[2023-06-13 10:10:56,845] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:10:56,847] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:10:56,848] [INFO] DQC Reference Directory: /var/lib/cwl/stge4760896-e473-45a1-8dc3-f5a516cfa2b3/dqc_reference
[2023-06-13 10:11:02,706] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:11:02,707] [INFO] Task started: Prodigal
[2023-06-13 10:11:02,707] [INFO] Running command: gunzip -c /var/lib/cwl/stg94bbd3e7-2bec-4bf4-82ad-77aa0bae448d/GCA_022738655.1_ASM2273865v1_genomic.fna.gz | prodigal -d GCA_022738655.1_ASM2273865v1_genomic.fna/cds.fna -a GCA_022738655.1_ASM2273865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:11:17,076] [INFO] Task succeeded: Prodigal
[2023-06-13 10:11:17,077] [INFO] Task started: HMMsearch
[2023-06-13 10:11:17,078] [INFO] Running command: hmmsearch --tblout GCA_022738655.1_ASM2273865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4760896-e473-45a1-8dc3-f5a516cfa2b3/dqc_reference/reference_markers.hmm GCA_022738655.1_ASM2273865v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:11:17,447] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:11:17,448] [INFO] Found 6/6 markers.
[2023-06-13 10:11:17,480] [INFO] Query marker FASTA was written to GCA_022738655.1_ASM2273865v1_genomic.fna/markers.fasta
[2023-06-13 10:11:17,481] [INFO] Task started: Blastn
[2023-06-13 10:11:17,481] [INFO] Running command: blastn -query GCA_022738655.1_ASM2273865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4760896-e473-45a1-8dc3-f5a516cfa2b3/dqc_reference/reference_markers.fasta -out GCA_022738655.1_ASM2273865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:22,370] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:22,376] [INFO] Selected 14 target genomes.
[2023-06-13 10:11:22,377] [INFO] Target genome list was writen to GCA_022738655.1_ASM2273865v1_genomic.fna/target_genomes.txt
[2023-06-13 10:11:22,379] [INFO] Task started: fastANI
[2023-06-13 10:11:22,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg94bbd3e7-2bec-4bf4-82ad-77aa0bae448d/GCA_022738655.1_ASM2273865v1_genomic.fna.gz --refList GCA_022738655.1_ASM2273865v1_genomic.fna/target_genomes.txt --output GCA_022738655.1_ASM2273865v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:11:28,956] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:28,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4760896-e473-45a1-8dc3-f5a516cfa2b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:11:28,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4760896-e473-45a1-8dc3-f5a516cfa2b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:11:28,970] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:11:28,970] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 10:11:28,970] [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_025151535.1	165179	165179	suspected-type	True	83.8264	310	552	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	83.7821	305	552	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	83.7553	314	552	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	82.0181	250	552	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.0306	62	552	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.8418	52	552	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.8418	52	552	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.7934	52	552	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:11:28,972] [INFO] DFAST Taxonomy check result was written to GCA_022738655.1_ASM2273865v1_genomic.fna/tc_result.tsv
[2023-06-13 10:11:28,973] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:11:28,973] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:11:28,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4760896-e473-45a1-8dc3-f5a516cfa2b3/dqc_reference/checkm_data
[2023-06-13 10:11:28,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:11:29,011] [INFO] Task started: CheckM
[2023-06-13 10:11:29,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022738655.1_ASM2273865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022738655.1_ASM2273865v1_genomic.fna/checkm_input GCA_022738655.1_ASM2273865v1_genomic.fna/checkm_result
[2023-06-13 10:12:18,229] [INFO] Task succeeded: CheckM
[2023-06-13 10:12:18,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.29%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 10:12:18,251] [INFO] ===== Completeness check finished =====
[2023-06-13 10:12:18,252] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:12:18,252] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022738655.1_ASM2273865v1_genomic.fna/markers.fasta)
[2023-06-13 10:12:18,252] [INFO] Task started: Blastn
[2023-06-13 10:12:18,253] [INFO] Running command: blastn -query GCA_022738655.1_ASM2273865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4760896-e473-45a1-8dc3-f5a516cfa2b3/dqc_reference/reference_markers_gtdb.fasta -out GCA_022738655.1_ASM2273865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:12:19,088] [INFO] Task succeeded: Blastn
[2023-06-13 10:12:19,096] [INFO] Selected 9 target genomes.
[2023-06-13 10:12:19,096] [INFO] Target genome list was writen to GCA_022738655.1_ASM2273865v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:12:19,098] [INFO] Task started: fastANI
[2023-06-13 10:12:19,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg94bbd3e7-2bec-4bf4-82ad-77aa0bae448d/GCA_022738655.1_ASM2273865v1_genomic.fna.gz --refList GCA_022738655.1_ASM2273865v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022738655.1_ASM2273865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:12:23,770] [INFO] Task succeeded: fastANI
[2023-06-13 10:12:23,780] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:12:23,781] [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	95.3767	439	552	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	94.3446	309	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCA_900551985.1	s__Prevotella sp900551985	93.7418	388	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_900544825.1	s__Prevotella sp900544825	93.5274	418	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCA_900765465.1	s__Prevotella sp900765465	91.722	255	552	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	86.2437	216	552	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	85.7334	354	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCF_015074785.1	s__Prevotella sp015074785	84.2865	322	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_019127135.1	s__Prevotella sp900551275	83.993	327	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
--------------------------------------------------------------------------------
[2023-06-13 10:12:23,783] [INFO] GTDB search result was written to GCA_022738655.1_ASM2273865v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:12:23,783] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:12:23,787] [INFO] DFAST_QC result json was written to GCA_022738655.1_ASM2273865v1_genomic.fna/dqc_result.json
[2023-06-13 10:12:23,788] [INFO] DFAST_QC completed!
[2023-06-13 10:12:23,788] [INFO] Total running time: 0h1m27s