[2023-06-13 15:57:54,532] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:57:54,542] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:57:54,542] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe105edd-2843-4870-ab60-e54e5820488a/dqc_reference
[2023-06-13 15:57:57,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:57:57,273] [INFO] Task started: Prodigal
[2023-06-13 15:57:57,273] [INFO] Running command: gunzip -c /var/lib/cwl/stgc067fbc9-4d84-4bf2-898e-cd20adcef10d/GCA_022744745.1_ASM2274474v1_genomic.fna.gz | prodigal -d GCA_022744745.1_ASM2274474v1_genomic.fna/cds.fna -a GCA_022744745.1_ASM2274474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:58:05,040] [INFO] Task succeeded: Prodigal
[2023-06-13 15:58:05,040] [INFO] Task started: HMMsearch
[2023-06-13 15:58:05,040] [INFO] Running command: hmmsearch --tblout GCA_022744745.1_ASM2274474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe105edd-2843-4870-ab60-e54e5820488a/dqc_reference/reference_markers.hmm GCA_022744745.1_ASM2274474v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:58:05,322] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:58:05,324] [INFO] Found 6/6 markers.
[2023-06-13 15:58:05,383] [INFO] Query marker FASTA was written to GCA_022744745.1_ASM2274474v1_genomic.fna/markers.fasta
[2023-06-13 15:58:05,384] [INFO] Task started: Blastn
[2023-06-13 15:58:05,384] [INFO] Running command: blastn -query GCA_022744745.1_ASM2274474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe105edd-2843-4870-ab60-e54e5820488a/dqc_reference/reference_markers.fasta -out GCA_022744745.1_ASM2274474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:58:06,044] [INFO] Task succeeded: Blastn
[2023-06-13 15:58:06,049] [INFO] Selected 26 target genomes.
[2023-06-13 15:58:06,050] [INFO] Target genome list was writen to GCA_022744745.1_ASM2274474v1_genomic.fna/target_genomes.txt
[2023-06-13 15:58:06,060] [INFO] Task started: fastANI
[2023-06-13 15:58:06,060] [INFO] Running command: fastANI --query /var/lib/cwl/stgc067fbc9-4d84-4bf2-898e-cd20adcef10d/GCA_022744745.1_ASM2274474v1_genomic.fna.gz --refList GCA_022744745.1_ASM2274474v1_genomic.fna/target_genomes.txt --output GCA_022744745.1_ASM2274474v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:58:20,663] [INFO] Task succeeded: fastANI
[2023-06-13 15:58:20,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe105edd-2843-4870-ab60-e54e5820488a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:58:20,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe105edd-2843-4870-ab60-e54e5820488a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:58:20,671] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:58:20,671] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:58:20,671] [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 copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	88.4784	125	779	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	88.3514	131	779	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	88.09	127	779	95	below_threshold
Dialister succinatiphilus	strain=YIT 11850	GCA_000242435.1	487173	487173	type	True	79.7087	139	779	95	below_threshold
Dialister invisus	strain=DSM 15470	GCA_000160055.1	218538	218538	type	True	79.5059	53	779	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:58:20,677] [INFO] DFAST Taxonomy check result was written to GCA_022744745.1_ASM2274474v1_genomic.fna/tc_result.tsv
[2023-06-13 15:58:20,678] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:58:20,678] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:58:20,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe105edd-2843-4870-ab60-e54e5820488a/dqc_reference/checkm_data
[2023-06-13 15:58:20,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:58:20,722] [INFO] Task started: CheckM
[2023-06-13 15:58:20,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022744745.1_ASM2274474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022744745.1_ASM2274474v1_genomic.fna/checkm_input GCA_022744745.1_ASM2274474v1_genomic.fna/checkm_result
[2023-06-13 15:58:51,591] [INFO] Task succeeded: CheckM
[2023-06-13 15:58:51,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 14.58%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:58:51,623] [INFO] ===== Completeness check finished =====
[2023-06-13 15:58:51,623] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:58:51,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022744745.1_ASM2274474v1_genomic.fna/markers.fasta)
[2023-06-13 15:58:51,624] [INFO] Task started: Blastn
[2023-06-13 15:58:51,624] [INFO] Running command: blastn -query GCA_022744745.1_ASM2274474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe105edd-2843-4870-ab60-e54e5820488a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022744745.1_ASM2274474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:58:52,717] [INFO] Task succeeded: Blastn
[2023-06-13 15:58:52,724] [INFO] Selected 14 target genomes.
[2023-06-13 15:58:52,724] [INFO] Target genome list was writen to GCA_022744745.1_ASM2274474v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:58:52,730] [INFO] Task started: fastANI
[2023-06-13 15:58:52,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgc067fbc9-4d84-4bf2-898e-cd20adcef10d/GCA_022744745.1_ASM2274474v1_genomic.fna.gz --refList GCA_022744745.1_ASM2274474v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022744745.1_ASM2274474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:59:03,661] [INFO] Task succeeded: fastANI
[2023-06-13 15:59:03,675] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:59:03,676] [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_000434475.1	s__Dialister sp000434475	95.6893	374	779	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	96.42	95.78	0.79	0.72	9	conclusive
GCA_900543455.1	s__Dialister sp900543455	93.3459	382	779	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543165.1	s__Dialister sp900543165	93.1994	391	779	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	98.68	98.63	0.86	0.84	3	-
GCF_015074785.1	s__Prevotella sp015074785	88.8675	144	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_019127135.1	s__Prevotella sp900551275	88.7853	140	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCA_900557255.1	s__Prevotella sp900557255	88.5465	102	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000157935.1	s__Prevotella copri	88.0867	133	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_900551985.1	s__Prevotella sp900551985	82.8535	98	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_900538805.1	s__Dialister sp900538805	79.5449	130	779	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	96.71	96.58	0.85	0.82	3	-
GCF_007164725.1	s__Dialister hominis	79.4107	145	779	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	99.17	99.05	0.95	0.90	7	-
GCA_002297935.1	s__Dialister sp002297935	79.2339	160	779	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541605.1	s__Dialister sp900541605	78.8156	141	779	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	98.13	96.92	0.86	0.81	3	-
GCA_900765565.1	s__Dialister sp900765565	78.2579	137	779	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister	95.0	99.94	99.94	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-13 15:59:03,680] [INFO] GTDB search result was written to GCA_022744745.1_ASM2274474v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:59:03,681] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:59:03,689] [INFO] DFAST_QC result json was written to GCA_022744745.1_ASM2274474v1_genomic.fna/dqc_result.json
[2023-06-13 15:59:03,690] [INFO] DFAST_QC completed!
[2023-06-13 15:59:03,690] [INFO] Total running time: 0h1m9s