[2024-01-25 19:00:50,744] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:50,746] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:50,746] [INFO] DQC Reference Directory: /var/lib/cwl/stg3266cda1-8098-439a-9cb1-9bfadcadf76b/dqc_reference
[2024-01-25 19:00:51,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:51,864] [INFO] Task started: Prodigal
[2024-01-25 19:00:51,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a2f5612-9a00-4502-99f2-b7fcc5cd4f61/GCF_003344635.1_ASM334463v1_genomic.fna.gz | prodigal -d GCF_003344635.1_ASM334463v1_genomic.fna/cds.fna -a GCF_003344635.1_ASM334463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:00,343] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:00,344] [INFO] Task started: HMMsearch
[2024-01-25 19:01:00,344] [INFO] Running command: hmmsearch --tblout GCF_003344635.1_ASM334463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3266cda1-8098-439a-9cb1-9bfadcadf76b/dqc_reference/reference_markers.hmm GCF_003344635.1_ASM334463v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:00,564] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:00,565] [INFO] Found 6/6 markers.
[2024-01-25 19:01:00,602] [INFO] Query marker FASTA was written to GCF_003344635.1_ASM334463v1_genomic.fna/markers.fasta
[2024-01-25 19:01:00,602] [INFO] Task started: Blastn
[2024-01-25 19:01:00,602] [INFO] Running command: blastn -query GCF_003344635.1_ASM334463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3266cda1-8098-439a-9cb1-9bfadcadf76b/dqc_reference/reference_markers.fasta -out GCF_003344635.1_ASM334463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:01,817] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:01,820] [INFO] Selected 12 target genomes.
[2024-01-25 19:01:01,820] [INFO] Target genome list was writen to GCF_003344635.1_ASM334463v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:01,832] [INFO] Task started: fastANI
[2024-01-25 19:01:01,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a2f5612-9a00-4502-99f2-b7fcc5cd4f61/GCF_003344635.1_ASM334463v1_genomic.fna.gz --refList GCF_003344635.1_ASM334463v1_genomic.fna/target_genomes.txt --output GCF_003344635.1_ASM334463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:14,162] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:14,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3266cda1-8098-439a-9cb1-9bfadcadf76b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:14,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3266cda1-8098-439a-9cb1-9bfadcadf76b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:14,171] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:01:14,171] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:01:14,171] [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
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	100.0	1097	1107	95	inconclusive
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	95.1475	966	1107	95	inconclusive
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	83.889	723	1107	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	83.0275	762	1107	95	below_threshold
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	78.6757	411	1107	95	below_threshold
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	78.3537	380	1107	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	78.1528	419	1107	95	below_threshold
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	77.9247	474	1107	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	77.6568	321	1107	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	77.3656	350	1107	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	77.3268	351	1107	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	77.2293	378	1107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:14,172] [INFO] DFAST Taxonomy check result was written to GCF_003344635.1_ASM334463v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:14,173] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:14,173] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:14,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3266cda1-8098-439a-9cb1-9bfadcadf76b/dqc_reference/checkm_data
[2024-01-25 19:01:14,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:14,213] [INFO] Task started: CheckM
[2024-01-25 19:01:14,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003344635.1_ASM334463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003344635.1_ASM334463v1_genomic.fna/checkm_input GCF_003344635.1_ASM334463v1_genomic.fna/checkm_result
[2024-01-25 19:02:00,686] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:00,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:00,747] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:00,747] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:00,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003344635.1_ASM334463v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:00,748] [INFO] Task started: Blastn
[2024-01-25 19:02:00,748] [INFO] Running command: blastn -query GCF_003344635.1_ASM334463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3266cda1-8098-439a-9cb1-9bfadcadf76b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003344635.1_ASM334463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:02,785] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:02,788] [INFO] Selected 11 target genomes.
[2024-01-25 19:02:02,788] [INFO] Target genome list was writen to GCF_003344635.1_ASM334463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:02,808] [INFO] Task started: fastANI
[2024-01-25 19:02:02,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a2f5612-9a00-4502-99f2-b7fcc5cd4f61/GCF_003344635.1_ASM334463v1_genomic.fna.gz --refList GCF_003344635.1_ASM334463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003344635.1_ASM334463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:13,065] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:13,073] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:13,073] [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_003344635.1	s__Desertihabitans aurantiacus	100.0	1097	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	conclusive
GCF_009742705.1	s__Auraticoccus cholistanensis	83.8723	724	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101785.1	s__Auraticoccus monumenti	83.0487	760	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876495.1	s__Friedmanniella capsulata	79.3084	551	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137855.1	s__Friedmanniella_A endophytica	79.0138	527	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362375.1	s__Enemella evansiae	78.7212	400	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.12	97.98	0.94	0.92	8	-
GCF_900110855.1	s__Friedmanniella flava	78.432	482	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408305.1	s__Naumannella cuiyingiana	78.3425	381	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Naumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408315.1	s__Microlunatus_A terrae	78.2679	467	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299835.1	s__Microlunatus_B speluncae	77.9027	477	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055925.1	s__Micropruina sp018055925	77.657	290	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:13,074] [INFO] GTDB search result was written to GCF_003344635.1_ASM334463v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:13,075] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:13,078] [INFO] DFAST_QC result json was written to GCF_003344635.1_ASM334463v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:13,078] [INFO] DFAST_QC completed!
[2024-01-25 19:02:13,078] [INFO] Total running time: 0h1m22s