[2024-01-24 13:45:41,685] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:41,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:41,687] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0826ed8-935c-4bfb-af50-f38a105b426d/dqc_reference
[2024-01-24 13:45:42,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:42,859] [INFO] Task started: Prodigal
[2024-01-24 13:45:42,859] [INFO] Running command: gunzip -c /var/lib/cwl/stgf54ee2c1-9432-44dd-9c3b-d41ed49879d5/GCF_000144405.1_ASM14440v1_genomic.fna.gz | prodigal -d GCF_000144405.1_ASM14440v1_genomic.fna/cds.fna -a GCF_000144405.1_ASM14440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:56,864] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:56,865] [INFO] Task started: HMMsearch
[2024-01-24 13:45:56,865] [INFO] Running command: hmmsearch --tblout GCF_000144405.1_ASM14440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0826ed8-935c-4bfb-af50-f38a105b426d/dqc_reference/reference_markers.hmm GCF_000144405.1_ASM14440v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:57,147] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:57,148] [INFO] Found 6/6 markers.
[2024-01-24 13:45:57,182] [INFO] Query marker FASTA was written to GCF_000144405.1_ASM14440v1_genomic.fna/markers.fasta
[2024-01-24 13:45:57,183] [INFO] Task started: Blastn
[2024-01-24 13:45:57,183] [INFO] Running command: blastn -query GCF_000144405.1_ASM14440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0826ed8-935c-4bfb-af50-f38a105b426d/dqc_reference/reference_markers.fasta -out GCF_000144405.1_ASM14440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:57,802] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:57,807] [INFO] Selected 9 target genomes.
[2024-01-24 13:45:57,807] [INFO] Target genome list was writen to GCF_000144405.1_ASM14440v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:57,828] [INFO] Task started: fastANI
[2024-01-24 13:45:57,829] [INFO] Running command: fastANI --query /var/lib/cwl/stgf54ee2c1-9432-44dd-9c3b-d41ed49879d5/GCF_000144405.1_ASM14440v1_genomic.fna.gz --refList GCF_000144405.1_ASM14440v1_genomic.fna/target_genomes.txt --output GCF_000144405.1_ASM14440v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:06,152] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:06,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0826ed8-935c-4bfb-af50-f38a105b426d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:06,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0826ed8-935c-4bfb-af50-f38a105b426d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:06,161] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:06,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:06,162] [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 melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	100.0	1054	1055	95	conclusive
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	99.9994	1053	1055	95	conclusive
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	88.2097	803	1055	95	below_threshold
Prevotella scopos	strain=JCM 17725	GCA_000614285.1	589437	589437	type	True	88.1855	775	1055	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	88.1533	810	1055	95	below_threshold
Prevotella scopos	strain=DSM 22613	GCA_900129535.1	589437	589437	type	True	88.1394	785	1055	95	below_threshold
Prevotella jejuni	strain=DSM 26989	GCA_900187995.1	1177574	1177574	type	True	86.7281	778	1055	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	81.2317	401	1055	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.319	55	1055	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:06,163] [INFO] DFAST Taxonomy check result was written to GCF_000144405.1_ASM14440v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:06,164] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:06,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:06,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0826ed8-935c-4bfb-af50-f38a105b426d/dqc_reference/checkm_data
[2024-01-24 13:46:06,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:06,197] [INFO] Task started: CheckM
[2024-01-24 13:46:06,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000144405.1_ASM14440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000144405.1_ASM14440v1_genomic.fna/checkm_input GCF_000144405.1_ASM14440v1_genomic.fna/checkm_result
[2024-01-24 13:46:53,103] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:53,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:53,131] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:53,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:53,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000144405.1_ASM14440v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:53,132] [INFO] Task started: Blastn
[2024-01-24 13:46:53,132] [INFO] Running command: blastn -query GCF_000144405.1_ASM14440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0826ed8-935c-4bfb-af50-f38a105b426d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000144405.1_ASM14440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:54,100] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:54,103] [INFO] Selected 8 target genomes.
[2024-01-24 13:46:54,103] [INFO] Target genome list was writen to GCF_000144405.1_ASM14440v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:54,116] [INFO] Task started: fastANI
[2024-01-24 13:46:54,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgf54ee2c1-9432-44dd-9c3b-d41ed49879d5/GCF_000144405.1_ASM14440v1_genomic.fna.gz --refList GCF_000144405.1_ASM14440v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000144405.1_ASM14440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:03,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:03,302] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:03,303] [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_000144405.1	s__Prevotella melaninogenica	100.0	1053	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	conclusive
GCF_018127965.1	s__Prevotella melaninogenica_B	94.8255	882	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.77	95.72	0.91	0.89	4	-
GCF_018127925.1	s__Prevotella melaninogenica_C	94.7233	888	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609775.1	s__Prevotella melaninogenica_A	90.8281	834	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018127785.1	s__Prevotella scopos	88.1514	803	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	-
GCF_018128065.1	s__Prevotella sp000467895	88.0647	774	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCF_900187995.1	s__Prevotella jejuni	86.7392	777	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.57	0.92	0.88	7	-
GCF_000257925.1	s__Prevotella sp000257925	81.6207	426	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:03,306] [INFO] GTDB search result was written to GCF_000144405.1_ASM14440v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:03,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:03,315] [INFO] DFAST_QC result json was written to GCF_000144405.1_ASM14440v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:03,316] [INFO] DFAST_QC completed!
[2024-01-24 13:47:03,316] [INFO] Total running time: 0h1m22s