[2024-01-25 20:02:05,868] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:05,869] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:05,870] [INFO] DQC Reference Directory: /var/lib/cwl/stga0cd938e-4b0e-4941-a831-ce60d87bd921/dqc_reference
[2024-01-25 20:02:07,088] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:07,089] [INFO] Task started: Prodigal
[2024-01-25 20:02:07,089] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dd4095a-cdbf-4966-9c66-50eda753d06c/GCF_011174705.1_ASM1117470v1_genomic.fna.gz | prodigal -d GCF_011174705.1_ASM1117470v1_genomic.fna/cds.fna -a GCF_011174705.1_ASM1117470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:16,603] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:16,603] [INFO] Task started: HMMsearch
[2024-01-25 20:02:16,603] [INFO] Running command: hmmsearch --tblout GCF_011174705.1_ASM1117470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0cd938e-4b0e-4941-a831-ce60d87bd921/dqc_reference/reference_markers.hmm GCF_011174705.1_ASM1117470v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:16,774] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:16,775] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1dd4095a-cdbf-4966-9c66-50eda753d06c/GCF_011174705.1_ASM1117470v1_genomic.fna.gz]
[2024-01-25 20:02:16,807] [INFO] Query marker FASTA was written to GCF_011174705.1_ASM1117470v1_genomic.fna/markers.fasta
[2024-01-25 20:02:16,807] [INFO] Task started: Blastn
[2024-01-25 20:02:16,807] [INFO] Running command: blastn -query GCF_011174705.1_ASM1117470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0cd938e-4b0e-4941-a831-ce60d87bd921/dqc_reference/reference_markers.fasta -out GCF_011174705.1_ASM1117470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:17,857] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:17,862] [INFO] Selected 14 target genomes.
[2024-01-25 20:02:17,863] [INFO] Target genome list was writen to GCF_011174705.1_ASM1117470v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:17,873] [INFO] Task started: fastANI
[2024-01-25 20:02:17,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dd4095a-cdbf-4966-9c66-50eda753d06c/GCF_011174705.1_ASM1117470v1_genomic.fna.gz --refList GCF_011174705.1_ASM1117470v1_genomic.fna/target_genomes.txt --output GCF_011174705.1_ASM1117470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:27,958] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:27,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0cd938e-4b0e-4941-a831-ce60d87bd921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:27,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0cd938e-4b0e-4941-a831-ce60d87bd921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:27,968] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:02:27,968] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:27,968] [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
Tessaracoccus coleopterorum	strain=HDW20	GCA_011174705.1	2714950	2714950	type	True	100.0	1195	1195	95	conclusive
Tessaracoccus aquimaris	strain=NSG39	GCA_001997345.1	1332264	1332264	type	True	82.6454	751	1195	95	below_threshold
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	82.1772	681	1195	95	below_threshold
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	81.7125	668	1195	95	below_threshold
Tessaracoccus bendigoensis	strain=DSM 12906	GCA_900141915.1	72764	72764	type	True	81.3422	605	1195	95	below_threshold
Tessaracoccus lapidicaptus	strain=IPBSL-7	GCA_001693815.1	1427523	1427523	type	True	80.3682	506	1195	95	below_threshold
Tessaracoccus flavus	strain=RP1	GCA_001997295.1	1610493	1610493	type	True	80.0698	485	1195	95	below_threshold
Tessaracoccus flavus	strain=RP1	GCA_900107385.1	1610493	1610493	type	True	80.0692	468	1195	95	below_threshold
Tessaracoccus oleiagri	strain=CGMCC 1.9159	GCA_900103275.1	686624	686624	type	True	79.1802	420	1195	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	78.4817	343	1195	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	78.2721	288	1195	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	77.0828	207	1195	95	below_threshold
Nocardioides gilvus	strain=XZ17	GCA_003194605.1	1735589	1735589	type	True	76.988	157	1195	95	below_threshold
Nocardioides panzhihuensis	strain=DSM 26487	GCA_013408335.1	860243	860243	type	True	76.7813	219	1195	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:27,969] [INFO] DFAST Taxonomy check result was written to GCF_011174705.1_ASM1117470v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:27,970] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:27,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:27,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0cd938e-4b0e-4941-a831-ce60d87bd921/dqc_reference/checkm_data
[2024-01-25 20:02:27,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:28,010] [INFO] Task started: CheckM
[2024-01-25 20:02:28,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011174705.1_ASM1117470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011174705.1_ASM1117470v1_genomic.fna/checkm_input GCF_011174705.1_ASM1117470v1_genomic.fna/checkm_result
[2024-01-25 20:03:05,812] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:05,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 4.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:05,833] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:05,834] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:05,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011174705.1_ASM1117470v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:05,834] [INFO] Task started: Blastn
[2024-01-25 20:03:05,834] [INFO] Running command: blastn -query GCF_011174705.1_ASM1117470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0cd938e-4b0e-4941-a831-ce60d87bd921/dqc_reference/reference_markers_gtdb.fasta -out GCF_011174705.1_ASM1117470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:07,631] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:07,634] [INFO] Selected 11 target genomes.
[2024-01-25 20:03:07,634] [INFO] Target genome list was writen to GCF_011174705.1_ASM1117470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:07,656] [INFO] Task started: fastANI
[2024-01-25 20:03:07,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dd4095a-cdbf-4966-9c66-50eda753d06c/GCF_011174705.1_ASM1117470v1_genomic.fna.gz --refList GCF_011174705.1_ASM1117470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011174705.1_ASM1117470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:17,079] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:17,087] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:17,087] [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_011174705.1	s__Arachnia coleopterorum	100.0	1195	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001997345.1	s__Arachnia aquimaris	82.6676	749	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998865.1	s__Arachnia flavescens	82.177	681	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489575.1	s__Arachnia defluvii	81.7229	667	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141915.1	s__Arachnia bendigoensis	81.3108	608	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012837465.1	s__Arachnia sp012837465	80.4594	400	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714275.1	s__Arachnia sp016714275	80.4064	537	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103275.1	s__Arachnia oleiagri	79.1839	420	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858265.1	s__Nocardioides sp009858265	76.9757	244	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408335.1	s__Nocardioides panzhihuensis	76.8351	220	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000960475.2	s__Nocardioides luteus_A	76.7328	247	1195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:17,088] [INFO] GTDB search result was written to GCF_011174705.1_ASM1117470v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:17,089] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:17,092] [INFO] DFAST_QC result json was written to GCF_011174705.1_ASM1117470v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:17,092] [INFO] DFAST_QC completed!
[2024-01-25 20:03:17,092] [INFO] Total running time: 0h1m11s