[2023-06-13 12:04:47,295] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:04:47,298] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:04:47,298] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2b03d63-8c3f-4ef5-8b36-1e0a7583f51c/dqc_reference
[2023-06-13 12:04:48,511] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:04:48,512] [INFO] Task started: Prodigal
[2023-06-13 12:04:48,512] [INFO] Running command: gunzip -c /var/lib/cwl/stg1eccaafc-73a8-4b34-b766-f4abfaf52fa4/GCA_022727765.1_ASM2272776v1_genomic.fna.gz | prodigal -d GCA_022727765.1_ASM2272776v1_genomic.fna/cds.fna -a GCA_022727765.1_ASM2272776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:05:01,321] [INFO] Task succeeded: Prodigal
[2023-06-13 12:05:01,321] [INFO] Task started: HMMsearch
[2023-06-13 12:05:01,321] [INFO] Running command: hmmsearch --tblout GCA_022727765.1_ASM2272776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2b03d63-8c3f-4ef5-8b36-1e0a7583f51c/dqc_reference/reference_markers.hmm GCA_022727765.1_ASM2272776v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:05:01,552] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:05:01,553] [INFO] Found 6/6 markers.
[2023-06-13 12:05:01,585] [INFO] Query marker FASTA was written to GCA_022727765.1_ASM2272776v1_genomic.fna/markers.fasta
[2023-06-13 12:05:01,586] [INFO] Task started: Blastn
[2023-06-13 12:05:01,586] [INFO] Running command: blastn -query GCA_022727765.1_ASM2272776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2b03d63-8c3f-4ef5-8b36-1e0a7583f51c/dqc_reference/reference_markers.fasta -out GCA_022727765.1_ASM2272776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:05:02,205] [INFO] Task succeeded: Blastn
[2023-06-13 12:05:02,211] [INFO] Selected 16 target genomes.
[2023-06-13 12:05:02,211] [INFO] Target genome list was writen to GCA_022727765.1_ASM2272776v1_genomic.fna/target_genomes.txt
[2023-06-13 12:05:02,213] [INFO] Task started: fastANI
[2023-06-13 12:05:02,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eccaafc-73a8-4b34-b766-f4abfaf52fa4/GCA_022727765.1_ASM2272776v1_genomic.fna.gz --refList GCA_022727765.1_ASM2272776v1_genomic.fna/target_genomes.txt --output GCA_022727765.1_ASM2272776v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:05:09,705] [INFO] Task succeeded: fastANI
[2023-06-13 12:05:09,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2b03d63-8c3f-4ef5-8b36-1e0a7583f51c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:05:09,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2b03d63-8c3f-4ef5-8b36-1e0a7583f51c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:05:09,715] [INFO] Found 4 fastANI hits (3 hits with ANI > threshold)
[2023-06-13 12:05:09,716] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 12:05:09,716] [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_000157935.1	165179	165179	suspected-type	True	95.3438	376	504	95	conclusive
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	95.2788	367	504	95	conclusive
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	95.1655	374	504	95	conclusive
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	81.9853	243	504	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 12:05:09,718] [INFO] DFAST Taxonomy check result was written to GCA_022727765.1_ASM2272776v1_genomic.fna/tc_result.tsv
[2023-06-13 12:05:09,719] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:05:09,719] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:05:09,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2b03d63-8c3f-4ef5-8b36-1e0a7583f51c/dqc_reference/checkm_data
[2023-06-13 12:05:09,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:05:09,753] [INFO] Task started: CheckM
[2023-06-13 12:05:09,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022727765.1_ASM2272776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022727765.1_ASM2272776v1_genomic.fna/checkm_input GCA_022727765.1_ASM2272776v1_genomic.fna/checkm_result
[2023-06-13 12:05:51,413] [INFO] Task succeeded: CheckM
[2023-06-13 12:05:51,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.68%
Contamintation: 1.14%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-13 12:05:51,447] [INFO] ===== Completeness check finished =====
[2023-06-13 12:05:51,447] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:05:51,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022727765.1_ASM2272776v1_genomic.fna/markers.fasta)
[2023-06-13 12:05:51,448] [INFO] Task started: Blastn
[2023-06-13 12:05:51,448] [INFO] Running command: blastn -query GCA_022727765.1_ASM2272776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2b03d63-8c3f-4ef5-8b36-1e0a7583f51c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022727765.1_ASM2272776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:05:52,420] [INFO] Task succeeded: Blastn
[2023-06-13 12:05:52,425] [INFO] Selected 11 target genomes.
[2023-06-13 12:05:52,426] [INFO] Target genome list was writen to GCA_022727765.1_ASM2272776v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:05:52,428] [INFO] Task started: fastANI
[2023-06-13 12:05:52,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eccaafc-73a8-4b34-b766-f4abfaf52fa4/GCA_022727765.1_ASM2272776v1_genomic.fna.gz --refList GCA_022727765.1_ASM2272776v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022727765.1_ASM2272776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:05:58,305] [INFO] Task succeeded: fastANI
[2023-06-13 12:05:58,319] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 12:05:58,319] [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	95.8639	429	504	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	95.7814	261	504	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	95.3438	376	504	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	94.6145	405	504	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	84.8153	331	504	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	84.1084	339	504	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	84.07	305	504	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	83.7985	284	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_900557035.1	s__Prevotella sp900557035	83.0496	248	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCA_900554835.1	s__Prevotella sp900554835	82.7833	239	504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765465.1	s__Prevotella sp900765465	82.6273	177	504	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 12:05:58,321] [INFO] GTDB search result was written to GCA_022727765.1_ASM2272776v1_genomic.fna/result_gtdb.tsv
[2023-06-13 12:05:58,322] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:05:58,325] [INFO] DFAST_QC result json was written to GCA_022727765.1_ASM2272776v1_genomic.fna/dqc_result.json
[2023-06-13 12:05:58,325] [INFO] DFAST_QC completed!
[2023-06-13 12:05:58,325] [INFO] Total running time: 0h1m11s