	GCA_014653785.1	2035533	2035533	type	True	85.6327	1129	1826	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	85.1815	1246	1826	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	84.8174	1070	1826	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	84.7106	1131	1826	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.0341	694	1826	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	78.9846	717	1826	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.7032	625	1826	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.7759	517	1826	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.7582	593	1826	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.6627	577	1826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:06,888] [INFO] DFAST Taxonomy check result was written to GCF_000515355.1_ASM51535v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:06,889] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:06,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:06,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12c0f348-eee4-4595-aaf8-e05243d53566/dqc_reference/checkm_data
[2024-01-25 20:05:06,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:06,950] [INFO] Task started: CheckM
[2024-01-25 20:05:06,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000515355.1_ASM51535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000515355.1_ASM51535v1_genomic.fna/checkm_input GCF_000515355.1_ASM51535v1_genomic.fna/checkm_result
[2024-01-25 20:05:40,657] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:40,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:40,675] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:40,675] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:40,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000515355.1_ASM51535v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:40,676] [INFO] Task started: Blastn
[2024-01-25 20:05:40,676] [INFO] Running command: blastn -query GCF_000515355.1_ASM51535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12c0f348-eee4-4595-aaf8-e05243d53566/dqc_reference/reference_markers_gtdb.fasta -out GCF_000515355.1_ASM51535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:42,669] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:42,672] [INFO] Selected 11 target genomes.
[2024-01-25 20:05:42,672] [INFO] Target genome list was writen to GCF_000515355.1_ASM51535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:42,689] [INFO] Task started: fastANI
[2024-01-25 20:05:42,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bcb1d2c-f7e4-4ee7-8787-20f4d5d7d7ef/GCF_000515355.1_ASM51535v1_genomic.fna.gz --refList GCF_000515355.1_ASM51535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000515355.1_ASM51535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:00,137] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:00,145] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:00,146] [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_000515355.1	s__Promicromonospora kroppenstedtii	99.9999	1813	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	97.09	97.09	0.84	0.84	2	conclusive
GCF_000385135.1	s__Promicromonospora sukumoe_B	93.8782	1506	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	95.99	95.99	0.93	0.93	2	-
GCF_014137995.1	s__Promicromonospora sukumoe	89.6427	1417	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550025.1	s__Promicromonospora thailandica	86.9166	1359	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058225.1	s__Promicromonospora sp003058225	86.784	1288	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	98.27	98.27	0.94	0.94	2	-
GCF_014653785.1	s__Promicromonospora soli	85.6262	1130	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900608595.1	s__Promicromonospora panici	85.595	1236	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096495.1	s__Promicromonospora sukumoe_A	85.5844	1261	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004695.1	s__Promicromonospora citrea	84.8357	1068	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	79.1081	731	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	78.9988	747	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:00,148] [INFO] GTDB search result was written to GCF_000515355.1_ASM51535v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:00,149] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:00,151] [INFO] DFAST_QC result json was written to GCF_000515355.1_ASM51535v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:00,151] [INFO] DFAST_QC completed!
[2024-01-25 20:06:00,151] [INFO] Total running time: 0h1m25s