[2024-01-25 18:51:05,755] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:05,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:05,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c96b279-d010-4bca-9670-982a59b4cbd0/dqc_reference
[2024-01-25 18:51:06,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:06,918] [INFO] Task started: Prodigal
[2024-01-25 18:51:06,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f9f29f8-e9df-41de-8e6e-cb79619deb67/GCF_014193425.1_ASM1419342v1_genomic.fna.gz | prodigal -d GCF_014193425.1_ASM1419342v1_genomic.fna/cds.fna -a GCF_014193425.1_ASM1419342v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:17,177] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:17,177] [INFO] Task started: HMMsearch
[2024-01-25 18:51:17,177] [INFO] Running command: hmmsearch --tblout GCF_014193425.1_ASM1419342v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c96b279-d010-4bca-9670-982a59b4cbd0/dqc_reference/reference_markers.hmm GCF_014193425.1_ASM1419342v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:17,389] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:17,390] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7f9f29f8-e9df-41de-8e6e-cb79619deb67/GCF_014193425.1_ASM1419342v1_genomic.fna.gz]
[2024-01-25 18:51:17,427] [INFO] Query marker FASTA was written to GCF_014193425.1_ASM1419342v1_genomic.fna/markers.fasta
[2024-01-25 18:51:17,427] [INFO] Task started: Blastn
[2024-01-25 18:51:17,427] [INFO] Running command: blastn -query GCF_014193425.1_ASM1419342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c96b279-d010-4bca-9670-982a59b4cbd0/dqc_reference/reference_markers.fasta -out GCF_014193425.1_ASM1419342v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:18,379] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:18,384] [INFO] Selected 13 target genomes.
[2024-01-25 18:51:18,384] [INFO] Target genome list was writen to GCF_014193425.1_ASM1419342v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:18,396] [INFO] Task started: fastANI
[2024-01-25 18:51:18,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9f29f8-e9df-41de-8e6e-cb79619deb67/GCF_014193425.1_ASM1419342v1_genomic.fna.gz --refList GCF_014193425.1_ASM1419342v1_genomic.fna/target_genomes.txt --output GCF_014193425.1_ASM1419342v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:31,813] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:31,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c96b279-d010-4bca-9670-982a59b4cbd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:31,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c96b279-d010-4bca-9670-982a59b4cbd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:31,822] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:51:31,822] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:31,823] [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
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	100.0	1444	1447	95	conclusive
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	84.6248	1015	1447	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	84.3369	1013	1447	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	79.0505	603	1447	95	below_threshold
Microlunatus phosphovorus	strain=NM-1	GCA_000270245.1	29405	29405	type	True	78.2286	422	1447	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	78.2049	433	1447	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	78.0616	506	1447	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.9994	526	1447	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	77.3975	395	1447	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.3524	462	1447	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	77.1883	306	1447	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	77.0222	408	1447	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	76.9951	404	1447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:31,824] [INFO] DFAST Taxonomy check result was written to GCF_014193425.1_ASM1419342v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:31,824] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:31,825] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:31,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c96b279-d010-4bca-9670-982a59b4cbd0/dqc_reference/checkm_data
[2024-01-25 18:51:31,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:31,865] [INFO] Task started: CheckM
[2024-01-25 18:51:31,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014193425.1_ASM1419342v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014193425.1_ASM1419342v1_genomic.fna/checkm_input GCF_014193425.1_ASM1419342v1_genomic.fna/checkm_result
[2024-01-25 18:52:26,187] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:26,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:26,208] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:26,208] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:26,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014193425.1_ASM1419342v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:26,209] [INFO] Task started: Blastn
[2024-01-25 18:52:26,209] [INFO] Running command: blastn -query GCF_014193425.1_ASM1419342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c96b279-d010-4bca-9670-982a59b4cbd0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014193425.1_ASM1419342v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:27,726] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:27,729] [INFO] Selected 6 target genomes.
[2024-01-25 18:52:27,730] [INFO] Target genome list was writen to GCF_014193425.1_ASM1419342v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:27,735] [INFO] Task started: fastANI
[2024-01-25 18:52:27,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9f29f8-e9df-41de-8e6e-cb79619deb67/GCF_014193425.1_ASM1419342v1_genomic.fna.gz --refList GCF_014193425.1_ASM1419342v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014193425.1_ASM1419342v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:34,931] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:34,939] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:34,939] [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_014193425.1	s__Friedmanniella antarctica	100.0	1443	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016907175.1	s__Friedmanniella spumicola	86.8096	1117	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105785.1	s__Friedmanniella sagamiharensis	84.5951	1016	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110855.1	s__Friedmanniella flava	84.3469	1012	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876495.1	s__Friedmanniella capsulata	80.3112	741	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105065.1	s__Friedmanniella luteola	79.9674	723	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:34,942] [INFO] GTDB search result was written to GCF_014193425.1_ASM1419342v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:34,943] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:34,946] [INFO] DFAST_QC result json was written to GCF_014193425.1_ASM1419342v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:34,946] [INFO] DFAST_QC completed!
[2024-01-25 18:52:34,946] [INFO] Total running time: 0h1m29s