[2023-06-13 10:10:49,202] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:10:49,204] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:10:49,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg244d3c1d-ef10-4080-9375-c4d57dcb2c00/dqc_reference
[2023-06-13 10:10:50,714] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:10:50,717] [INFO] Task started: Prodigal
[2023-06-13 10:10:50,717] [INFO] Running command: gunzip -c /var/lib/cwl/stg3506cba9-c23d-43e1-bfc8-dc0799fd3e95/GCA_022741825.1_ASM2274182v1_genomic.fna.gz | prodigal -d GCA_022741825.1_ASM2274182v1_genomic.fna/cds.fna -a GCA_022741825.1_ASM2274182v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:11:05,469] [INFO] Task succeeded: Prodigal
[2023-06-13 10:11:05,469] [INFO] Task started: HMMsearch
[2023-06-13 10:11:05,469] [INFO] Running command: hmmsearch --tblout GCA_022741825.1_ASM2274182v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg244d3c1d-ef10-4080-9375-c4d57dcb2c00/dqc_reference/reference_markers.hmm GCA_022741825.1_ASM2274182v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:11:05,735] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:11:05,737] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3506cba9-c23d-43e1-bfc8-dc0799fd3e95/GCA_022741825.1_ASM2274182v1_genomic.fna.gz]
[2023-06-13 10:11:05,771] [INFO] Query marker FASTA was written to GCA_022741825.1_ASM2274182v1_genomic.fna/markers.fasta
[2023-06-13 10:11:05,771] [INFO] Task started: Blastn
[2023-06-13 10:11:05,772] [INFO] Running command: blastn -query GCA_022741825.1_ASM2274182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg244d3c1d-ef10-4080-9375-c4d57dcb2c00/dqc_reference/reference_markers.fasta -out GCA_022741825.1_ASM2274182v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:06,418] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:06,422] [INFO] Selected 16 target genomes.
[2023-06-13 10:11:06,423] [INFO] Target genome list was writen to GCA_022741825.1_ASM2274182v1_genomic.fna/target_genomes.txt
[2023-06-13 10:11:06,424] [INFO] Task started: fastANI
[2023-06-13 10:11:06,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg3506cba9-c23d-43e1-bfc8-dc0799fd3e95/GCA_022741825.1_ASM2274182v1_genomic.fna.gz --refList GCA_022741825.1_ASM2274182v1_genomic.fna/target_genomes.txt --output GCA_022741825.1_ASM2274182v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:11:14,749] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:14,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg244d3c1d-ef10-4080-9375-c4d57dcb2c00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:11:14,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg244d3c1d-ef10-4080-9375-c4d57dcb2c00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:11:14,765] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:11:14,765] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 10:11:14,765] [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	83.4404	423	735	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	83.412	435	735	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	83.3057	435	735	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	81.3045	345	735	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.5795	53	735	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	77.5795	53	735	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.0048	65	735	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.9251	76	735	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.6835	69	735	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.5623	73	735	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.2164	53	735	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:11:14,803] [INFO] DFAST Taxonomy check result was written to GCA_022741825.1_ASM2274182v1_genomic.fna/tc_result.tsv
[2023-06-13 10:11:14,804] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:11:14,804] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:11:14,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg244d3c1d-ef10-4080-9375-c4d57dcb2c00/dqc_reference/checkm_data
[2023-06-13 10:11:14,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:11:14,839] [INFO] Task started: CheckM
[2023-06-13 10:11:14,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022741825.1_ASM2274182v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022741825.1_ASM2274182v1_genomic.fna/checkm_input GCA_022741825.1_ASM2274182v1_genomic.fna/checkm_result
[2023-06-13 10:12:00,768] [INFO] Task succeeded: CheckM
[2023-06-13 10:12:00,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.73%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 10:12:00,793] [INFO] ===== Completeness check finished =====
[2023-06-13 10:12:00,793] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:12:00,794] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022741825.1_ASM2274182v1_genomic.fna/markers.fasta)
[2023-06-13 10:12:00,794] [INFO] Task started: Blastn
[2023-06-13 10:12:00,794] [INFO] Running command: blastn -query GCA_022741825.1_ASM2274182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg244d3c1d-ef10-4080-9375-c4d57dcb2c00/dqc_reference/reference_markers_gtdb.fasta -out GCA_022741825.1_ASM2274182v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:12:01,632] [INFO] Task succeeded: Blastn
[2023-06-13 10:12:01,637] [INFO] Selected 7 target genomes.
[2023-06-13 10:12:01,637] [INFO] Target genome list was writen to GCA_022741825.1_ASM2274182v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:12:01,638] [INFO] Task started: fastANI
[2023-06-13 10:12:01,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg3506cba9-c23d-43e1-bfc8-dc0799fd3e95/GCA_022741825.1_ASM2274182v1_genomic.fna.gz --refList GCA_022741825.1_ASM2274182v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022741825.1_ASM2274182v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:12:06,090] [INFO] Task succeeded: fastANI
[2023-06-13 10:12:06,100] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:12:06,100] [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_002224675.1	s__Prevotella copri_A	95.7571	599	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	conclusive
GCA_900557035.1	s__Prevotella sp900557035	94.3305	431	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCA_900544825.1	s__Prevotella sp900544825	93.9298	567	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCA_900551985.1	s__Prevotella sp900551985	93.8298	520	735	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	91.7822	355	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556795.1	s__Prevotella sp900556795	86.3878	296	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.39	96.16	0.81	0.77	3	-
GCF_009494395.1	s__Prevotella sp900546535	85.4366	498	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
--------------------------------------------------------------------------------
[2023-06-13 10:12:06,102] [INFO] GTDB search result was written to GCA_022741825.1_ASM2274182v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:12:06,102] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:12:06,105] [INFO] DFAST_QC result json was written to GCA_022741825.1_ASM2274182v1_genomic.fna/dqc_result.json
[2023-06-13 10:12:06,106] [INFO] DFAST_QC completed!
[2023-06-13 10:12:06,106] [INFO] Total running time: 0h1m17s