[2024-01-24 15:06:36,898] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:37,011] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:37,011] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bda2568-98e3-43de-a038-b23f2a9e2f21/dqc_reference
[2024-01-24 15:06:38,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,421] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,421] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5838f2f-1479-448a-ae94-0db3a610abbd/GCF_900187045.1_51485_B01_genomic.fna.gz | prodigal -d GCF_900187045.1_51485_B01_genomic.fna/cds.fna -a GCF_900187045.1_51485_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:47,611] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:47,612] [INFO] Task started: HMMsearch
[2024-01-24 15:06:47,612] [INFO] Running command: hmmsearch --tblout GCF_900187045.1_51485_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bda2568-98e3-43de-a038-b23f2a9e2f21/dqc_reference/reference_markers.hmm GCF_900187045.1_51485_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:47,895] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:47,903] [INFO] Found 6/6 markers.
[2024-01-24 15:06:47,932] [INFO] Query marker FASTA was written to GCF_900187045.1_51485_B01_genomic.fna/markers.fasta
[2024-01-24 15:06:47,932] [INFO] Task started: Blastn
[2024-01-24 15:06:47,932] [INFO] Running command: blastn -query GCF_900187045.1_51485_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bda2568-98e3-43de-a038-b23f2a9e2f21/dqc_reference/reference_markers.fasta -out GCF_900187045.1_51485_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:48,893] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:48,896] [INFO] Selected 21 target genomes.
[2024-01-24 15:06:48,897] [INFO] Target genome list was writen to GCF_900187045.1_51485_B01_genomic.fna/target_genomes.txt
[2024-01-24 15:06:48,904] [INFO] Task started: fastANI
[2024-01-24 15:06:48,905] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5838f2f-1479-448a-ae94-0db3a610abbd/GCF_900187045.1_51485_B01_genomic.fna.gz --refList GCF_900187045.1_51485_B01_genomic.fna/target_genomes.txt --output GCF_900187045.1_51485_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:02,461] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:02,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bda2568-98e3-43de-a038-b23f2a9e2f21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:02,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bda2568-98e3-43de-a038-b23f2a9e2f21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:02,471] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:07:02,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:02,472] [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
Dermatophilus congolensis	strain=NCTC13039	GCA_900187045.1	1863	1863	type	True	100.0	873	875	95	conclusive
Dermatophilus congolensis	strain=DSM 44180	GCA_000429885.1	1863	1863	type	True	99.9931	865	875	95	conclusive
Gephyromycinifex aptenodytis	strain=NJES-13	GCA_012277275.1	2716227	2716227	type	True	77.4842	104	875	95	below_threshold
Janibacter cremeus	strain=DSM 26154	GCA_013409205.1	1285192	1285192	type	True	77.2902	55	875	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	77.2655	53	875	95	below_threshold
Kineosphaera limosa	strain=DSM 14548	GCA_013409325.1	111564	111564	type	True	77.1268	110	875	95	below_threshold
Kineosphaera limosa	strain=NBRC 100340	GCA_000298215.1	111564	111564	type	True	76.7942	102	875	95	below_threshold
Flexivirga caeni	strain=BO-16	GCA_003724155.1	2294115	2294115	type	True	76.7473	57	875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:02,473] [INFO] DFAST Taxonomy check result was written to GCF_900187045.1_51485_B01_genomic.fna/tc_result.tsv
[2024-01-24 15:07:02,474] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:02,474] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:02,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bda2568-98e3-43de-a038-b23f2a9e2f21/dqc_reference/checkm_data
[2024-01-24 15:07:02,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:02,503] [INFO] Task started: CheckM
[2024-01-24 15:07:02,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187045.1_51485_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187045.1_51485_B01_genomic.fna/checkm_input GCF_900187045.1_51485_B01_genomic.fna/checkm_result
[2024-01-24 15:07:32,796] [INFO] Task succeeded: CheckM
[2024-01-24 15:07:32,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:07:32,819] [INFO] ===== Completeness check finished =====
[2024-01-24 15:07:32,819] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:07:32,820] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187045.1_51485_B01_genomic.fna/markers.fasta)
[2024-01-24 15:07:32,820] [INFO] Task started: Blastn
[2024-01-24 15:07:32,820] [INFO] Running command: blastn -query GCF_900187045.1_51485_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bda2568-98e3-43de-a038-b23f2a9e2f21/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187045.1_51485_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:34,004] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:34,007] [INFO] Selected 21 target genomes.
[2024-01-24 15:07:34,008] [INFO] Target genome list was writen to GCF_900187045.1_51485_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:07:34,052] [INFO] Task started: fastANI
[2024-01-24 15:07:34,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5838f2f-1479-448a-ae94-0db3a610abbd/GCF_900187045.1_51485_B01_genomic.fna.gz --refList GCF_900187045.1_51485_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900187045.1_51485_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:07:47,021] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:47,036] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:07:47,037] [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_900187045.1	s__Dermatophilus congolensis	100.0	873	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Dermatophilus	95.0	99.70	99.67	0.98	0.97	33	conclusive
GCF_900447215.1	s__Dermatophilus congolensis_A	94.9144	833	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Dermatophilus	95.0	98.32	98.28	0.97	0.96	10	-
GCF_004295485.1	s__Janibacter limosus_A	77.7285	56	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715095.1	s__Yimella lutea	77.5703	62	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	98.40	98.40	0.90	0.90	2	-
GCF_012277275.1	s__Mobilicoccus sp012277275	77.3587	104	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Mobilicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386865.1	s__Yimella indica	77.1363	76	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409205.1	s__Janibacter cremeus	77.033	54	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003724155.1	s__Flexivirga caeni	76.7473	57	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646815.1	s__Terrabacter tumescens	76.41	72	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:07:47,038] [INFO] GTDB search result was written to GCF_900187045.1_51485_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 15:07:47,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:07:47,042] [INFO] DFAST_QC result json was written to GCF_900187045.1_51485_B01_genomic.fna/dqc_result.json
[2024-01-24 15:07:47,042] [INFO] DFAST_QC completed!
[2024-01-24 15:07:47,042] [INFO] Total running time: 0h1m10s