[2023-06-29 16:34:59,306] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:34:59,309] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:34:59,310] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe5826d2-752a-40f4-91ec-755207df9354/dqc_reference
[2023-06-29 16:35:00,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:35:00,535] [INFO] Task started: Prodigal
[2023-06-29 16:35:00,535] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd131729-5302-4964-9f5e-aea4183948d1/GCA_023708465.1_ASM2370846v1_genomic.fna.gz | prodigal -d GCA_023708465.1_ASM2370846v1_genomic.fna/cds.fna -a GCA_023708465.1_ASM2370846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:35:16,810] [INFO] Task succeeded: Prodigal
[2023-06-29 16:35:16,811] [INFO] Task started: HMMsearch
[2023-06-29 16:35:16,811] [INFO] Running command: hmmsearch --tblout GCA_023708465.1_ASM2370846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe5826d2-752a-40f4-91ec-755207df9354/dqc_reference/reference_markers.hmm GCA_023708465.1_ASM2370846v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:35:17,063] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:35:17,065] [INFO] Found 6/6 markers.
[2023-06-29 16:35:17,099] [INFO] Query marker FASTA was written to GCA_023708465.1_ASM2370846v1_genomic.fna/markers.fasta
[2023-06-29 16:35:17,100] [INFO] Task started: Blastn
[2023-06-29 16:35:17,100] [INFO] Running command: blastn -query GCA_023708465.1_ASM2370846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe5826d2-752a-40f4-91ec-755207df9354/dqc_reference/reference_markers.fasta -out GCA_023708465.1_ASM2370846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:35:17,706] [INFO] Task succeeded: Blastn
[2023-06-29 16:35:17,711] [INFO] Selected 15 target genomes.
[2023-06-29 16:35:17,711] [INFO] Target genome list was writen to GCA_023708465.1_ASM2370846v1_genomic.fna/target_genomes.txt
[2023-06-29 16:35:17,712] [INFO] Task started: fastANI
[2023-06-29 16:35:17,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd131729-5302-4964-9f5e-aea4183948d1/GCA_023708465.1_ASM2370846v1_genomic.fna.gz --refList GCA_023708465.1_ASM2370846v1_genomic.fna/target_genomes.txt --output GCA_023708465.1_ASM2370846v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:35:26,428] [INFO] Task succeeded: fastANI
[2023-06-29 16:35:26,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe5826d2-752a-40f4-91ec-755207df9354/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:35:26,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe5826d2-752a-40f4-91ec-755207df9354/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:35:26,446] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2023-06-29 16:35:26,446] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 16:35:26,447] [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	96.553	692	990	95	conclusive
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	96.3523	715	990	95	conclusive
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	96.3371	719	990	95	conclusive
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	83.9335	488	990	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	78.6239	123	990	95	below_threshold
Prevotella bivia	strain=DSM 20514	GCA_000262545.1	28125	28125	type	True	78.3921	63	990	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	78.0197	97	990	95	below_threshold
Prevotella bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	77.9414	112	990	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	77.8876	76	990	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	77.8627	90	990	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.7334	71	990	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	77.3168	86	990	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	77.3124	82	990	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.6345	97	990	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:35:26,449] [INFO] DFAST Taxonomy check result was written to GCA_023708465.1_ASM2370846v1_genomic.fna/tc_result.tsv
[2023-06-29 16:35:26,450] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:35:26,450] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:35:26,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe5826d2-752a-40f4-91ec-755207df9354/dqc_reference/checkm_data
[2023-06-29 16:35:26,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:35:26,491] [INFO] Task started: CheckM
[2023-06-29 16:35:26,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708465.1_ASM2370846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708465.1_ASM2370846v1_genomic.fna/checkm_input GCA_023708465.1_ASM2370846v1_genomic.fna/checkm_result
[2023-06-29 16:36:15,580] [INFO] Task succeeded: CheckM
[2023-06-29 16:36:15,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:36:15,603] [INFO] ===== Completeness check finished =====
[2023-06-29 16:36:15,604] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:36:15,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708465.1_ASM2370846v1_genomic.fna/markers.fasta)
[2023-06-29 16:36:15,604] [INFO] Task started: Blastn
[2023-06-29 16:36:15,605] [INFO] Running command: blastn -query GCA_023708465.1_ASM2370846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe5826d2-752a-40f4-91ec-755207df9354/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708465.1_ASM2370846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:36:16,447] [INFO] Task succeeded: Blastn
[2023-06-29 16:36:16,452] [INFO] Selected 10 target genomes.
[2023-06-29 16:36:16,452] [INFO] Target genome list was writen to GCA_023708465.1_ASM2370846v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:36:16,453] [INFO] Task started: fastANI
[2023-06-29 16:36:16,453] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd131729-5302-4964-9f5e-aea4183948d1/GCA_023708465.1_ASM2370846v1_genomic.fna.gz --refList GCA_023708465.1_ASM2370846v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708465.1_ASM2370846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:36:23,539] [INFO] Task succeeded: fastANI
[2023-06-29 16:36:23,552] [INFO] Found 10 fastANI hits (3 hits with ANI > circumscription radius)
[2023-06-29 16:36:23,553] [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_000157935.1	s__Prevotella copri	96.398	717	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	inconclusive
GCF_015074785.1	s__Prevotella sp015074785	96.0534	748	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	inconclusive
GCF_019127135.1	s__Prevotella sp900551275	95.0599	744	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	inconclusive
GCA_900557255.1	s__Prevotella sp900557255	94.4585	406	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009494395.1	s__Prevotella sp900546535	87.2174	657	990	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	86.7551	667	990	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	86.4944	583	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	-
GCA_900544825.1	s__Prevotella sp900544825	86.4882	570	990	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	85.9235	521	990	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	83.2596	302	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:36:23,555] [INFO] GTDB search result was written to GCA_023708465.1_ASM2370846v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:36:23,555] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:36:23,559] [INFO] DFAST_QC result json was written to GCA_023708465.1_ASM2370846v1_genomic.fna/dqc_result.json
[2023-06-29 16:36:23,559] [INFO] DFAST_QC completed!
[2023-06-29 16:36:23,559] [INFO] Total running time: 0h1m24s