[2024-01-24 10:47:54,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,175] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,175] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c48eab5-6812-4589-93d9-19133a7e6f7a/dqc_reference
[2024-01-24 10:48:03,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,344] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg744e2522-f25e-44ec-8a57-4dc5e2be3f72/GCF_003261635.1_ASM326163v1_genomic.fna.gz | prodigal -d GCF_003261635.1_ASM326163v1_genomic.fna/cds.fna -a GCF_003261635.1_ASM326163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:25,762] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:25,762] [INFO] Task started: HMMsearch
[2024-01-24 10:48:25,763] [INFO] Running command: hmmsearch --tblout GCF_003261635.1_ASM326163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c48eab5-6812-4589-93d9-19133a7e6f7a/dqc_reference/reference_markers.hmm GCF_003261635.1_ASM326163v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:26,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:26,124] [INFO] Found 6/6 markers.
[2024-01-24 10:48:26,192] [INFO] Query marker FASTA was written to GCF_003261635.1_ASM326163v1_genomic.fna/markers.fasta
[2024-01-24 10:48:26,193] [INFO] Task started: Blastn
[2024-01-24 10:48:26,193] [INFO] Running command: blastn -query GCF_003261635.1_ASM326163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c48eab5-6812-4589-93d9-19133a7e6f7a/dqc_reference/reference_markers.fasta -out GCF_003261635.1_ASM326163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:27,361] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:27,364] [INFO] Selected 14 target genomes.
[2024-01-24 10:48:27,364] [INFO] Target genome list was writen to GCF_003261635.1_ASM326163v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:27,370] [INFO] Task started: fastANI
[2024-01-24 10:48:27,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg744e2522-f25e-44ec-8a57-4dc5e2be3f72/GCF_003261635.1_ASM326163v1_genomic.fna.gz --refList GCF_003261635.1_ASM326163v1_genomic.fna/target_genomes.txt --output GCF_003261635.1_ASM326163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:53,123] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:53,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c48eab5-6812-4589-93d9-19133a7e6f7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:53,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c48eab5-6812-4589-93d9-19133a7e6f7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:53,136] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:53,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:53,137] [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
Kribbella monticola	strain=NEAU-SW521	GCA_003261635.1	2185285	2185285	type	True	100.0	2642	2644	95	conclusive
Kribbella catacumbae	strain=DSM 19601	GCA_000372465.1	460086	460086	type	True	83.8011	1727	2644	95	below_threshold
Kribbella flavida	strain=DSM 17836	GCA_000024345.1	182640	182640	type	True	83.4393	1594	2644	95	below_threshold
Kribbella italica	strain=DSM 28967	GCA_014205135.1	1540520	1540520	type	True	83.3217	1668	2644	95	below_threshold
Kribbella amoyensis	strain=DSM 24683	GCA_007828865.1	996641	996641	type	True	82.9297	1588	2644	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	82.8255	1384	2644	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	82.6114	1579	2644	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	82.4216	1536	2644	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	82.3434	1483	2644	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	82.3383	1509	2644	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	82.2365	1543	2644	95	below_threshold
Kribbella solani	strain=DSM 17294	GCA_014205295.1	236067	236067	type	True	81.9135	1385	2644	95	below_threshold
Kribbella antibiotica	strain=JCM 13523	GCA_004349055.1	190195	190195	type	True	81.7871	1416	2644	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.7739	514	2644	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:53,138] [INFO] DFAST Taxonomy check result was written to GCF_003261635.1_ASM326163v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:53,139] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:53,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:53,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c48eab5-6812-4589-93d9-19133a7e6f7a/dqc_reference/checkm_data
[2024-01-24 10:48:53,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:53,211] [INFO] Task started: CheckM
[2024-01-24 10:48:53,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003261635.1_ASM326163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003261635.1_ASM326163v1_genomic.fna/checkm_input GCF_003261635.1_ASM326163v1_genomic.fna/checkm_result
[2024-01-24 10:50:02,578] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:02,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:02,614] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:02,615] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:02,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003261635.1_ASM326163v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:02,615] [INFO] Task started: Blastn
[2024-01-24 10:50:02,616] [INFO] Running command: blastn -query GCF_003261635.1_ASM326163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c48eab5-6812-4589-93d9-19133a7e6f7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003261635.1_ASM326163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:04,424] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:04,428] [INFO] Selected 11 target genomes.
[2024-01-24 10:50:04,429] [INFO] Target genome list was writen to GCF_003261635.1_ASM326163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:04,455] [INFO] Task started: fastANI
[2024-01-24 10:50:04,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg744e2522-f25e-44ec-8a57-4dc5e2be3f72/GCF_003261635.1_ASM326163v1_genomic.fna.gz --refList GCF_003261635.1_ASM326163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003261635.1_ASM326163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:26,681] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:26,696] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:26,696] [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_003261635.1	s__Kribbella monticola	100.0	2642	2644	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004365175.1	s__Kribbella sp004365175	93.3644	2382	2644	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217565.1	s__Kribbella qitaiheensis	87.4734	1995	2644	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345365.1	s__Kribbella sp004345365	83.9414	1700	2644	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	95.33	95.31	0.84	0.84	3	-
GCF_000372465.1	s__Kribbella catacumbae	83.7931	1730	2644	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984195.1	s__Kribbella sp001984195	83.484	1621	2644	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024345.1	s__Kribbella flavida	83.4516	1591	2644	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205135.1	s__Kribbella italica	83.3112	1670	2644	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361855.1	s__Kribbella sp004361855	83.0934	1625	2644	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828865.1	s__Kribbella amoyensis	82.9508	1584	2644	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366075.1	s__Kribbella sp004366075	82.339	1532	2644	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	97.22	95.50	0.92	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:26,697] [INFO] GTDB search result was written to GCF_003261635.1_ASM326163v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:26,698] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:26,704] [INFO] DFAST_QC result json was written to GCF_003261635.1_ASM326163v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:26,704] [INFO] DFAST_QC completed!
[2024-01-24 10:50:26,704] [INFO] Total running time: 0h2m33s