[2023-06-19 15:07:29,298] [INFO] DFAST_QC pipeline started.
[2023-06-19 15:07:29,311] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 15:07:29,311] [INFO] DQC Reference Directory: /var/lib/cwl/stg21f838ae-a4ee-47fe-b26a-4c6238470bda/dqc_reference
[2023-06-19 15:07:30,924] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 15:07:30,925] [INFO] Task started: Prodigal
[2023-06-19 15:07:30,925] [INFO] Running command: gunzip -c /var/lib/cwl/stg16a102b6-c6eb-4784-94d0-5c9324c2ef5e/GCA_018065005.1_ASM1806500v1_genomic.fna.gz | prodigal -d GCA_018065005.1_ASM1806500v1_genomic.fna/cds.fna -a GCA_018065005.1_ASM1806500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 15:07:47,667] [INFO] Task succeeded: Prodigal
[2023-06-19 15:07:47,667] [INFO] Task started: HMMsearch
[2023-06-19 15:07:47,667] [INFO] Running command: hmmsearch --tblout GCA_018065005.1_ASM1806500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21f838ae-a4ee-47fe-b26a-4c6238470bda/dqc_reference/reference_markers.hmm GCA_018065005.1_ASM1806500v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 15:07:47,936] [INFO] Task succeeded: HMMsearch
[2023-06-19 15:07:47,937] [INFO] Found 6/6 markers.
[2023-06-19 15:07:47,974] [INFO] Query marker FASTA was written to GCA_018065005.1_ASM1806500v1_genomic.fna/markers.fasta
[2023-06-19 15:07:47,974] [INFO] Task started: Blastn
[2023-06-19 15:07:47,975] [INFO] Running command: blastn -query GCA_018065005.1_ASM1806500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21f838ae-a4ee-47fe-b26a-4c6238470bda/dqc_reference/reference_markers.fasta -out GCA_018065005.1_ASM1806500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:07:48,623] [INFO] Task succeeded: Blastn
[2023-06-19 15:07:48,630] [INFO] Selected 38 target genomes.
[2023-06-19 15:07:48,630] [INFO] Target genome list was writen to GCA_018065005.1_ASM1806500v1_genomic.fna/target_genomes.txt
[2023-06-19 15:07:48,637] [INFO] Task started: fastANI
[2023-06-19 15:07:48,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg16a102b6-c6eb-4784-94d0-5c9324c2ef5e/GCA_018065005.1_ASM1806500v1_genomic.fna.gz --refList GCA_018065005.1_ASM1806500v1_genomic.fna/target_genomes.txt --output GCA_018065005.1_ASM1806500v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 15:08:09,507] [INFO] Task succeeded: fastANI
[2023-06-19 15:08:09,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21f838ae-a4ee-47fe-b26a-4c6238470bda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 15:08:09,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21f838ae-a4ee-47fe-b26a-4c6238470bda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 15:08:09,521] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 15:08:09,521] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 15:08:09,521] [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
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.8621	53	767	95	below_threshold
Prevotellamassilia timonensis	strain=Marseille-P2831	GCA_900106785.1	1852370	1852370	type	True	76.7355	55	767	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.7317	56	767	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.6865	54	767	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.6653	53	767	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.5109	53	767	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.4733	53	767	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.4124	52	767	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 15:08:09,524] [INFO] DFAST Taxonomy check result was written to GCA_018065005.1_ASM1806500v1_genomic.fna/tc_result.tsv
[2023-06-19 15:08:09,524] [INFO] ===== Taxonomy check completed =====
[2023-06-19 15:08:09,525] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 15:08:09,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21f838ae-a4ee-47fe-b26a-4c6238470bda/dqc_reference/checkm_data
[2023-06-19 15:08:09,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 15:08:09,560] [INFO] Task started: CheckM
[2023-06-19 15:08:09,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018065005.1_ASM1806500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018065005.1_ASM1806500v1_genomic.fna/checkm_input GCA_018065005.1_ASM1806500v1_genomic.fna/checkm_result
[2023-06-19 15:08:57,341] [INFO] Task succeeded: CheckM
[2023-06-19 15:08:57,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 15:08:57,370] [INFO] ===== Completeness check finished =====
[2023-06-19 15:08:57,371] [INFO] ===== Start GTDB Search =====
[2023-06-19 15:08:57,371] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018065005.1_ASM1806500v1_genomic.fna/markers.fasta)
[2023-06-19 15:08:57,371] [INFO] Task started: Blastn
[2023-06-19 15:08:57,371] [INFO] Running command: blastn -query GCA_018065005.1_ASM1806500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21f838ae-a4ee-47fe-b26a-4c6238470bda/dqc_reference/reference_markers_gtdb.fasta -out GCA_018065005.1_ASM1806500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:08:58,285] [INFO] Task succeeded: Blastn
[2023-06-19 15:08:58,291] [INFO] Selected 33 target genomes.
[2023-06-19 15:08:58,292] [INFO] Target genome list was writen to GCA_018065005.1_ASM1806500v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 15:08:58,346] [INFO] Task started: fastANI
[2023-06-19 15:08:58,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg16a102b6-c6eb-4784-94d0-5c9324c2ef5e/GCA_018065005.1_ASM1806500v1_genomic.fna.gz --refList GCA_018065005.1_ASM1806500v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018065005.1_ASM1806500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 15:09:12,764] [INFO] Task succeeded: fastANI
[2023-06-19 15:09:12,787] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 15:09:12,787] [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_018065005.1	s__UBA4372 sp018065005	100.0	762	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018064685.1	s__UBA4372 sp018064685	78.4075	179	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784475.1	s__UBA4372 sp902784475	77.9517	91	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320435.1	s__UBA4372 sp900320435	77.6661	88	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.93	95.36	0.84	0.75	10	-
GCA_017524545.1	s__UBA4372 sp017524545	77.5911	124	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779845.1	s__UBA4372 sp902779845	77.4671	101	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	95.82	95.27	0.82	0.79	4	-
GCA_017453445.1	s__UBA4372 sp017453445	77.301	108	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.06	98.06	0.83	0.83	2	-
GCA_902791295.1	s__UBA4372 sp902791295	77.2683	89	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233765.1	s__UBA4372 sp905233765	77.2665	96	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017379075.1	s__UBA4372 sp017379075	77.0512	85	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	95.81	95.71	0.83	0.83	3	-
GCA_016292545.1	s__UBA4372 sp016292545	77.0199	96	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017559845.1	s__UBA4372 sp017559845	77.0165	86	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788315.1	s__UBA4372 sp902788315	76.9347	93	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.21	97.94	0.89	0.88	4	-
GCA_017445145.1	s__UBA4372 sp017445145	76.8186	104	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617235.1	s__UBA4372 sp017617235	76.7676	66	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016280855.1	s__UBA4372 sp016280855	76.6984	63	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016285055.1	s__Prevotella sp016285055	76.6173	80	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019052365.1	s__Prevotella sp000434975	76.6083	60	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCA_900316285.1	s__Prevotella sp900316285	76.4448	62	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.02	95.37	0.87	0.79	21	-
GCA_902781315.1	s__Prevotella sp902781315	76.3333	76	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.55	96.55	0.79	0.79	2	-
GCA_017478085.1	s__Prevotella sp017478085	76.2357	54	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 15:09:12,790] [INFO] GTDB search result was written to GCA_018065005.1_ASM1806500v1_genomic.fna/result_gtdb.tsv
[2023-06-19 15:09:12,791] [INFO] ===== GTDB Search completed =====
[2023-06-19 15:09:12,795] [INFO] DFAST_QC result json was written to GCA_018065005.1_ASM1806500v1_genomic.fna/dqc_result.json
[2023-06-19 15:09:12,795] [INFO] DFAST_QC completed!
[2023-06-19 15:09:12,795] [INFO] Total running time: 0h1m43s