[2023-06-28 23:57:38,595] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:57:38,597] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:57:38,598] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc95a04c-fe6e-4e35-8a44-e45b1a402e6e/dqc_reference
[2023-06-28 23:57:39,903] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:57:39,904] [INFO] Task started: Prodigal
[2023-06-28 23:57:39,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg133321ce-2dc7-42bf-9772-9380a8daf406/GCA_017412965.1_ASM1741296v1_genomic.fna.gz | prodigal -d GCA_017412965.1_ASM1741296v1_genomic.fna/cds.fna -a GCA_017412965.1_ASM1741296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:57:50,972] [INFO] Task succeeded: Prodigal
[2023-06-28 23:57:50,973] [INFO] Task started: HMMsearch
[2023-06-28 23:57:50,973] [INFO] Running command: hmmsearch --tblout GCA_017412965.1_ASM1741296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc95a04c-fe6e-4e35-8a44-e45b1a402e6e/dqc_reference/reference_markers.hmm GCA_017412965.1_ASM1741296v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:57:51,204] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:57:51,206] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg133321ce-2dc7-42bf-9772-9380a8daf406/GCA_017412965.1_ASM1741296v1_genomic.fna.gz]
[2023-06-28 23:57:51,237] [INFO] Query marker FASTA was written to GCA_017412965.1_ASM1741296v1_genomic.fna/markers.fasta
[2023-06-28 23:57:51,238] [INFO] Task started: Blastn
[2023-06-28 23:57:51,238] [INFO] Running command: blastn -query GCA_017412965.1_ASM1741296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc95a04c-fe6e-4e35-8a44-e45b1a402e6e/dqc_reference/reference_markers.fasta -out GCA_017412965.1_ASM1741296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:57:51,820] [INFO] Task succeeded: Blastn
[2023-06-28 23:57:51,823] [INFO] Selected 12 target genomes.
[2023-06-28 23:57:51,824] [INFO] Target genome list was writen to GCA_017412965.1_ASM1741296v1_genomic.fna/target_genomes.txt
[2023-06-28 23:57:51,825] [INFO] Task started: fastANI
[2023-06-28 23:57:51,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg133321ce-2dc7-42bf-9772-9380a8daf406/GCA_017412965.1_ASM1741296v1_genomic.fna.gz --refList GCA_017412965.1_ASM1741296v1_genomic.fna/target_genomes.txt --output GCA_017412965.1_ASM1741296v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:57:58,581] [INFO] Task succeeded: fastANI
[2023-06-28 23:57:58,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc95a04c-fe6e-4e35-8a44-e45b1a402e6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:57:58,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc95a04c-fe6e-4e35-8a44-e45b1a402e6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:57:58,589] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2023-06-28 23:57:58,589] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 23:57:58,589] [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	97.4032	559	607	95	conclusive
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	97.3806	558	607	95	conclusive
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.0542	123	607	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.6327	75	607	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.601	76	607	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.5994	76	607	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:57:58,591] [INFO] DFAST Taxonomy check result was written to GCA_017412965.1_ASM1741296v1_genomic.fna/tc_result.tsv
[2023-06-28 23:57:58,592] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:57:58,592] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:57:58,592] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc95a04c-fe6e-4e35-8a44-e45b1a402e6e/dqc_reference/checkm_data
[2023-06-28 23:57:58,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:57:58,622] [INFO] Task started: CheckM
[2023-06-28 23:57:58,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017412965.1_ASM1741296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017412965.1_ASM1741296v1_genomic.fna/checkm_input GCA_017412965.1_ASM1741296v1_genomic.fna/checkm_result
[2023-06-28 23:58:34,820] [INFO] Task succeeded: CheckM
[2023-06-28 23:58:34,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 23:58:34,846] [INFO] ===== Completeness check finished =====
[2023-06-28 23:58:34,846] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:58:34,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017412965.1_ASM1741296v1_genomic.fna/markers.fasta)
[2023-06-28 23:58:34,847] [INFO] Task started: Blastn
[2023-06-28 23:58:34,847] [INFO] Running command: blastn -query GCA_017412965.1_ASM1741296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc95a04c-fe6e-4e35-8a44-e45b1a402e6e/dqc_reference/reference_markers_gtdb.fasta -out GCA_017412965.1_ASM1741296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:58:35,667] [INFO] Task succeeded: Blastn
[2023-06-28 23:58:35,673] [INFO] Selected 5 target genomes.
[2023-06-28 23:58:35,673] [INFO] Target genome list was writen to GCA_017412965.1_ASM1741296v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:58:35,707] [INFO] Task started: fastANI
[2023-06-28 23:58:35,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg133321ce-2dc7-42bf-9772-9380a8daf406/GCA_017412965.1_ASM1741296v1_genomic.fna.gz --refList GCA_017412965.1_ASM1741296v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017412965.1_ASM1741296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:58:39,216] [INFO] Task succeeded: fastANI
[2023-06-28 23:58:39,228] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:58:39,228] [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_000025925.1	s__Prevotella ruminicola	97.4032	559	607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.74	96.82	0.88	0.80	15	conclusive
GCF_900107775.1	s__Prevotella ruminicola_C	94.5778	562	607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.61	0.89	0.89	3	-
GCF_000687715.1	s__Prevotella ruminicola_B	94.0307	562	607	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	90.1953	486	607	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	88.7265	527	607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:58:39,230] [INFO] GTDB search result was written to GCA_017412965.1_ASM1741296v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:58:39,230] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:58:39,233] [INFO] DFAST_QC result json was written to GCA_017412965.1_ASM1741296v1_genomic.fna/dqc_result.json
[2023-06-28 23:58:39,233] [INFO] DFAST_QC completed!
[2023-06-28 23:58:39,233] [INFO] Total running time: 0h1m1s