[2024-01-24 10:47:06,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,596] [INFO] DQC Reference Directory: /var/lib/cwl/stgb64ada89-8c01-409a-b8f6-1574e167c478/dqc_reference
[2024-01-24 10:47:12,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,795] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,796] [INFO] Running command: gunzip -c /var/lib/cwl/stg38f298f2-16f0-4dd0-8651-1afa549a7296/GCF_017349295.1_ASM1734929v1_genomic.fna.gz | prodigal -d GCF_017349295.1_ASM1734929v1_genomic.fna/cds.fna -a GCF_017349295.1_ASM1734929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:25,903] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:25,903] [INFO] Task started: HMMsearch
[2024-01-24 10:47:25,903] [INFO] Running command: hmmsearch --tblout GCF_017349295.1_ASM1734929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb64ada89-8c01-409a-b8f6-1574e167c478/dqc_reference/reference_markers.hmm GCF_017349295.1_ASM1734929v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:26,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:26,233] [INFO] Found 6/6 markers.
[2024-01-24 10:47:26,272] [INFO] Query marker FASTA was written to GCF_017349295.1_ASM1734929v1_genomic.fna/markers.fasta
[2024-01-24 10:47:26,273] [INFO] Task started: Blastn
[2024-01-24 10:47:26,273] [INFO] Running command: blastn -query GCF_017349295.1_ASM1734929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb64ada89-8c01-409a-b8f6-1574e167c478/dqc_reference/reference_markers.fasta -out GCF_017349295.1_ASM1734929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:27,518] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:27,521] [INFO] Selected 13 target genomes.
[2024-01-24 10:47:27,521] [INFO] Target genome list was writen to GCF_017349295.1_ASM1734929v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:28,424] [INFO] Task started: fastANI
[2024-01-24 10:47:28,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg38f298f2-16f0-4dd0-8651-1afa549a7296/GCF_017349295.1_ASM1734929v1_genomic.fna.gz --refList GCF_017349295.1_ASM1734929v1_genomic.fna/target_genomes.txt --output GCF_017349295.1_ASM1734929v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:42,968] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:42,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb64ada89-8c01-409a-b8f6-1574e167c478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:42,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb64ada89-8c01-409a-b8f6-1574e167c478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:42,995] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:42,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:42,996] [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
Myceligenerans salitolerans	strain=XHU 5031	GCA_017349295.1	1230528	1230528	type	True	100.0	1505	1506	95	conclusive
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	88.1117	1210	1506	95	below_threshold
Myceligenerans indicum	strain=I2	GCA_016742955.1	2593663	2593663	type	True	85.2477	1083	1506	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	80.2241	737	1506	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	80.0939	774	1506	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	79.9153	741	1506	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	79.8648	838	1506	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	79.7236	799	1506	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	78.8418	524	1506	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.3992	459	1506	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.2745	454	1506	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	78.1682	437	1506	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.6337	467	1506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:43,000] [INFO] DFAST Taxonomy check result was written to GCF_017349295.1_ASM1734929v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:43,001] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:43,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:43,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb64ada89-8c01-409a-b8f6-1574e167c478/dqc_reference/checkm_data
[2024-01-24 10:47:43,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:43,058] [INFO] Task started: CheckM
[2024-01-24 10:47:43,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017349295.1_ASM1734929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017349295.1_ASM1734929v1_genomic.fna/checkm_input GCF_017349295.1_ASM1734929v1_genomic.fna/checkm_result
[2024-01-24 10:48:54,590] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:54,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:54,610] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:54,610] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:54,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017349295.1_ASM1734929v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:54,611] [INFO] Task started: Blastn
[2024-01-24 10:48:54,612] [INFO] Running command: blastn -query GCF_017349295.1_ASM1734929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb64ada89-8c01-409a-b8f6-1574e167c478/dqc_reference/reference_markers_gtdb.fasta -out GCF_017349295.1_ASM1734929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:56,416] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:56,420] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:56,420] [INFO] Target genome list was writen to GCF_017349295.1_ASM1734929v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:56,475] [INFO] Task started: fastANI
[2024-01-24 10:48:56,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg38f298f2-16f0-4dd0-8651-1afa549a7296/GCF_017349295.1_ASM1734929v1_genomic.fna.gz --refList GCF_017349295.1_ASM1734929v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017349295.1_ASM1734929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:10,745] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:10,756] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:10,757] [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_017349295.1	s__Myceligenerans salitolerans	100.0	1505	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003814695.1	s__Myceligenerans xiligouense	88.076	1214	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014892515.1	s__Myceligenerans sp014892515	87.948	1220	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016742955.1	s__Myceligenerans indicum	85.2506	1083	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004695.1	s__Promicromonospora citrea	80.2373	735	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCF_003550025.1	s__Promicromonospora thailandica	80.141	811	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215105.1	s__Isoptericola variabilis_A	80.0112	574	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_014137995.1	s__Promicromonospora sukumoe	79.9272	832	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385135.1	s__Promicromonospora sukumoe_B	79.8668	823	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	95.99	95.99	0.93	0.93	2	-
GCF_001750215.1	s__Xylanimonas variabilis_A	79.6571	443	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016921195.1	s__Cellulosimicrobium cellulans_F	79.045	570	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	79.0393	551	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	-
GCA_009783295.1	s__Xylanimonas sp009783295	78.9676	518	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:10,762] [INFO] GTDB search result was written to GCF_017349295.1_ASM1734929v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:10,763] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:10,767] [INFO] DFAST_QC result json was written to GCF_017349295.1_ASM1734929v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:10,767] [INFO] DFAST_QC completed!
[2024-01-24 10:49:10,767] [INFO] Total running time: 0h2m4s