[2024-01-25 20:13:35,868] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:35,879] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:35,879] [INFO] DQC Reference Directory: /var/lib/cwl/stgcef16d95-50d8-423d-a3e0-e2715c9f4260/dqc_reference
[2024-01-25 20:13:37,042] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:37,042] [INFO] Task started: Prodigal
[2024-01-25 20:13:37,042] [INFO] Running command: gunzip -c /var/lib/cwl/stgff34b0e4-6bbd-44eb-83b8-f44a2ea5714b/GCF_003327535.1_ASM332753v1_genomic.fna.gz | prodigal -d GCF_003327535.1_ASM332753v1_genomic.fna/cds.fna -a GCF_003327535.1_ASM332753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:46,880] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:46,880] [INFO] Task started: HMMsearch
[2024-01-25 20:13:46,880] [INFO] Running command: hmmsearch --tblout GCF_003327535.1_ASM332753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcef16d95-50d8-423d-a3e0-e2715c9f4260/dqc_reference/reference_markers.hmm GCF_003327535.1_ASM332753v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:47,115] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:47,116] [INFO] Found 6/6 markers.
[2024-01-25 20:13:47,155] [INFO] Query marker FASTA was written to GCF_003327535.1_ASM332753v1_genomic.fna/markers.fasta
[2024-01-25 20:13:47,155] [INFO] Task started: Blastn
[2024-01-25 20:13:47,155] [INFO] Running command: blastn -query GCF_003327535.1_ASM332753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcef16d95-50d8-423d-a3e0-e2715c9f4260/dqc_reference/reference_markers.fasta -out GCF_003327535.1_ASM332753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:48,396] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:48,401] [INFO] Selected 12 target genomes.
[2024-01-25 20:13:48,402] [INFO] Target genome list was writen to GCF_003327535.1_ASM332753v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:48,419] [INFO] Task started: fastANI
[2024-01-25 20:13:48,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgff34b0e4-6bbd-44eb-83b8-f44a2ea5714b/GCF_003327535.1_ASM332753v1_genomic.fna.gz --refList GCF_003327535.1_ASM332753v1_genomic.fna/target_genomes.txt --output GCF_003327535.1_ASM332753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:00,219] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:00,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcef16d95-50d8-423d-a3e0-e2715c9f4260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:00,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcef16d95-50d8-423d-a3e0-e2715c9f4260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:00,228] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:14:00,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:00,228] [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 brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	100.0	1337	1337	95	conclusive
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	94.9595	932	1337	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	83.619	871	1337	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	83.0343	934	1337	95	below_threshold
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	78.6847	485	1337	95	below_threshold
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	78.2653	445	1337	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	78.0721	515	1337	95	below_threshold
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	77.8969	549	1337	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	77.4054	391	1337	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	77.2893	427	1337	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	77.1881	431	1337	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.1614	472	1337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:00,230] [INFO] DFAST Taxonomy check result was written to GCF_003327535.1_ASM332753v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:00,230] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:00,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:00,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcef16d95-50d8-423d-a3e0-e2715c9f4260/dqc_reference/checkm_data
[2024-01-25 20:14:00,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:00,281] [INFO] Task started: CheckM
[2024-01-25 20:14:00,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003327535.1_ASM332753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003327535.1_ASM332753v1_genomic.fna/checkm_input GCF_003327535.1_ASM332753v1_genomic.fna/checkm_result
[2024-01-25 20:15:00,748] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:00,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:00,767] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:00,767] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:00,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003327535.1_ASM332753v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:00,768] [INFO] Task started: Blastn
[2024-01-25 20:15:00,768] [INFO] Running command: blastn -query GCF_003327535.1_ASM332753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcef16d95-50d8-423d-a3e0-e2715c9f4260/dqc_reference/reference_markers_gtdb.fasta -out GCF_003327535.1_ASM332753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:02,666] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:02,670] [INFO] Selected 12 target genomes.
[2024-01-25 20:15:02,670] [INFO] Target genome list was writen to GCF_003327535.1_ASM332753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:02,699] [INFO] Task started: fastANI
[2024-01-25 20:15:02,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgff34b0e4-6bbd-44eb-83b8-f44a2ea5714b/GCF_003327535.1_ASM332753v1_genomic.fna.gz --refList GCF_003327535.1_ASM332753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003327535.1_ASM332753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:13,785] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:13,793] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:15:13,794] [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	94.9595	932	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_009742705.1	s__Auraticoccus cholistanensis	83.6316	870	1337	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	83.0221	936	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137855.1	s__Friedmanniella_A endophytica	79.1179	588	1337	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_017876495.1	s__Friedmanniella capsulata	79.0618	651	1337	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	78.7978	618	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362375.1	s__Enemella evansiae	78.6217	480	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.12	97.98	0.94	0.92	8	-
GCF_013408315.1	s__Microlunatus_A terrae	78.3992	532	1337	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_900110855.1	s__Friedmanniella flava	78.2863	590	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002250625.1	s__Enemella sp002250625	78.2533	468	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.13	98.13	0.89	0.89	2	-
GCF_013408305.1	s__Naumannella cuiyingiana	78.2439	448	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Naumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055925.1	s__Micropruina sp018055925	77.612	357	1337	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 20:15:13,796] [INFO] GTDB search result was written to GCF_003327535.1_ASM332753v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:13,796] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:13,800] [INFO] DFAST_QC result json was written to GCF_003327535.1_ASM332753v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:13,801] [INFO] DFAST_QC completed!
[2024-01-25 20:15:13,801] [INFO] Total running time: 0h1m38s