[2023-06-13 16:35:32,649] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:35:32,653] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:35:32,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg4132f131-4988-4b5c-998e-b260ce999cb3/dqc_reference
[2023-06-13 16:35:34,020] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:35:34,021] [INFO] Task started: Prodigal
[2023-06-13 16:35:34,021] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd6ba05f-cea5-4e5c-8ca2-310eb5fd3fd8/GCA_022744325.1_ASM2274432v1_genomic.fna.gz | prodigal -d GCA_022744325.1_ASM2274432v1_genomic.fna/cds.fna -a GCA_022744325.1_ASM2274432v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:35:45,256] [INFO] Task succeeded: Prodigal
[2023-06-13 16:35:45,256] [INFO] Task started: HMMsearch
[2023-06-13 16:35:45,256] [INFO] Running command: hmmsearch --tblout GCA_022744325.1_ASM2274432v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4132f131-4988-4b5c-998e-b260ce999cb3/dqc_reference/reference_markers.hmm GCA_022744325.1_ASM2274432v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:35:45,500] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:35:45,501] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfd6ba05f-cea5-4e5c-8ca2-310eb5fd3fd8/GCA_022744325.1_ASM2274432v1_genomic.fna.gz]
[2023-06-13 16:35:45,525] [INFO] Query marker FASTA was written to GCA_022744325.1_ASM2274432v1_genomic.fna/markers.fasta
[2023-06-13 16:35:45,525] [INFO] Task started: Blastn
[2023-06-13 16:35:45,525] [INFO] Running command: blastn -query GCA_022744325.1_ASM2274432v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4132f131-4988-4b5c-998e-b260ce999cb3/dqc_reference/reference_markers.fasta -out GCA_022744325.1_ASM2274432v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:35:46,063] [INFO] Task succeeded: Blastn
[2023-06-13 16:35:46,066] [INFO] Selected 15 target genomes.
[2023-06-13 16:35:46,066] [INFO] Target genome list was writen to GCA_022744325.1_ASM2274432v1_genomic.fna/target_genomes.txt
[2023-06-13 16:35:46,067] [INFO] Task started: fastANI
[2023-06-13 16:35:46,067] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd6ba05f-cea5-4e5c-8ca2-310eb5fd3fd8/GCA_022744325.1_ASM2274432v1_genomic.fna.gz --refList GCA_022744325.1_ASM2274432v1_genomic.fna/target_genomes.txt --output GCA_022744325.1_ASM2274432v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:35:54,482] [INFO] Task succeeded: fastANI
[2023-06-13 16:35:54,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4132f131-4988-4b5c-998e-b260ce999cb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:35:54,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4132f131-4988-4b5c-998e-b260ce999cb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:35:54,493] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2023-06-13 16:35:54,493] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 16:35:54,493] [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 copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	95.3974	520	704	95	conclusive
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	95.3643	525	704	95	conclusive
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	95.3164	534	704	95	conclusive
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	81.4754	354	704	95	below_threshold
Prevotella bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	76.959	54	704	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.8091	54	704	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.8091	54	704	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 16:35:54,495] [INFO] DFAST Taxonomy check result was written to GCA_022744325.1_ASM2274432v1_genomic.fna/tc_result.tsv
[2023-06-13 16:35:54,495] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:35:54,495] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:35:54,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4132f131-4988-4b5c-998e-b260ce999cb3/dqc_reference/checkm_data
[2023-06-13 16:35:54,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:35:54,526] [INFO] Task started: CheckM
[2023-06-13 16:35:54,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022744325.1_ASM2274432v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022744325.1_ASM2274432v1_genomic.fna/checkm_input GCA_022744325.1_ASM2274432v1_genomic.fna/checkm_result
[2023-06-13 16:36:29,704] [INFO] Task succeeded: CheckM
[2023-06-13 16:36:29,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.55%
Contamintation: 12.50%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-13 16:36:29,734] [INFO] ===== Completeness check finished =====
[2023-06-13 16:36:29,734] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:36:29,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022744325.1_ASM2274432v1_genomic.fna/markers.fasta)
[2023-06-13 16:36:29,735] [INFO] Task started: Blastn
[2023-06-13 16:36:29,735] [INFO] Running command: blastn -query GCA_022744325.1_ASM2274432v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4132f131-4988-4b5c-998e-b260ce999cb3/dqc_reference/reference_markers_gtdb.fasta -out GCA_022744325.1_ASM2274432v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:36:30,457] [INFO] Task succeeded: Blastn
[2023-06-13 16:36:30,460] [INFO] Selected 9 target genomes.
[2023-06-13 16:36:30,460] [INFO] Target genome list was writen to GCA_022744325.1_ASM2274432v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:36:30,461] [INFO] Task started: fastANI
[2023-06-13 16:36:30,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd6ba05f-cea5-4e5c-8ca2-310eb5fd3fd8/GCA_022744325.1_ASM2274432v1_genomic.fna.gz --refList GCA_022744325.1_ASM2274432v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022744325.1_ASM2274432v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:36:36,235] [INFO] Task succeeded: fastANI
[2023-06-13 16:36:36,242] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 16:36:36,242] [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_015074785.1	s__Prevotella sp015074785	96.0927	589	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	inconclusive
GCA_900557255.1	s__Prevotella sp900557255	95.3572	346	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000157935.1	s__Prevotella copri	95.3164	534	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCF_019127135.1	s__Prevotella sp900551275	94.5817	561	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCF_009494395.1	s__Prevotella sp900546535	84.7528	457	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCA_019249655.1	s__Prevotella sp900767615	84.3658	458	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCF_002224675.1	s__Prevotella copri_A	83.8206	413	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	-
GCA_900551985.1	s__Prevotella sp900551985	83.2805	380	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_900765465.1	s__Prevotella sp900765465	82.7102	256	704	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 16:36:36,244] [INFO] GTDB search result was written to GCA_022744325.1_ASM2274432v1_genomic.fna/result_gtdb.tsv
[2023-06-13 16:36:36,244] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:36:36,247] [INFO] DFAST_QC result json was written to GCA_022744325.1_ASM2274432v1_genomic.fna/dqc_result.json
[2023-06-13 16:36:36,247] [INFO] DFAST_QC completed!
[2023-06-13 16:36:36,247] [INFO] Total running time: 0h1m4s