[2024-01-24 12:07:06,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,756] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2a8f2e5-6151-4fe0-be95-89712a2cc6b2/dqc_reference
[2024-01-24 12:07:07,984] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,984] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,985] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa8453ab-4fc2-40f5-93e5-9dc8a51cb644/GCF_021044565.1_ASM2104456v1_genomic.fna.gz | prodigal -d GCF_021044565.1_ASM2104456v1_genomic.fna/cds.fna -a GCF_021044565.1_ASM2104456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:20,790] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:20,790] [INFO] Task started: HMMsearch
[2024-01-24 12:07:20,791] [INFO] Running command: hmmsearch --tblout GCF_021044565.1_ASM2104456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2a8f2e5-6151-4fe0-be95-89712a2cc6b2/dqc_reference/reference_markers.hmm GCF_021044565.1_ASM2104456v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:21,123] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:21,125] [INFO] Found 6/6 markers.
[2024-01-24 12:07:21,164] [INFO] Query marker FASTA was written to GCF_021044565.1_ASM2104456v1_genomic.fna/markers.fasta
[2024-01-24 12:07:21,165] [INFO] Task started: Blastn
[2024-01-24 12:07:21,165] [INFO] Running command: blastn -query GCF_021044565.1_ASM2104456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2a8f2e5-6151-4fe0-be95-89712a2cc6b2/dqc_reference/reference_markers.fasta -out GCF_021044565.1_ASM2104456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:22,134] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:22,138] [INFO] Selected 11 target genomes.
[2024-01-24 12:07:22,138] [INFO] Target genome list was writen to GCF_021044565.1_ASM2104456v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:22,143] [INFO] Task started: fastANI
[2024-01-24 12:07:22,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa8453ab-4fc2-40f5-93e5-9dc8a51cb644/GCF_021044565.1_ASM2104456v1_genomic.fna.gz --refList GCF_021044565.1_ASM2104456v1_genomic.fna/target_genomes.txt --output GCF_021044565.1_ASM2104456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:31,128] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:31,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2a8f2e5-6151-4fe0-be95-89712a2cc6b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:31,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2a8f2e5-6151-4fe0-be95-89712a2cc6b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:31,144] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:31,144] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:31,144] [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
Subtercola lobariae	strain=9583b	GCA_016881145.1	1588641	1588641	type	True	82.7077	811	1439	95	below_threshold
Subtercola lobariae	strain=CGMCC 1.12976	GCA_014640255.1	1588641	1588641	type	True	82.6867	806	1439	95	below_threshold
Subtercola vilae	strain=DB165	GCA_004923255.1	2056433	2056433	type	True	81.3889	626	1439	95	below_threshold
Subtercola boreus	strain=K300	GCA_003399685.1	120213	120213	suspected-type	True	80.6703	640	1439	95	below_threshold
Subtercola frigoramans	strain=DSM 13057	GCA_016907385.1	120298	120298	type	True	80.67	557	1439	95	below_threshold
Subtercola boreus	strain=DSM 13056	GCA_006716115.1	120213	120213	suspected-type	True	80.6332	639	1439	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	79.011	452	1439	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.3044	365	1439	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.0913	338	1439	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.0745	322	1439	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	77.9659	343	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:31,147] [INFO] DFAST Taxonomy check result was written to GCF_021044565.1_ASM2104456v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:31,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:31,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:31,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2a8f2e5-6151-4fe0-be95-89712a2cc6b2/dqc_reference/checkm_data
[2024-01-24 12:07:31,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:31,193] [INFO] Task started: CheckM
[2024-01-24 12:07:31,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021044565.1_ASM2104456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021044565.1_ASM2104456v1_genomic.fna/checkm_input GCF_021044565.1_ASM2104456v1_genomic.fna/checkm_result
[2024-01-24 12:08:12,091] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:12,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:12,115] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:12,115] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:12,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021044565.1_ASM2104456v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:12,116] [INFO] Task started: Blastn
[2024-01-24 12:08:12,116] [INFO] Running command: blastn -query GCF_021044565.1_ASM2104456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2a8f2e5-6151-4fe0-be95-89712a2cc6b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_021044565.1_ASM2104456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:13,603] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:13,607] [INFO] Selected 10 target genomes.
[2024-01-24 12:08:13,607] [INFO] Target genome list was writen to GCF_021044565.1_ASM2104456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:13,616] [INFO] Task started: fastANI
[2024-01-24 12:08:13,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa8453ab-4fc2-40f5-93e5-9dc8a51cb644/GCF_021044565.1_ASM2104456v1_genomic.fna.gz --refList GCF_021044565.1_ASM2104456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021044565.1_ASM2104456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:21,313] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:21,325] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:08:21,326] [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_014640255.1	s__Subtercola lobariae	82.702	804	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004923255.1	s__Subtercola vilae	81.3739	627	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002931235.1	s__Subtercola sp002931235	81.0916	579	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399645.1	s__Subtercola boreus_A	80.8962	572	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	100.00	100.00	0.99	0.99	3	-
GCF_016907385.1	s__Subtercola frigoramans	80.7157	559	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018889995.1	s__Subtercola sp018889995	80.6732	561	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716115.1	s__Subtercola boreus	80.6367	639	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003399625.1	s__Subtercola boreus_C	80.4704	573	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399635.1	s__Subtercola boreus_B	80.3642	581	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297105.1	s__Herbiconiux sp004297105	78.9189	438	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:21,332] [INFO] GTDB search result was written to GCF_021044565.1_ASM2104456v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:21,332] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:21,337] [INFO] DFAST_QC result json was written to GCF_021044565.1_ASM2104456v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:21,337] [INFO] DFAST_QC completed!
[2024-01-24 12:08:21,337] [INFO] Total running time: 0h1m15s