[2023-06-13 21:59:05,760] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:59:05,764] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:59:05,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f392e54-0af9-45b8-9b1b-1589706f993c/dqc_reference
[2023-06-13 21:59:07,008] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:59:07,009] [INFO] Task started: Prodigal
[2023-06-13 21:59:07,009] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a9645fd-753e-4296-9f2e-5235051e694e/GCA_022738795.1_ASM2273879v1_genomic.fna.gz | prodigal -d GCA_022738795.1_ASM2273879v1_genomic.fna/cds.fna -a GCA_022738795.1_ASM2273879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:59:20,332] [INFO] Task succeeded: Prodigal
[2023-06-13 21:59:20,332] [INFO] Task started: HMMsearch
[2023-06-13 21:59:20,332] [INFO] Running command: hmmsearch --tblout GCA_022738795.1_ASM2273879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f392e54-0af9-45b8-9b1b-1589706f993c/dqc_reference/reference_markers.hmm GCA_022738795.1_ASM2273879v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:59:20,512] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:59:20,514] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1a9645fd-753e-4296-9f2e-5235051e694e/GCA_022738795.1_ASM2273879v1_genomic.fna.gz]
[2023-06-13 21:59:20,540] [INFO] Query marker FASTA was written to GCA_022738795.1_ASM2273879v1_genomic.fna/markers.fasta
[2023-06-13 21:59:20,541] [INFO] Task started: Blastn
[2023-06-13 21:59:20,541] [INFO] Running command: blastn -query GCA_022738795.1_ASM2273879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f392e54-0af9-45b8-9b1b-1589706f993c/dqc_reference/reference_markers.fasta -out GCA_022738795.1_ASM2273879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:59:21,097] [INFO] Task succeeded: Blastn
[2023-06-13 21:59:21,101] [INFO] Selected 16 target genomes.
[2023-06-13 21:59:21,102] [INFO] Target genome list was writen to GCA_022738795.1_ASM2273879v1_genomic.fna/target_genomes.txt
[2023-06-13 21:59:21,103] [INFO] Task started: fastANI
[2023-06-13 21:59:21,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a9645fd-753e-4296-9f2e-5235051e694e/GCA_022738795.1_ASM2273879v1_genomic.fna.gz --refList GCA_022738795.1_ASM2273879v1_genomic.fna/target_genomes.txt --output GCA_022738795.1_ASM2273879v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:59:28,532] [INFO] Task succeeded: fastANI
[2023-06-13 21:59:28,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f392e54-0af9-45b8-9b1b-1589706f993c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:59:28,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f392e54-0af9-45b8-9b1b-1589706f993c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:59:28,541] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:59:28,541] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:59:28,542] [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_009495405.1	165179	165179	suspected-type	True	80.4445	204	466	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	80.3488	210	466	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	80.231	214	466	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	79.9412	186	466	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.2295	63	466	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.2178	65	466	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.7858	66	466	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:59:28,545] [INFO] DFAST Taxonomy check result was written to GCA_022738795.1_ASM2273879v1_genomic.fna/tc_result.tsv
[2023-06-13 21:59:28,546] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:59:28,546] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:59:28,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f392e54-0af9-45b8-9b1b-1589706f993c/dqc_reference/checkm_data
[2023-06-13 21:59:28,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:59:28,576] [INFO] Task started: CheckM
[2023-06-13 21:59:28,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022738795.1_ASM2273879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022738795.1_ASM2273879v1_genomic.fna/checkm_input GCA_022738795.1_ASM2273879v1_genomic.fna/checkm_result
[2023-06-13 22:00:09,160] [INFO] Task succeeded: CheckM
[2023-06-13 22:00:09,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.30%
Contamintation: 9.72%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 22:00:09,183] [INFO] ===== Completeness check finished =====
[2023-06-13 22:00:09,183] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:00:09,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022738795.1_ASM2273879v1_genomic.fna/markers.fasta)
[2023-06-13 22:00:09,184] [INFO] Task started: Blastn
[2023-06-13 22:00:09,184] [INFO] Running command: blastn -query GCA_022738795.1_ASM2273879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f392e54-0af9-45b8-9b1b-1589706f993c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022738795.1_ASM2273879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:00:09,956] [INFO] Task succeeded: Blastn
[2023-06-13 22:00:09,960] [INFO] Selected 14 target genomes.
[2023-06-13 22:00:09,960] [INFO] Target genome list was writen to GCA_022738795.1_ASM2273879v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:00:09,961] [INFO] Task started: fastANI
[2023-06-13 22:00:09,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a9645fd-753e-4296-9f2e-5235051e694e/GCA_022738795.1_ASM2273879v1_genomic.fna.gz --refList GCA_022738795.1_ASM2273879v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022738795.1_ASM2273879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:00:17,411] [INFO] Task succeeded: fastANI
[2023-06-13 22:00:17,423] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 22:00:17,424] [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_009495355.1	s__Prevotella sp900313215	96.865	365	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.34	96.92	0.81	0.74	15	conclusive
GCA_900556395.1	s__Prevotella sp900556395	85.9326	297	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.81	0.83	0.82	3	-
GCA_002439605.1	s__Prevotella sp002439605	84.3595	265	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.57	99.57	0.81	0.81	2	-
GCF_002224675.1	s__Prevotella copri_A	82.4645	221	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	-
GCA_900544825.1	s__Prevotella sp900544825	82.4611	208	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCF_015074785.1	s__Prevotella sp015074785	81.0187	241	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_009494395.1	s__Prevotella sp900546535	80.6763	230	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCF_000157935.1	s__Prevotella copri	80.3489	210	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_900555035.1	s__Prevotella sp900555035	80.2987	184	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765465.1	s__Prevotella sp900765465	80.153	118	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556795.1	s__Prevotella sp900556795	79.7284	135	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.39	96.16	0.81	0.77	3	-
GCA_002451555.1	s__Prevotella sp002451555	79.1157	184	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.47	99.47	0.85	0.85	2	-
GCA_900548535.1	s__Prevotella sp900548535	79.0995	186	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436035.1	s__Prevotella sp000436035	79.0709	180	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.58	97.92	0.86	0.81	4	-
--------------------------------------------------------------------------------
[2023-06-13 22:00:17,426] [INFO] GTDB search result was written to GCA_022738795.1_ASM2273879v1_genomic.fna/result_gtdb.tsv
[2023-06-13 22:00:17,427] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:00:17,431] [INFO] DFAST_QC result json was written to GCA_022738795.1_ASM2273879v1_genomic.fna/dqc_result.json
[2023-06-13 22:00:17,431] [INFO] DFAST_QC completed!
[2023-06-13 22:00:17,431] [INFO] Total running time: 0h1m12s