[2023-06-13 22:41:37,790] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:41:37,793] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:41:37,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a66e9a5-5e22-42d0-88f6-da2ab350195a/dqc_reference
[2023-06-13 22:41:39,164] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:41:39,165] [INFO] Task started: Prodigal
[2023-06-13 22:41:39,166] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c6070f6-7eb3-4635-8381-d432172e7f69/GCA_022722515.1_ASM2272251v1_genomic.fna.gz | prodigal -d GCA_022722515.1_ASM2272251v1_genomic.fna/cds.fna -a GCA_022722515.1_ASM2272251v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:41:56,902] [INFO] Task succeeded: Prodigal
[2023-06-13 22:41:56,903] [INFO] Task started: HMMsearch
[2023-06-13 22:41:56,903] [INFO] Running command: hmmsearch --tblout GCA_022722515.1_ASM2272251v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a66e9a5-5e22-42d0-88f6-da2ab350195a/dqc_reference/reference_markers.hmm GCA_022722515.1_ASM2272251v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:41:57,127] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:41:57,129] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5c6070f6-7eb3-4635-8381-d432172e7f69/GCA_022722515.1_ASM2272251v1_genomic.fna.gz]
[2023-06-13 22:41:57,162] [INFO] Query marker FASTA was written to GCA_022722515.1_ASM2272251v1_genomic.fna/markers.fasta
[2023-06-13 22:41:57,162] [INFO] Task started: Blastn
[2023-06-13 22:41:57,163] [INFO] Running command: blastn -query GCA_022722515.1_ASM2272251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a66e9a5-5e22-42d0-88f6-da2ab350195a/dqc_reference/reference_markers.fasta -out GCA_022722515.1_ASM2272251v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:41:57,744] [INFO] Task succeeded: Blastn
[2023-06-13 22:41:57,749] [INFO] Selected 14 target genomes.
[2023-06-13 22:41:57,749] [INFO] Target genome list was writen to GCA_022722515.1_ASM2272251v1_genomic.fna/target_genomes.txt
[2023-06-13 22:41:57,751] [INFO] Task started: fastANI
[2023-06-13 22:41:57,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c6070f6-7eb3-4635-8381-d432172e7f69/GCA_022722515.1_ASM2272251v1_genomic.fna.gz --refList GCA_022722515.1_ASM2272251v1_genomic.fna/target_genomes.txt --output GCA_022722515.1_ASM2272251v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:42:05,728] [INFO] Task succeeded: fastANI
[2023-06-13 22:42:05,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a66e9a5-5e22-42d0-88f6-da2ab350195a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:42:05,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a66e9a5-5e22-42d0-88f6-da2ab350195a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:42:05,742] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:42:05,742] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 22:42:05,742] [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_000157935.1	165179	165179	suspected-type	True	85.1323	561	975	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	85.0856	551	975	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	84.8762	574	975	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	83.3546	475	975	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	78.1301	135	975	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.418	62	975	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.2346	125	975	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.1871	127	975	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.1402	111	975	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.8248	104	975	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.7822	72	975	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	76.5686	52	975	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	76.4907	54	975	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 22:42:05,745] [INFO] DFAST Taxonomy check result was written to GCA_022722515.1_ASM2272251v1_genomic.fna/tc_result.tsv
[2023-06-13 22:42:05,745] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:42:05,745] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:42:05,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a66e9a5-5e22-42d0-88f6-da2ab350195a/dqc_reference/checkm_data
[2023-06-13 22:42:05,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:42:05,785] [INFO] Task started: CheckM
[2023-06-13 22:42:05,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022722515.1_ASM2272251v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022722515.1_ASM2272251v1_genomic.fna/checkm_input GCA_022722515.1_ASM2272251v1_genomic.fna/checkm_result
[2023-06-13 22:42:57,455] [INFO] Task succeeded: CheckM
[2023-06-13 22:42:57,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.55%
Contamintation: 9.72%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 22:42:57,493] [INFO] ===== Completeness check finished =====
[2023-06-13 22:42:57,493] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:42:57,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022722515.1_ASM2272251v1_genomic.fna/markers.fasta)
[2023-06-13 22:42:57,494] [INFO] Task started: Blastn
[2023-06-13 22:42:57,494] [INFO] Running command: blastn -query GCA_022722515.1_ASM2272251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a66e9a5-5e22-42d0-88f6-da2ab350195a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022722515.1_ASM2272251v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:42:58,305] [INFO] Task succeeded: Blastn
[2023-06-13 22:42:58,309] [INFO] Selected 7 target genomes.
[2023-06-13 22:42:58,309] [INFO] Target genome list was writen to GCA_022722515.1_ASM2272251v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:42:58,310] [INFO] Task started: fastANI
[2023-06-13 22:42:58,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c6070f6-7eb3-4635-8381-d432172e7f69/GCA_022722515.1_ASM2272251v1_genomic.fna.gz --refList GCA_022722515.1_ASM2272251v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022722515.1_ASM2272251v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:43:02,872] [INFO] Task succeeded: fastANI
[2023-06-13 22:43:02,880] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 22:43:02,880] [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_002224675.1	s__Prevotella copri_A	95.7979	741	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	conclusive
GCA_900557035.1	s__Prevotella sp900557035	94.3225	492	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCA_900544825.1	s__Prevotella sp900544825	94.003	711	975	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	93.7874	626	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_900765465.1	s__Prevotella sp900765465	91.8087	388	975	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	86.9455	628	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCA_900556795.1	s__Prevotella sp900556795	86.8672	341	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.39	96.16	0.81	0.77	3	-
--------------------------------------------------------------------------------
[2023-06-13 22:43:02,882] [INFO] GTDB search result was written to GCA_022722515.1_ASM2272251v1_genomic.fna/result_gtdb.tsv
[2023-06-13 22:43:02,884] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:43:02,902] [INFO] DFAST_QC result json was written to GCA_022722515.1_ASM2272251v1_genomic.fna/dqc_result.json
[2023-06-13 22:43:02,903] [INFO] DFAST_QC completed!
[2023-06-13 22:43:02,903] [INFO] Total running time: 0h1m25s