[2024-01-24 11:44:23,375] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,377] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,377] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4402365-7c8d-4666-b119-3180144e7c62/dqc_reference
[2024-01-24 11:44:26,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,343] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,343] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b149d80-52c1-4637-b5af-3c047939aa94/GCF_018390535.1_ASM1839053v1_genomic.fna.gz | prodigal -d GCF_018390535.1_ASM1839053v1_genomic.fna/cds.fna -a GCF_018390535.1_ASM1839053v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:48,277] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:48,278] [INFO] Task started: HMMsearch
[2024-01-24 11:44:48,278] [INFO] Running command: hmmsearch --tblout GCF_018390535.1_ASM1839053v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4402365-7c8d-4666-b119-3180144e7c62/dqc_reference/reference_markers.hmm GCF_018390535.1_ASM1839053v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:48,564] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:48,566] [INFO] Found 6/6 markers.
[2024-01-24 11:44:48,604] [INFO] Query marker FASTA was written to GCF_018390535.1_ASM1839053v1_genomic.fna/markers.fasta
[2024-01-24 11:44:48,604] [INFO] Task started: Blastn
[2024-01-24 11:44:48,605] [INFO] Running command: blastn -query GCF_018390535.1_ASM1839053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4402365-7c8d-4666-b119-3180144e7c62/dqc_reference/reference_markers.fasta -out GCF_018390535.1_ASM1839053v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:49,227] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:49,234] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:49,234] [INFO] Target genome list was writen to GCF_018390535.1_ASM1839053v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:49,244] [INFO] Task started: fastANI
[2024-01-24 11:44:49,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b149d80-52c1-4637-b5af-3c047939aa94/GCF_018390535.1_ASM1839053v1_genomic.fna.gz --refList GCF_018390535.1_ASM1839053v1_genomic.fna/target_genomes.txt --output GCF_018390535.1_ASM1839053v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:00,295] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:00,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4402365-7c8d-4666-b119-3180144e7c62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:00,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4402365-7c8d-4666-b119-3180144e7c62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:00,313] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:00,313] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:00,314] [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
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	100.0	1347	1347	95	conclusive
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	87.6507	803	1347	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	87.6232	813	1347	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	85.2883	793	1347	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	85.2049	807	1347	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	85.0763	860	1347	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	85.0336	863	1347	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	85.0132	871	1347	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	80.9003	547	1347	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	80.449	512	1347	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	80.3626	554	1347	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	80.0645	484	1347	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	78.3667	109	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:00,315] [INFO] DFAST Taxonomy check result was written to GCF_018390535.1_ASM1839053v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:00,316] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:00,316] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:00,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4402365-7c8d-4666-b119-3180144e7c62/dqc_reference/checkm_data
[2024-01-24 11:45:00,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:00,360] [INFO] Task started: CheckM
[2024-01-24 11:45:00,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018390535.1_ASM1839053v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018390535.1_ASM1839053v1_genomic.fna/checkm_input GCF_018390535.1_ASM1839053v1_genomic.fna/checkm_result
[2024-01-24 11:46:00,900] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:00,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:00,924] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:00,924] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:00,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018390535.1_ASM1839053v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:00,925] [INFO] Task started: Blastn
[2024-01-24 11:46:00,926] [INFO] Running command: blastn -query GCF_018390535.1_ASM1839053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4402365-7c8d-4666-b119-3180144e7c62/dqc_reference/reference_markers_gtdb.fasta -out GCF_018390535.1_ASM1839053v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:01,766] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:01,770] [INFO] Selected 12 target genomes.
[2024-01-24 11:46:01,770] [INFO] Target genome list was writen to GCF_018390535.1_ASM1839053v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:01,780] [INFO] Task started: fastANI
[2024-01-24 11:46:01,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b149d80-52c1-4637-b5af-3c047939aa94/GCF_018390535.1_ASM1839053v1_genomic.fna.gz --refList GCF_018390535.1_ASM1839053v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018390535.1_ASM1839053v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:13,470] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:13,483] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:13,483] [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_003438615.1	s__Bacteroides sp003545565	99.6724	1187	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	conclusive
GCF_900129655.1	s__Bacteroides clarus	87.6232	813	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_000154525.1	s__Bacteroides stercoris	85.2883	793	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_000155815.1	s__Bacteroides eggerthii	85.0566	862	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCF_000374365.1	s__Bacteroides gallinarum	83.7755	856	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_910578895.1	s__Bacteroides sp910578895	83.0687	652	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215345.1	s__Bacteroides sp905215345	80.8293	656	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142015.1	s__Bacteroides stercorirosoris	80.1271	477	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.49	98.12	0.84	0.77	7	-
GCA_905207245.1	s__Bacteroides sp905207245	79.2015	437	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555635.1	s__Bacteroides sp900555635	79.0886	422	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.02	98.02	0.75	0.75	2	-
GCF_000969835.1	s__Parabacteroides goldsteinii	78.3827	108	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
GCA_900557355.1	s__Bacteroides sp900557355	77.8648	225	1347	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.57	98.57	0.54	0.54	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:13,485] [INFO] GTDB search result was written to GCF_018390535.1_ASM1839053v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:13,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:13,489] [INFO] DFAST_QC result json was written to GCF_018390535.1_ASM1839053v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:13,489] [INFO] DFAST_QC completed!
[2024-01-24 11:46:13,489] [INFO] Total running time: 0h1m50s