[2023-06-13 21:20:32,332] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:20:32,335] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:20:32,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg785561c3-8a44-4ce0-9402-3ee80f1310e0/dqc_reference
[2023-06-13 21:20:33,482] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:20:33,483] [INFO] Task started: Prodigal
[2023-06-13 21:20:33,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg08107410-d1d3-41b2-bbd1-f1648862f7ca/GCA_022744025.1_ASM2274402v1_genomic.fna.gz | prodigal -d GCA_022744025.1_ASM2274402v1_genomic.fna/cds.fna -a GCA_022744025.1_ASM2274402v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:20:45,785] [INFO] Task succeeded: Prodigal
[2023-06-13 21:20:45,785] [INFO] Task started: HMMsearch
[2023-06-13 21:20:45,786] [INFO] Running command: hmmsearch --tblout GCA_022744025.1_ASM2274402v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg785561c3-8a44-4ce0-9402-3ee80f1310e0/dqc_reference/reference_markers.hmm GCA_022744025.1_ASM2274402v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:20:46,062] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:20:46,063] [INFO] Found 6/6 markers.
[2023-06-13 21:20:46,089] [INFO] Query marker FASTA was written to GCA_022744025.1_ASM2274402v1_genomic.fna/markers.fasta
[2023-06-13 21:20:46,089] [INFO] Task started: Blastn
[2023-06-13 21:20:46,089] [INFO] Running command: blastn -query GCA_022744025.1_ASM2274402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg785561c3-8a44-4ce0-9402-3ee80f1310e0/dqc_reference/reference_markers.fasta -out GCA_022744025.1_ASM2274402v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:20:46,628] [INFO] Task succeeded: Blastn
[2023-06-13 21:20:46,632] [INFO] Selected 23 target genomes.
[2023-06-13 21:20:46,632] [INFO] Target genome list was writen to GCA_022744025.1_ASM2274402v1_genomic.fna/target_genomes.txt
[2023-06-13 21:20:46,633] [INFO] Task started: fastANI
[2023-06-13 21:20:46,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg08107410-d1d3-41b2-bbd1-f1648862f7ca/GCA_022744025.1_ASM2274402v1_genomic.fna.gz --refList GCA_022744025.1_ASM2274402v1_genomic.fna/target_genomes.txt --output GCA_022744025.1_ASM2274402v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:20:57,111] [INFO] Task succeeded: fastANI
[2023-06-13 21:20:57,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg785561c3-8a44-4ce0-9402-3ee80f1310e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:20:57,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg785561c3-8a44-4ce0-9402-3ee80f1310e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:20:57,121] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 21:20:57,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 21:20:57,121] [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 hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	97.5703	709	821	95	conclusive
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	81.2642	373	821	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	81.2527	382	821	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	81.2189	370	821	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	77.4055	66	821	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	77.1869	60	821	95	below_threshold
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	77.1431	61	821	95	below_threshold
Prevotella scopos	strain=DSM 22613	GCA_900129535.1	589437	589437	type	True	77.1042	62	821	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.0968	101	821	95	below_threshold
Prevotella jejuni	strain=DSM 26989	GCA_900187995.1	1177574	1177574	type	True	77.0729	56	821	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.9699	68	821	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.6735	66	821	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.4822	52	821	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	76.3952	69	821	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:20:57,123] [INFO] DFAST Taxonomy check result was written to GCA_022744025.1_ASM2274402v1_genomic.fna/tc_result.tsv
[2023-06-13 21:20:57,124] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:20:57,124] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:20:57,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg785561c3-8a44-4ce0-9402-3ee80f1310e0/dqc_reference/checkm_data
[2023-06-13 21:20:57,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:20:57,156] [INFO] Task started: CheckM
[2023-06-13 21:20:57,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022744025.1_ASM2274402v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022744025.1_ASM2274402v1_genomic.fna/checkm_input GCA_022744025.1_ASM2274402v1_genomic.fna/checkm_result
[2023-06-13 21:21:35,482] [INFO] Task succeeded: CheckM
[2023-06-13 21:21:35,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.84%
Contamintation: 1.85%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 21:21:35,505] [INFO] ===== Completeness check finished =====
[2023-06-13 21:21:35,505] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:21:35,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022744025.1_ASM2274402v1_genomic.fna/markers.fasta)
[2023-06-13 21:21:35,507] [INFO] Task started: Blastn
[2023-06-13 21:21:35,507] [INFO] Running command: blastn -query GCA_022744025.1_ASM2274402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg785561c3-8a44-4ce0-9402-3ee80f1310e0/dqc_reference/reference_markers_gtdb.fasta -out GCA_022744025.1_ASM2274402v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:21:36,282] [INFO] Task succeeded: Blastn
[2023-06-13 21:21:36,286] [INFO] Selected 16 target genomes.
[2023-06-13 21:21:36,286] [INFO] Target genome list was writen to GCA_022744025.1_ASM2274402v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:21:36,287] [INFO] Task started: fastANI
[2023-06-13 21:21:36,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg08107410-d1d3-41b2-bbd1-f1648862f7ca/GCA_022744025.1_ASM2274402v1_genomic.fna.gz --refList GCA_022744025.1_ASM2274402v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022744025.1_ASM2274402v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:21:45,798] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:45,808] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 21:21:45,808] [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_004535825.1	s__Prevotella hominis	97.5703	709	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.52	95.16	0.76	0.66	13	conclusive
GCA_900554835.1	s__Prevotella sp900554835	94.5481	592	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015074785.1	s__Prevotella sp015074785	81.6421	394	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCA_019249655.1	s__Prevotella sp900767615	81.365	403	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCA_900551985.1	s__Prevotella sp900551985	81.302	346	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_000436035.1	s__Prevotella sp000436035	81.2942	403	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.58	97.92	0.86	0.81	4	-
GCF_000157935.1	s__Prevotella copri	81.2351	383	821	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	81.1587	404	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCF_002224675.1	s__Prevotella copri_A	81.107	407	821	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	81.0858	373	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCA_900555035.1	s__Prevotella sp900555035	80.828	335	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557035.1	s__Prevotella sp900557035	80.667	284	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCA_002451555.1	s__Prevotella sp002451555	80.601	395	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.47	99.47	0.85	0.85	2	-
GCF_009495355.1	s__Prevotella sp900313215	80.1091	317	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.34	96.92	0.81	0.74	15	-
GCF_900142525.1	s__Prevotella ruminicola_A	76.532	62	821	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 21:21:45,810] [INFO] GTDB search result was written to GCA_022744025.1_ASM2274402v1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:21:45,811] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:21:45,814] [INFO] DFAST_QC result json was written to GCA_022744025.1_ASM2274402v1_genomic.fna/dqc_result.json
[2023-06-13 21:21:45,814] [INFO] DFAST_QC completed!
[2023-06-13 21:21:45,814] [INFO] Total running time: 0h1m13s