[2023-06-30 10:05:48,333] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:05:48,339] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:05:48,339] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9f6d821-0bc3-44dd-811c-d708add26f4a/dqc_reference
[2023-06-30 10:05:50,877] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:05:50,877] [INFO] Task started: Prodigal
[2023-06-30 10:05:50,878] [INFO] Running command: gunzip -c /var/lib/cwl/stg64a33576-e5b0-415a-aba9-e17f9320113a/GCA_024691965.1_ASM2469196v1_genomic.fna.gz | prodigal -d GCA_024691965.1_ASM2469196v1_genomic.fna/cds.fna -a GCA_024691965.1_ASM2469196v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:06:05,438] [INFO] Task succeeded: Prodigal
[2023-06-30 10:06:05,439] [INFO] Task started: HMMsearch
[2023-06-30 10:06:05,439] [INFO] Running command: hmmsearch --tblout GCA_024691965.1_ASM2469196v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9f6d821-0bc3-44dd-811c-d708add26f4a/dqc_reference/reference_markers.hmm GCA_024691965.1_ASM2469196v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:06:05,690] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:06:05,692] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg64a33576-e5b0-415a-aba9-e17f9320113a/GCA_024691965.1_ASM2469196v1_genomic.fna.gz]
[2023-06-30 10:06:05,741] [INFO] Query marker FASTA was written to GCA_024691965.1_ASM2469196v1_genomic.fna/markers.fasta
[2023-06-30 10:06:05,741] [INFO] Task started: Blastn
[2023-06-30 10:06:05,742] [INFO] Running command: blastn -query GCA_024691965.1_ASM2469196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f6d821-0bc3-44dd-811c-d708add26f4a/dqc_reference/reference_markers.fasta -out GCA_024691965.1_ASM2469196v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:06:06,361] [INFO] Task succeeded: Blastn
[2023-06-30 10:06:06,366] [INFO] Selected 21 target genomes.
[2023-06-30 10:06:06,367] [INFO] Target genome list was writen to GCA_024691965.1_ASM2469196v1_genomic.fna/target_genomes.txt
[2023-06-30 10:06:06,368] [INFO] Task started: fastANI
[2023-06-30 10:06:06,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg64a33576-e5b0-415a-aba9-e17f9320113a/GCA_024691965.1_ASM2469196v1_genomic.fna.gz --refList GCA_024691965.1_ASM2469196v1_genomic.fna/target_genomes.txt --output GCA_024691965.1_ASM2469196v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:06:16,018] [INFO] Task succeeded: fastANI
[2023-06-30 10:06:16,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9f6d821-0bc3-44dd-811c-d708add26f4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:06:16,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9f6d821-0bc3-44dd-811c-d708add26f4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:06:16,031] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:06:16,031] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 10:06:16,031] [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 ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	79.3891	278	854	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	79.3351	282	854	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.134	160	854	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.0122	87	854	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.8579	88	854	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.4842	55	854	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.3432	62	854	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.2462	56	854	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.2271	67	854	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.0476	61	854	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:06:16,033] [INFO] DFAST Taxonomy check result was written to GCA_024691965.1_ASM2469196v1_genomic.fna/tc_result.tsv
[2023-06-30 10:06:16,034] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:06:16,034] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:06:16,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9f6d821-0bc3-44dd-811c-d708add26f4a/dqc_reference/checkm_data
[2023-06-30 10:06:16,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:06:16,067] [INFO] Task started: CheckM
[2023-06-30 10:06:16,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024691965.1_ASM2469196v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024691965.1_ASM2469196v1_genomic.fna/checkm_input GCA_024691965.1_ASM2469196v1_genomic.fna/checkm_result
[2023-06-30 10:07:01,811] [INFO] Task succeeded: CheckM
[2023-06-30 10:07:01,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.06%
Contamintation: 9.47%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-30 10:07:01,838] [INFO] ===== Completeness check finished =====
[2023-06-30 10:07:01,838] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:07:01,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024691965.1_ASM2469196v1_genomic.fna/markers.fasta)
[2023-06-30 10:07:01,839] [INFO] Task started: Blastn
[2023-06-30 10:07:01,839] [INFO] Running command: blastn -query GCA_024691965.1_ASM2469196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f6d821-0bc3-44dd-811c-d708add26f4a/dqc_reference/reference_markers_gtdb.fasta -out GCA_024691965.1_ASM2469196v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:07:02,773] [INFO] Task succeeded: Blastn
[2023-06-30 10:07:02,778] [INFO] Selected 20 target genomes.
[2023-06-30 10:07:02,778] [INFO] Target genome list was writen to GCA_024691965.1_ASM2469196v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:07:02,783] [INFO] Task started: fastANI
[2023-06-30 10:07:02,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg64a33576-e5b0-415a-aba9-e17f9320113a/GCA_024691965.1_ASM2469196v1_genomic.fna.gz --refList GCA_024691965.1_ASM2469196v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024691965.1_ASM2469196v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:07:16,035] [INFO] Task succeeded: fastANI
[2023-06-30 10:07:16,058] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:07:16,058] [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
GCA_016283605.1	s__Prevotella sp016283605	97.4686	568	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016290175.1	s__Prevotella sp016290175	80.8886	383	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785945.1	s__Prevotella sp902785945	80.7211	408	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017964785.1	s__Prevotella sp017964785	80.3992	367	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233555.1	s__Prevotella sp905233555	80.3139	366	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902763615.1	s__Prevotella sp902763615	80.2677	348	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784565.1	s__Prevotella sp902784565	80.1966	351	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.90	0.76	0.76	2	-
GCA_017618275.1	s__Prevotella sp017618275	80.1779	366	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017965725.1	s__Prevotella sp017965725	80.079	329	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016284635.1	s__Prevotella sp016284635	79.9417	331	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017556145.1	s__Prevotella sp017556145	79.6242	345	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551005.1	s__Prevotella sp017551005	79.6023	329	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017650905.1	s__Prevotella sp017650905	79.5393	292	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017518935.1	s__Prevotella sp017518935	79.52	325	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789415.1	s__Prevotella sp902789415	79.0542	251	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060625.1	s__Prevotella ruminicola_D	79.0029	276	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142525.1	s__Prevotella ruminicola_A	78.9972	274	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315035.1	s__Prevotella sp900315035	78.8921	286	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.18	98.35	0.94	0.89	3	-
GCA_002351725.1	s__Prevotella sp002351725	78.7738	229	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.82	95.50	0.81	0.76	9	-
GCA_902799655.1	s__Prevotella sp902799655	78.2873	206	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 10:07:16,061] [INFO] GTDB search result was written to GCA_024691965.1_ASM2469196v1_genomic.fna/result_gtdb.tsv
[2023-06-30 10:07:16,061] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:07:16,066] [INFO] DFAST_QC result json was written to GCA_024691965.1_ASM2469196v1_genomic.fna/dqc_result.json
[2023-06-30 10:07:16,066] [INFO] DFAST_QC completed!
[2023-06-30 10:07:16,066] [INFO] Total running time: 0h1m28s