[2023-06-29 13:53:43,595] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:53:43,597] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:53:43,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg8353ba86-5431-4f55-b7fb-e84b9f9dac11/dqc_reference
[2023-06-29 13:53:44,931] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:53:44,932] [INFO] Task started: Prodigal
[2023-06-29 13:53:44,932] [INFO] Running command: gunzip -c /var/lib/cwl/stgf55a4526-bc44-42ca-9bba-68cd1f984397/GCA_021624865.1_ASM2162486v1_genomic.fna.gz | prodigal -d GCA_021624865.1_ASM2162486v1_genomic.fna/cds.fna -a GCA_021624865.1_ASM2162486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:54:02,800] [INFO] Task succeeded: Prodigal
[2023-06-29 13:54:02,800] [INFO] Task started: HMMsearch
[2023-06-29 13:54:02,800] [INFO] Running command: hmmsearch --tblout GCA_021624865.1_ASM2162486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8353ba86-5431-4f55-b7fb-e84b9f9dac11/dqc_reference/reference_markers.hmm GCA_021624865.1_ASM2162486v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:54:03,074] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:54:03,075] [INFO] Found 6/6 markers.
[2023-06-29 13:54:03,107] [INFO] Query marker FASTA was written to GCA_021624865.1_ASM2162486v1_genomic.fna/markers.fasta
[2023-06-29 13:54:03,108] [INFO] Task started: Blastn
[2023-06-29 13:54:03,108] [INFO] Running command: blastn -query GCA_021624865.1_ASM2162486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8353ba86-5431-4f55-b7fb-e84b9f9dac11/dqc_reference/reference_markers.fasta -out GCA_021624865.1_ASM2162486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:54:03,704] [INFO] Task succeeded: Blastn
[2023-06-29 13:54:03,708] [INFO] Selected 14 target genomes.
[2023-06-29 13:54:03,708] [INFO] Target genome list was writen to GCA_021624865.1_ASM2162486v1_genomic.fna/target_genomes.txt
[2023-06-29 13:54:03,709] [INFO] Task started: fastANI
[2023-06-29 13:54:03,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgf55a4526-bc44-42ca-9bba-68cd1f984397/GCA_021624865.1_ASM2162486v1_genomic.fna.gz --refList GCA_021624865.1_ASM2162486v1_genomic.fna/target_genomes.txt --output GCA_021624865.1_ASM2162486v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:54:13,226] [INFO] Task succeeded: fastANI
[2023-06-29 13:54:13,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8353ba86-5431-4f55-b7fb-e84b9f9dac11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:54:13,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8353ba86-5431-4f55-b7fb-e84b9f9dac11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:54:13,242] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:54:13,242] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:54:13,242] [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	94.4933	802	1149	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	94.4527	787	1149	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	94.3932	814	1149	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	84.3529	576	1149	95	below_threshold
Prevotella bivia	strain=DSM 20514	GCA_000262545.1	28125	28125	type	True	78.1702	63	1149	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	78.0525	79	1149	95	below_threshold
Prevotella veroralis	strain=DSM 19559	GCA_000377625.1	28137	28137	type	True	77.8418	80	1149	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.7102	138	1149	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	77.2049	76	1149	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.0841	88	1149	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:54:13,244] [INFO] DFAST Taxonomy check result was written to GCA_021624865.1_ASM2162486v1_genomic.fna/tc_result.tsv
[2023-06-29 13:54:13,245] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:54:13,245] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:54:13,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8353ba86-5431-4f55-b7fb-e84b9f9dac11/dqc_reference/checkm_data
[2023-06-29 13:54:13,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:54:13,287] [INFO] Task started: CheckM
[2023-06-29 13:54:13,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021624865.1_ASM2162486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021624865.1_ASM2162486v1_genomic.fna/checkm_input GCA_021624865.1_ASM2162486v1_genomic.fna/checkm_result
[2023-06-29 13:55:06,737] [INFO] Task succeeded: CheckM
[2023-06-29 13:55:06,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:55:06,760] [INFO] ===== Completeness check finished =====
[2023-06-29 13:55:06,760] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:55:06,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021624865.1_ASM2162486v1_genomic.fna/markers.fasta)
[2023-06-29 13:55:06,761] [INFO] Task started: Blastn
[2023-06-29 13:55:06,761] [INFO] Running command: blastn -query GCA_021624865.1_ASM2162486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8353ba86-5431-4f55-b7fb-e84b9f9dac11/dqc_reference/reference_markers_gtdb.fasta -out GCA_021624865.1_ASM2162486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:55:07,628] [INFO] Task succeeded: Blastn
[2023-06-29 13:55:07,633] [INFO] Selected 12 target genomes.
[2023-06-29 13:55:07,634] [INFO] Target genome list was writen to GCA_021624865.1_ASM2162486v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:55:07,635] [INFO] Task started: fastANI
[2023-06-29 13:55:07,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgf55a4526-bc44-42ca-9bba-68cd1f984397/GCA_021624865.1_ASM2162486v1_genomic.fna.gz --refList GCA_021624865.1_ASM2162486v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021624865.1_ASM2162486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:55:16,888] [INFO] Task succeeded: fastANI
[2023-06-29 13:55:16,908] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:55:16,908] [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_019127135.1	s__Prevotella sp900551275	96.8851	916	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	conclusive
GCF_015074785.1	s__Prevotella sp015074785	94.6639	887	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_000157935.1	s__Prevotella copri	94.3687	815	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_900557255.1	s__Prevotella sp900557255	93.2106	504	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009494395.1	s__Prevotella sp900546535	87.7241	750	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCF_002224675.1	s__Prevotella copri_A	87.3344	704	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	-
GCA_019249655.1	s__Prevotella sp900767615	87.0934	727	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCA_900544825.1	s__Prevotella sp900544825	86.4671	637	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCA_900551985.1	s__Prevotella sp900551985	86.159	588	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_900556795.1	s__Prevotella sp900556795	85.5161	354	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.39	96.16	0.81	0.77	3	-
GCA_900557035.1	s__Prevotella sp900557035	84.5261	436	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCA_900765465.1	s__Prevotella sp900765465	83.2065	322	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:55:16,911] [INFO] GTDB search result was written to GCA_021624865.1_ASM2162486v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:55:16,911] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:55:16,915] [INFO] DFAST_QC result json was written to GCA_021624865.1_ASM2162486v1_genomic.fna/dqc_result.json
[2023-06-29 13:55:16,915] [INFO] DFAST_QC completed!
[2023-06-29 13:55:16,915] [INFO] Total running time: 0h1m33s