[2024-01-24 11:51:37,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:37,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:37,237] [INFO] DQC Reference Directory: /var/lib/cwl/stgf388ae0c-655e-4008-9186-a07014eca387/dqc_reference
[2024-01-24 11:51:38,498] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,499] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,499] [INFO] Running command: gunzip -c /var/lib/cwl/stge5910c75-7c50-4fb7-86dc-fc4d936744a1/GCF_013004105.1_ASM1300410v1_genomic.fna.gz | prodigal -d GCF_013004105.1_ASM1300410v1_genomic.fna/cds.fna -a GCF_013004105.1_ASM1300410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:55,813] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:55,814] [INFO] Task started: HMMsearch
[2024-01-24 11:51:55,814] [INFO] Running command: hmmsearch --tblout GCF_013004105.1_ASM1300410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf388ae0c-655e-4008-9186-a07014eca387/dqc_reference/reference_markers.hmm GCF_013004105.1_ASM1300410v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:56,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:56,109] [INFO] Found 6/6 markers.
[2024-01-24 11:51:56,160] [INFO] Query marker FASTA was written to GCF_013004105.1_ASM1300410v1_genomic.fna/markers.fasta
[2024-01-24 11:51:56,160] [INFO] Task started: Blastn
[2024-01-24 11:51:56,161] [INFO] Running command: blastn -query GCF_013004105.1_ASM1300410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf388ae0c-655e-4008-9186-a07014eca387/dqc_reference/reference_markers.fasta -out GCF_013004105.1_ASM1300410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:56,817] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:56,822] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:56,823] [INFO] Target genome list was writen to GCF_013004105.1_ASM1300410v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:56,832] [INFO] Task started: fastANI
[2024-01-24 11:51:56,832] [INFO] Running command: fastANI --query /var/lib/cwl/stge5910c75-7c50-4fb7-86dc-fc4d936744a1/GCF_013004105.1_ASM1300410v1_genomic.fna.gz --refList GCF_013004105.1_ASM1300410v1_genomic.fna/target_genomes.txt --output GCF_013004105.1_ASM1300410v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:09,690] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:09,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf388ae0c-655e-4008-9186-a07014eca387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:09,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf388ae0c-655e-4008-9186-a07014eca387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:09,699] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:09,699] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:09,699] [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
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	100.0	1726	1726	95	conclusive
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	78.6673	482	1726	95	below_threshold
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	78.4595	516	1726	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	76.3221	329	1726	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.8973	100	1726	95	below_threshold
Rhodococcus jostii	strain=DSM 44719	GCA_900105375.1	132919	132919	type	True	74.8047	74	1726	95	below_threshold
Rhodococcus jostii	strain=NBRC 16295	GCA_001894825.1	132919	132919	type	True	74.7805	71	1726	95	below_threshold
Quadrisphaera granulorum	strain=DSM 44889	GCA_900218025.1	317664	317664	type	True	74.7316	55	1726	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:09,702] [INFO] DFAST Taxonomy check result was written to GCF_013004105.1_ASM1300410v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:09,702] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:09,703] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:09,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf388ae0c-655e-4008-9186-a07014eca387/dqc_reference/checkm_data
[2024-01-24 11:52:09,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:09,756] [INFO] Task started: CheckM
[2024-01-24 11:52:09,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013004105.1_ASM1300410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013004105.1_ASM1300410v1_genomic.fna/checkm_input GCF_013004105.1_ASM1300410v1_genomic.fna/checkm_result
[2024-01-24 11:53:06,888] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:06,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:06,911] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:06,911] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:06,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013004105.1_ASM1300410v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:06,912] [INFO] Task started: Blastn
[2024-01-24 11:53:06,912] [INFO] Running command: blastn -query GCF_013004105.1_ASM1300410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf388ae0c-655e-4008-9186-a07014eca387/dqc_reference/reference_markers_gtdb.fasta -out GCF_013004105.1_ASM1300410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:07,925] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:07,929] [INFO] Selected 10 target genomes.
[2024-01-24 11:53:07,929] [INFO] Target genome list was writen to GCF_013004105.1_ASM1300410v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:07,939] [INFO] Task started: fastANI
[2024-01-24 11:53:07,939] [INFO] Running command: fastANI --query /var/lib/cwl/stge5910c75-7c50-4fb7-86dc-fc4d936744a1/GCF_013004105.1_ASM1300410v1_genomic.fna.gz --refList GCF_013004105.1_ASM1300410v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013004105.1_ASM1300410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:16,893] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:16,907] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:16,907] [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_013004105.1	s__Gemmatimonas sp013004105	100.0	1726	1726	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002737115.1	s__Gemmatimonas sp002737115	84.7803	539	1726	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	97.83	97.76	0.72	0.69	3	-
GCA_903894655.1	s__Gemmatimonas sp903894655	84.7331	670	1726	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903900795.1	s__Gemmatimonas sp903900795	84.6696	765	1726	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010305.1	s__Gemmatimonas aurantiaca	78.663	483	1726	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002483225.1	s__Gemmatimonas sp002483225	78.5971	503	1726	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	97.70	97.70	0.96	0.96	2	-
GCA_016741895.1	s__Gemmatimonas sp016741895	78.591	453	1726	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695095.2	s__Gemmatimonas phototrophica	78.4364	515	1726	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720905.1	s__Gemmatimonas sp016720905	77.7787	421	1726	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794735.1	s__SCN-70-22 sp016794735	76.4142	110	1726	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:16,909] [INFO] GTDB search result was written to GCF_013004105.1_ASM1300410v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:16,909] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:16,912] [INFO] DFAST_QC result json was written to GCF_013004105.1_ASM1300410v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:16,912] [INFO] DFAST_QC completed!
[2024-01-24 11:53:16,912] [INFO] Total running time: 0h1m40s