[2023-06-28 11:09:48,324] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:09:48,334] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:09:48,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg1af90b08-28ce-4759-9e78-41ab57159e3f/dqc_reference
[2023-06-28 11:09:49,634] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:09:49,635] [INFO] Task started: Prodigal
[2023-06-28 11:09:49,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg80c5e030-31e7-4cf3-8117-014c16adc07b/GCA_017619335.1_ASM1761933v1_genomic.fna.gz | prodigal -d GCA_017619335.1_ASM1761933v1_genomic.fna/cds.fna -a GCA_017619335.1_ASM1761933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:10:11,119] [INFO] Task succeeded: Prodigal
[2023-06-28 11:10:11,120] [INFO] Task started: HMMsearch
[2023-06-28 11:10:11,120] [INFO] Running command: hmmsearch --tblout GCA_017619335.1_ASM1761933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1af90b08-28ce-4759-9e78-41ab57159e3f/dqc_reference/reference_markers.hmm GCA_017619335.1_ASM1761933v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:10:11,378] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:10:11,379] [INFO] Found 6/6 markers.
[2023-06-28 11:10:11,413] [INFO] Query marker FASTA was written to GCA_017619335.1_ASM1761933v1_genomic.fna/markers.fasta
[2023-06-28 11:10:11,413] [INFO] Task started: Blastn
[2023-06-28 11:10:11,414] [INFO] Running command: blastn -query GCA_017619335.1_ASM1761933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af90b08-28ce-4759-9e78-41ab57159e3f/dqc_reference/reference_markers.fasta -out GCA_017619335.1_ASM1761933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:10:12,016] [INFO] Task succeeded: Blastn
[2023-06-28 11:10:12,020] [INFO] Selected 29 target genomes.
[2023-06-28 11:10:12,020] [INFO] Target genome list was writen to GCA_017619335.1_ASM1761933v1_genomic.fna/target_genomes.txt
[2023-06-28 11:10:12,022] [INFO] Task started: fastANI
[2023-06-28 11:10:12,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg80c5e030-31e7-4cf3-8117-014c16adc07b/GCA_017619335.1_ASM1761933v1_genomic.fna.gz --refList GCA_017619335.1_ASM1761933v1_genomic.fna/target_genomes.txt --output GCA_017619335.1_ASM1761933v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:10:26,464] [INFO] Task succeeded: fastANI
[2023-06-28 11:10:26,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1af90b08-28ce-4759-9e78-41ab57159e3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:10:26,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1af90b08-28ce-4759-9e78-41ab57159e3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:10:26,476] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:10:26,476] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 11:10:26,476] [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_000220215.1	52227	52227	type	True	76.25	63	1143	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.2229	64	1143	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	75.9637	60	1143	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	75.5798	58	1143	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 11:10:26,478] [INFO] DFAST Taxonomy check result was written to GCA_017619335.1_ASM1761933v1_genomic.fna/tc_result.tsv
[2023-06-28 11:10:26,479] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:10:26,479] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:10:26,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1af90b08-28ce-4759-9e78-41ab57159e3f/dqc_reference/checkm_data
[2023-06-28 11:10:26,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:10:26,522] [INFO] Task started: CheckM
[2023-06-28 11:10:26,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017619335.1_ASM1761933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017619335.1_ASM1761933v1_genomic.fna/checkm_input GCA_017619335.1_ASM1761933v1_genomic.fna/checkm_result
[2023-06-28 11:11:28,207] [INFO] Task succeeded: CheckM
[2023-06-28 11:11:28,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:11:28,235] [INFO] ===== Completeness check finished =====
[2023-06-28 11:11:28,235] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:11:28,236] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017619335.1_ASM1761933v1_genomic.fna/markers.fasta)
[2023-06-28 11:11:28,236] [INFO] Task started: Blastn
[2023-06-28 11:11:28,236] [INFO] Running command: blastn -query GCA_017619335.1_ASM1761933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af90b08-28ce-4759-9e78-41ab57159e3f/dqc_reference/reference_markers_gtdb.fasta -out GCA_017619335.1_ASM1761933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:11:29,078] [INFO] Task succeeded: Blastn
[2023-06-28 11:11:29,095] [INFO] Selected 16 target genomes.
[2023-06-28 11:11:29,096] [INFO] Target genome list was writen to GCA_017619335.1_ASM1761933v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:11:29,102] [INFO] Task started: fastANI
[2023-06-28 11:11:29,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg80c5e030-31e7-4cf3-8117-014c16adc07b/GCA_017619335.1_ASM1761933v1_genomic.fna.gz --refList GCA_017619335.1_ASM1761933v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017619335.1_ASM1761933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:11:38,987] [INFO] Task succeeded: fastANI
[2023-06-28 11:11:38,999] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:11:38,999] [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_017619335.1	s__UBA4372 sp017619335	100.0	1135	1143	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_017455585.1	s__UBA4372 sp017455585	80.6926	452	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316355.1	s__UBA4372 sp900316355	79.3988	302	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.71	97.42	0.94	0.87	3	-
GCA_902779845.1	s__UBA4372 sp902779845	79.3375	299	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	95.82	95.27	0.82	0.79	4	-
GCA_902771725.1	s__UBA4372 sp902771725	78.9522	388	1143	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	78.8859	278	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318115.1	s__UBA4372 sp900318115	78.8333	369	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.30	96.55	0.83	0.74	7	-
GCA_902779165.1	s__UBA4372 sp902779165	78.7909	353	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.70	97.51	0.80	0.77	4	-
GCA_017965425.1	s__UBA4372 sp017965425	78.7586	284	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017535725.1	s__UBA4372 sp017535725	78.7007	289	1143	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	78.3268	243	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783885.1	s__UBA4372 sp902783885	78.1404	201	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016286165.1	s__UBA4372 sp016286165	78.0497	272	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236985.1	s__UBA4372 sp905236985	77.8974	262	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803195.1	s__UBA4372 sp902803195	77.8351	221	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 11:11:39,001] [INFO] GTDB search result was written to GCA_017619335.1_ASM1761933v1_genomic.fna/result_gtdb.tsv
[2023-06-28 11:11:39,002] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:11:39,005] [INFO] DFAST_QC result json was written to GCA_017619335.1_ASM1761933v1_genomic.fna/dqc_result.json
[2023-06-28 11:11:39,005] [INFO] DFAST_QC completed!
[2023-06-28 11:11:39,005] [INFO] Total running time: 0h1m51s