[2023-06-17 11:44:19,571] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:44:19,573] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:44:19,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg55dc8b27-6f9d-4f39-8edf-35043c905cf2/dqc_reference
[2023-06-17 11:44:20,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:44:20,892] [INFO] Task started: Prodigal
[2023-06-17 11:44:20,892] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9eac5fa-215e-477c-9227-a186d2dc429d/GCA_028693585.1_ASM2869358v1_genomic.fna.gz | prodigal -d GCA_028693585.1_ASM2869358v1_genomic.fna/cds.fna -a GCA_028693585.1_ASM2869358v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:44:34,232] [INFO] Task succeeded: Prodigal
[2023-06-17 11:44:34,232] [INFO] Task started: HMMsearch
[2023-06-17 11:44:34,232] [INFO] Running command: hmmsearch --tblout GCA_028693585.1_ASM2869358v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55dc8b27-6f9d-4f39-8edf-35043c905cf2/dqc_reference/reference_markers.hmm GCA_028693585.1_ASM2869358v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:44:34,555] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:44:34,556] [INFO] Found 6/6 markers.
[2023-06-17 11:44:34,586] [INFO] Query marker FASTA was written to GCA_028693585.1_ASM2869358v1_genomic.fna/markers.fasta
[2023-06-17 11:44:34,586] [INFO] Task started: Blastn
[2023-06-17 11:44:34,587] [INFO] Running command: blastn -query GCA_028693585.1_ASM2869358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55dc8b27-6f9d-4f39-8edf-35043c905cf2/dqc_reference/reference_markers.fasta -out GCA_028693585.1_ASM2869358v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:44:35,192] [INFO] Task succeeded: Blastn
[2023-06-17 11:44:35,196] [INFO] Selected 24 target genomes.
[2023-06-17 11:44:35,197] [INFO] Target genome list was writen to GCA_028693585.1_ASM2869358v1_genomic.fna/target_genomes.txt
[2023-06-17 11:44:35,198] [INFO] Task started: fastANI
[2023-06-17 11:44:35,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9eac5fa-215e-477c-9227-a186d2dc429d/GCA_028693585.1_ASM2869358v1_genomic.fna.gz --refList GCA_028693585.1_ASM2869358v1_genomic.fna/target_genomes.txt --output GCA_028693585.1_ASM2869358v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:44:53,963] [INFO] Task succeeded: fastANI
[2023-06-17 11:44:53,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55dc8b27-6f9d-4f39-8edf-35043c905cf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:44:53,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55dc8b27-6f9d-4f39-8edf-35043c905cf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:44:53,976] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:44:53,976] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:44:53,976] [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
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	77.5498	140	952	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	77.531	139	952	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	77.4688	125	952	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	77.4441	110	952	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	77.4437	138	952	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	77.3867	112	952	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	77.3041	152	952	95	below_threshold
Parabacteroides faecis	strain=DSM 102983	GCA_014199665.1	1217282	1217282	type	True	77.2894	146	952	95	below_threshold
Parabacteroides faecis	strain=JCM 18682	GCA_014647375.1	1217282	1217282	type	True	77.277	149	952	95	below_threshold
Parabacteroides bouchesdurhonensis	strain=Marseille-P3763	GCA_900186615.1	1936995	1936995	type	True	77.2227	119	952	95	below_threshold
Massilibacteroides vaginae	strain=MV12	GCA_900178525.1	1673718	1673718	type	True	76.9173	73	952	95	below_threshold
Parabacteroides pacaensis	strain=Marseille-P4001	GCA_900292045.1	2086575	2086575	type	True	76.8387	98	952	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:44:53,979] [INFO] DFAST Taxonomy check result was written to GCA_028693585.1_ASM2869358v1_genomic.fna/tc_result.tsv
[2023-06-17 11:44:53,979] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:44:53,980] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:44:53,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55dc8b27-6f9d-4f39-8edf-35043c905cf2/dqc_reference/checkm_data
[2023-06-17 11:44:53,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:44:54,025] [INFO] Task started: CheckM
[2023-06-17 11:44:54,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028693585.1_ASM2869358v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028693585.1_ASM2869358v1_genomic.fna/checkm_input GCA_028693585.1_ASM2869358v1_genomic.fna/checkm_result
[2023-06-17 11:45:35,052] [INFO] Task succeeded: CheckM
[2023-06-17 11:45:35,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:45:35,077] [INFO] ===== Completeness check finished =====
[2023-06-17 11:45:35,078] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:45:35,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028693585.1_ASM2869358v1_genomic.fna/markers.fasta)
[2023-06-17 11:45:35,078] [INFO] Task started: Blastn
[2023-06-17 11:45:35,078] [INFO] Running command: blastn -query GCA_028693585.1_ASM2869358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55dc8b27-6f9d-4f39-8edf-35043c905cf2/dqc_reference/reference_markers_gtdb.fasta -out GCA_028693585.1_ASM2869358v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:45:35,886] [INFO] Task succeeded: Blastn
[2023-06-17 11:45:35,892] [INFO] Selected 22 target genomes.
[2023-06-17 11:45:35,892] [INFO] Target genome list was writen to GCA_028693585.1_ASM2869358v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:45:35,904] [INFO] Task started: fastANI
[2023-06-17 11:45:35,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9eac5fa-215e-477c-9227-a186d2dc429d/GCA_028693585.1_ASM2869358v1_genomic.fna.gz --refList GCA_028693585.1_ASM2869358v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028693585.1_ASM2869358v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:45:51,399] [INFO] Task succeeded: fastANI
[2023-06-17 11:45:51,422] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:45:51,422] [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
GCA_018054455.1	s__Macellibacteroides sp018054455	98.8772	754	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Macellibacteroides	95.0	98.91	97.71	0.78	0.74	5	conclusive
GCF_013409575.1	s__Macellibacteroides fermentans	80.1889	462	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Macellibacteroides	95.0	96.90	95.56	0.80	0.74	5	-
GCF_015550595.1	s__Parabacteroides sp900540715	77.766	141	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCF_003473295.1	s__Parabacteroides sp003473295	77.4757	112	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000969835.1	s__Parabacteroides goldsteinii	77.4411	125	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
GCF_003480915.1	s__Parabacteroides sp003480915	77.4097	133	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.39	97.67	0.93	0.87	5	-
GCF_900128505.1	s__Parabacteroides timonensis	77.2915	152	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.14	96.11	0.85	0.79	3	-
GCF_900186615.1	s__Parabacteroides bouchesdurhonensis	77.2064	119	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.72	97.72	0.92	0.92	3	-
GCF_900108035.1	s__Parabacteroides chinchillae	77.1946	119	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.95	97.95	0.87	0.87	3	-
GCF_010500925.1	s__Barb7 sp010500925	77.0067	79	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Barb7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541965.1	s__Parabacteroides sp900541965	76.945	114	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.98	99.95	0.94	0.89	3	-
GCF_900178525.1	s__Massilibacteroides vaginae	76.928	71	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Massilibacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552465.1	s__Parabacteroides sp900552465	76.5754	84	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.92	99.92	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-17 11:45:51,424] [INFO] GTDB search result was written to GCA_028693585.1_ASM2869358v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:45:51,425] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:45:51,429] [INFO] DFAST_QC result json was written to GCA_028693585.1_ASM2869358v1_genomic.fna/dqc_result.json
[2023-06-17 11:45:51,429] [INFO] DFAST_QC completed!
[2023-06-17 11:45:51,429] [INFO] Total running time: 0h1m32s