[2023-06-14 02:10:52,071] [INFO] DFAST_QC pipeline started.
[2023-06-14 02:10:52,074] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 02:10:52,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f7e5adb-46bd-4caf-9bf8-fc1468fcafc3/dqc_reference
[2023-06-14 02:10:53,453] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 02:10:53,454] [INFO] Task started: Prodigal
[2023-06-14 02:10:53,454] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9a9629d-4af5-41a9-b2e2-bed3dca27b24/GCA_022649285.1_ASM2264928v1_genomic.fna.gz | prodigal -d GCA_022649285.1_ASM2264928v1_genomic.fna/cds.fna -a GCA_022649285.1_ASM2264928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 02:11:05,181] [INFO] Task succeeded: Prodigal
[2023-06-14 02:11:05,181] [INFO] Task started: HMMsearch
[2023-06-14 02:11:05,182] [INFO] Running command: hmmsearch --tblout GCA_022649285.1_ASM2264928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f7e5adb-46bd-4caf-9bf8-fc1468fcafc3/dqc_reference/reference_markers.hmm GCA_022649285.1_ASM2264928v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 02:11:05,419] [INFO] Task succeeded: HMMsearch
[2023-06-14 02:11:05,421] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf9a9629d-4af5-41a9-b2e2-bed3dca27b24/GCA_022649285.1_ASM2264928v1_genomic.fna.gz]
[2023-06-14 02:11:05,450] [INFO] Query marker FASTA was written to GCA_022649285.1_ASM2264928v1_genomic.fna/markers.fasta
[2023-06-14 02:11:05,450] [INFO] Task started: Blastn
[2023-06-14 02:11:05,450] [INFO] Running command: blastn -query GCA_022649285.1_ASM2264928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f7e5adb-46bd-4caf-9bf8-fc1468fcafc3/dqc_reference/reference_markers.fasta -out GCA_022649285.1_ASM2264928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 02:11:06,060] [INFO] Task succeeded: Blastn
[2023-06-14 02:11:06,064] [INFO] Selected 25 target genomes.
[2023-06-14 02:11:06,065] [INFO] Target genome list was writen to GCA_022649285.1_ASM2264928v1_genomic.fna/target_genomes.txt
[2023-06-14 02:11:06,066] [INFO] Task started: fastANI
[2023-06-14 02:11:06,066] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9a9629d-4af5-41a9-b2e2-bed3dca27b24/GCA_022649285.1_ASM2264928v1_genomic.fna.gz --refList GCA_022649285.1_ASM2264928v1_genomic.fna/target_genomes.txt --output GCA_022649285.1_ASM2264928v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 02:11:20,004] [INFO] Task succeeded: fastANI
[2023-06-14 02:11:20,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f7e5adb-46bd-4caf-9bf8-fc1468fcafc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 02:11:20,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f7e5adb-46bd-4caf-9bf8-fc1468fcafc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 02:11:20,020] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 02:11:20,020] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 02:11:20,020] [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 cerevisiae	strain=DSM 100619	GCA_024054555.1	2053716	2053716	type	True	80.2599	368	796	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.8062	56	796	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	76.7277	58	796	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.4286	50	796	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.3202	52	796	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.2755	52	796	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.2533	54	796	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 02:11:20,022] [INFO] DFAST Taxonomy check result was written to GCA_022649285.1_ASM2264928v1_genomic.fna/tc_result.tsv
[2023-06-14 02:11:20,023] [INFO] ===== Taxonomy check completed =====
[2023-06-14 02:11:20,023] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 02:11:20,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f7e5adb-46bd-4caf-9bf8-fc1468fcafc3/dqc_reference/checkm_data
[2023-06-14 02:11:20,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 02:11:20,056] [INFO] Task started: CheckM
[2023-06-14 02:11:20,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022649285.1_ASM2264928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022649285.1_ASM2264928v1_genomic.fna/checkm_input GCA_022649285.1_ASM2264928v1_genomic.fna/checkm_result
[2023-06-14 02:11:58,767] [INFO] Task succeeded: CheckM
[2023-06-14 02:11:58,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 02:11:58,792] [INFO] ===== Completeness check finished =====
[2023-06-14 02:11:58,793] [INFO] ===== Start GTDB Search =====
[2023-06-14 02:11:58,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022649285.1_ASM2264928v1_genomic.fna/markers.fasta)
[2023-06-14 02:11:58,793] [INFO] Task started: Blastn
[2023-06-14 02:11:58,793] [INFO] Running command: blastn -query GCA_022649285.1_ASM2264928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f7e5adb-46bd-4caf-9bf8-fc1468fcafc3/dqc_reference/reference_markers_gtdb.fasta -out GCA_022649285.1_ASM2264928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 02:11:59,787] [INFO] Task succeeded: Blastn
[2023-06-14 02:11:59,792] [INFO] Selected 23 target genomes.
[2023-06-14 02:11:59,792] [INFO] Target genome list was writen to GCA_022649285.1_ASM2264928v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 02:11:59,795] [INFO] Task started: fastANI
[2023-06-14 02:11:59,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9a9629d-4af5-41a9-b2e2-bed3dca27b24/GCA_022649285.1_ASM2264928v1_genomic.fna.gz --refList GCA_022649285.1_ASM2264928v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022649285.1_ASM2264928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 02:12:10,395] [INFO] Task succeeded: fastANI
[2023-06-14 02:12:10,409] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 02:12:10,409] [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_002409785.1	s__Prevotella sp002409785	99.2291	674	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.35	99.13	0.87	0.82	3	conclusive
GCA_003483565.1	s__Prevotella sp003483565	78.4805	66	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.31	99.31	0.72	0.72	2	-
GCF_000426565.1	s__Prevotella albensis	76.731	59	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.96	99.96	1.00	1.00	2	-
GCF_019127135.1	s__Prevotella sp900551275	76.3886	57	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCF_000424185.1	s__Prevotella sp000424185	76.3864	62	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015074785.1	s__Prevotella sp015074785	76.3232	52	796	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	76.2998	54	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCF_009494395.1	s__Prevotella sp900546535	76.0247	55	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
--------------------------------------------------------------------------------
[2023-06-14 02:12:10,411] [INFO] GTDB search result was written to GCA_022649285.1_ASM2264928v1_genomic.fna/result_gtdb.tsv
[2023-06-14 02:12:10,412] [INFO] ===== GTDB Search completed =====
[2023-06-14 02:12:10,415] [INFO] DFAST_QC result json was written to GCA_022649285.1_ASM2264928v1_genomic.fna/dqc_result.json
[2023-06-14 02:12:10,416] [INFO] DFAST_QC completed!
[2023-06-14 02:12:10,416] [INFO] Total running time: 0h1m18s