[2024-01-24 14:12:45,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:45,968] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:45,968] [INFO] DQC Reference Directory: /var/lib/cwl/stg27a16499-7e16-4a42-97cc-9190af44bee4/dqc_reference
[2024-01-24 14:12:47,213] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:47,213] [INFO] Task started: Prodigal
[2024-01-24 14:12:47,214] [INFO] Running command: gunzip -c /var/lib/cwl/stg73ffcd66-a503-4c58-afdb-26e85fa6ee29/GCF_009695775.1_ASM969577v1_genomic.fna.gz | prodigal -d GCF_009695775.1_ASM969577v1_genomic.fna/cds.fna -a GCF_009695775.1_ASM969577v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:10,046] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:10,047] [INFO] Task started: HMMsearch
[2024-01-24 14:13:10,047] [INFO] Running command: hmmsearch --tblout GCF_009695775.1_ASM969577v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27a16499-7e16-4a42-97cc-9190af44bee4/dqc_reference/reference_markers.hmm GCF_009695775.1_ASM969577v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:10,305] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:10,307] [INFO] Found 6/6 markers.
[2024-01-24 14:13:10,343] [INFO] Query marker FASTA was written to GCF_009695775.1_ASM969577v1_genomic.fna/markers.fasta
[2024-01-24 14:13:10,343] [INFO] Task started: Blastn
[2024-01-24 14:13:10,343] [INFO] Running command: blastn -query GCF_009695775.1_ASM969577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27a16499-7e16-4a42-97cc-9190af44bee4/dqc_reference/reference_markers.fasta -out GCF_009695775.1_ASM969577v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:10,957] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:10,961] [INFO] Selected 13 target genomes.
[2024-01-24 14:13:10,961] [INFO] Target genome list was writen to GCF_009695775.1_ASM969577v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:10,969] [INFO] Task started: fastANI
[2024-01-24 14:13:10,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg73ffcd66-a503-4c58-afdb-26e85fa6ee29/GCF_009695775.1_ASM969577v1_genomic.fna.gz --refList GCF_009695775.1_ASM969577v1_genomic.fna/target_genomes.txt --output GCF_009695775.1_ASM969577v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:18,247] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:18,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27a16499-7e16-4a42-97cc-9190af44bee4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:18,248] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27a16499-7e16-4a42-97cc-9190af44bee4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:18,263] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:18,263] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:18,264] [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 mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	100.0	1242	1251	95	conclusive
Prevotella multisaccharivorax	strain=DSM 17128	GCA_000218235.1	310514	310514	type	True	78.8186	175	1251	95	below_threshold
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	78.7593	176	1251	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.9998	189	1251	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.4618	117	1251	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.442	127	1251	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.3525	112	1251	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.3044	197	1251	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	77.2074	191	1251	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.204	192	1251	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.8046	108	1251	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.749	109	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:18,265] [INFO] DFAST Taxonomy check result was written to GCF_009695775.1_ASM969577v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:18,266] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:18,266] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:18,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27a16499-7e16-4a42-97cc-9190af44bee4/dqc_reference/checkm_data
[2024-01-24 14:13:18,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:18,306] [INFO] Task started: CheckM
[2024-01-24 14:13:18,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695775.1_ASM969577v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695775.1_ASM969577v1_genomic.fna/checkm_input GCF_009695775.1_ASM969577v1_genomic.fna/checkm_result
[2024-01-24 14:14:25,016] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:25,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:25,035] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:25,035] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:25,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695775.1_ASM969577v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:25,036] [INFO] Task started: Blastn
[2024-01-24 14:14:25,036] [INFO] Running command: blastn -query GCF_009695775.1_ASM969577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27a16499-7e16-4a42-97cc-9190af44bee4/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695775.1_ASM969577v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:25,936] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:25,939] [INFO] Selected 7 target genomes.
[2024-01-24 14:14:25,939] [INFO] Target genome list was writen to GCF_009695775.1_ASM969577v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:25,945] [INFO] Task started: fastANI
[2024-01-24 14:14:25,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg73ffcd66-a503-4c58-afdb-26e85fa6ee29/GCF_009695775.1_ASM969577v1_genomic.fna.gz --refList GCF_009695775.1_ASM969577v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695775.1_ASM969577v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:31,616] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:31,623] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:31,623] [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_009695775.1	s__Prevotella mizrahii	100.0	1242	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.87	0.87	0.84	6	conclusive
GCA_002481295.1	s__Prevotella sp002481295	93.4054	746	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	96.70	0.87	0.78	4	-
GCA_900317685.1	s__Prevotella sp900317685	89.5968	789	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.13	96.10	0.84	0.76	12	-
GCA_900540375.1	s__Prevotella sp900540375	88.0321	763	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.83	98.80	0.92	0.91	3	-
GCA_900546345.1	s__Prevotella sp900546345	85.0097	730	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018789675.1	s__Prevotella sp002300055	77.9985	189	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.15	99.02	0.92	0.90	6	-
GCA_902801375.1	s__Prevotella sp902801375	76.8526	100	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.75	97.75	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:31,631] [INFO] GTDB search result was written to GCF_009695775.1_ASM969577v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:31,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:31,637] [INFO] DFAST_QC result json was written to GCF_009695775.1_ASM969577v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:31,637] [INFO] DFAST_QC completed!
[2024-01-24 14:14:31,637] [INFO] Total running time: 0h1m46s