[2023-06-29 14:27:03,610] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:27:03,615] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:27:03,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg62a8cc19-09b7-4307-ae35-dd2b1fe6d808/dqc_reference
[2023-06-29 14:27:04,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:27:04,953] [INFO] Task started: Prodigal
[2023-06-29 14:27:04,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg40d9ff49-f4d4-46b3-a5c4-4658b0f04b7d/GCA_021622745.1_ASM2162274v1_genomic.fna.gz | prodigal -d GCA_021622745.1_ASM2162274v1_genomic.fna/cds.fna -a GCA_021622745.1_ASM2162274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:27:20,256] [INFO] Task succeeded: Prodigal
[2023-06-29 14:27:20,256] [INFO] Task started: HMMsearch
[2023-06-29 14:27:20,256] [INFO] Running command: hmmsearch --tblout GCA_021622745.1_ASM2162274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62a8cc19-09b7-4307-ae35-dd2b1fe6d808/dqc_reference/reference_markers.hmm GCA_021622745.1_ASM2162274v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:27:20,484] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:27:20,485] [INFO] Found 6/6 markers.
[2023-06-29 14:27:20,512] [INFO] Query marker FASTA was written to GCA_021622745.1_ASM2162274v1_genomic.fna/markers.fasta
[2023-06-29 14:27:20,513] [INFO] Task started: Blastn
[2023-06-29 14:27:20,513] [INFO] Running command: blastn -query GCA_021622745.1_ASM2162274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62a8cc19-09b7-4307-ae35-dd2b1fe6d808/dqc_reference/reference_markers.fasta -out GCA_021622745.1_ASM2162274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:27:21,126] [INFO] Task succeeded: Blastn
[2023-06-29 14:27:21,130] [INFO] Selected 27 target genomes.
[2023-06-29 14:27:21,130] [INFO] Target genome list was writen to GCA_021622745.1_ASM2162274v1_genomic.fna/target_genomes.txt
[2023-06-29 14:27:21,131] [INFO] Task started: fastANI
[2023-06-29 14:27:21,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg40d9ff49-f4d4-46b3-a5c4-4658b0f04b7d/GCA_021622745.1_ASM2162274v1_genomic.fna.gz --refList GCA_021622745.1_ASM2162274v1_genomic.fna/target_genomes.txt --output GCA_021622745.1_ASM2162274v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:27:35,692] [INFO] Task succeeded: fastANI
[2023-06-29 14:27:35,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62a8cc19-09b7-4307-ae35-dd2b1fe6d808/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:27:35,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62a8cc19-09b7-4307-ae35-dd2b1fe6d808/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:27:35,703] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:27:35,703] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:27:35,704] [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 stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	78.9062	238	807	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	78.4245	129	807	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	78.3535	132	807	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	78.262	130	807	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	78.2199	79	807	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.7897	74	807	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.6939	99	807	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	76.5331	75	807	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.5087	76	807	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.4821	53	807	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.3974	53	807	95	below_threshold
Prevotella fusca	strain=JCM 17724	GCA_000614245.1	589436	589436	type	True	76.3523	54	807	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:27:35,706] [INFO] DFAST Taxonomy check result was written to GCA_021622745.1_ASM2162274v1_genomic.fna/tc_result.tsv
[2023-06-29 14:27:35,706] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:27:35,706] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:27:35,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62a8cc19-09b7-4307-ae35-dd2b1fe6d808/dqc_reference/checkm_data
[2023-06-29 14:27:35,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:27:35,738] [INFO] Task started: CheckM
[2023-06-29 14:27:35,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021622745.1_ASM2162274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021622745.1_ASM2162274v1_genomic.fna/checkm_input GCA_021622745.1_ASM2162274v1_genomic.fna/checkm_result
[2023-06-29 14:28:21,921] [INFO] Task succeeded: CheckM
[2023-06-29 14:28:21,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 6.72%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 14:28:21,947] [INFO] ===== Completeness check finished =====
[2023-06-29 14:28:21,947] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:28:21,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021622745.1_ASM2162274v1_genomic.fna/markers.fasta)
[2023-06-29 14:28:21,948] [INFO] Task started: Blastn
[2023-06-29 14:28:21,948] [INFO] Running command: blastn -query GCA_021622745.1_ASM2162274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62a8cc19-09b7-4307-ae35-dd2b1fe6d808/dqc_reference/reference_markers_gtdb.fasta -out GCA_021622745.1_ASM2162274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:28:22,768] [INFO] Task succeeded: Blastn
[2023-06-29 14:28:22,773] [INFO] Selected 9 target genomes.
[2023-06-29 14:28:22,773] [INFO] Target genome list was writen to GCA_021622745.1_ASM2162274v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:28:22,775] [INFO] Task started: fastANI
[2023-06-29 14:28:22,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg40d9ff49-f4d4-46b3-a5c4-4658b0f04b7d/GCA_021622745.1_ASM2162274v1_genomic.fna.gz --refList GCA_021622745.1_ASM2162274v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021622745.1_ASM2162274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:28:28,059] [INFO] Task succeeded: fastANI
[2023-06-29 14:28:28,072] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:28:28,072] [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_900290275.1	s__Prevotella sp900290275	97.718	709	807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.80	97.71	0.90	0.86	4	conclusive
GCA_900553155.1	s__Prevotella sp900553155	85.5452	371	807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
GCA_900552515.1	s__Prevotella sp900552515	80.8051	277	807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.50	0.85	0.85	3	-
GCA_900550035.1	s__Prevotella sp900550035	80.6523	369	807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCA_900544495.1	s__Prevotella sp900544495	80.5402	323	807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_900546575.1	s__Prevotella sp900546575	80.3395	323	807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCF_002265625.1	s__Prevotella sp002265625	79.8579	284	807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCF_019052365.1	s__Prevotella sp000434975	79.0809	247	807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCF_000235885.1	s__Prevotella stercorea	78.8846	239	807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	-
--------------------------------------------------------------------------------
[2023-06-29 14:28:28,079] [INFO] GTDB search result was written to GCA_021622745.1_ASM2162274v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:28:28,080] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:28:28,084] [INFO] DFAST_QC result json was written to GCA_021622745.1_ASM2162274v1_genomic.fna/dqc_result.json
[2023-06-29 14:28:28,084] [INFO] DFAST_QC completed!
[2023-06-29 14:28:28,084] [INFO] Total running time: 0h1m24s