[2024-01-25 19:39:05,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:05,635] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:05,635] [INFO] DQC Reference Directory: /var/lib/cwl/stge5db2d65-5c28-4da4-ad40-1396730cdd31/dqc_reference
[2024-01-25 19:39:06,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:06,789] [INFO] Task started: Prodigal
[2024-01-25 19:39:06,790] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8979fc1-12d7-40b4-a470-60a4394ab96e/GCF_000585355.1_ASM58535v1_genomic.fna.gz | prodigal -d GCF_000585355.1_ASM58535v1_genomic.fna/cds.fna -a GCF_000585355.1_ASM58535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:18,235] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:18,236] [INFO] Task started: HMMsearch
[2024-01-25 19:39:18,236] [INFO] Running command: hmmsearch --tblout GCF_000585355.1_ASM58535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5db2d65-5c28-4da4-ad40-1396730cdd31/dqc_reference/reference_markers.hmm GCF_000585355.1_ASM58535v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:18,495] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:18,500] [INFO] Found 6/6 markers.
[2024-01-25 19:39:18,540] [INFO] Query marker FASTA was written to GCF_000585355.1_ASM58535v1_genomic.fna/markers.fasta
[2024-01-25 19:39:18,540] [INFO] Task started: Blastn
[2024-01-25 19:39:18,541] [INFO] Running command: blastn -query GCF_000585355.1_ASM58535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5db2d65-5c28-4da4-ad40-1396730cdd31/dqc_reference/reference_markers.fasta -out GCF_000585355.1_ASM58535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:19,145] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:19,152] [INFO] Selected 25 target genomes.
[2024-01-25 19:39:19,152] [INFO] Target genome list was writen to GCF_000585355.1_ASM58535v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:19,164] [INFO] Task started: fastANI
[2024-01-25 19:39:19,164] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8979fc1-12d7-40b4-a470-60a4394ab96e/GCF_000585355.1_ASM58535v1_genomic.fna.gz --refList GCF_000585355.1_ASM58535v1_genomic.fna/target_genomes.txt --output GCF_000585355.1_ASM58535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:32,700] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:32,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5db2d65-5c28-4da4-ad40-1396730cdd31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:32,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5db2d65-5c28-4da4-ad40-1396730cdd31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:32,706] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:39:32,706] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:32,706] [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 oryzae	strain=DSM 17970	GCA_000585355.1	185293	185293	type	True	100.0	1095	1095	95	conclusive
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	79.4366	179	1095	95	below_threshold
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	79.3696	53	1095	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.6299	70	1095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:32,708] [INFO] DFAST Taxonomy check result was written to GCF_000585355.1_ASM58535v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:32,708] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:32,708] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:32,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5db2d65-5c28-4da4-ad40-1396730cdd31/dqc_reference/checkm_data
[2024-01-25 19:39:32,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:32,744] [INFO] Task started: CheckM
[2024-01-25 19:39:32,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000585355.1_ASM58535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000585355.1_ASM58535v1_genomic.fna/checkm_input GCF_000585355.1_ASM58535v1_genomic.fna/checkm_result
[2024-01-25 19:40:08,315] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:08,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:08,359] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:08,360] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:08,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000585355.1_ASM58535v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:08,361] [INFO] Task started: Blastn
[2024-01-25 19:40:08,361] [INFO] Running command: blastn -query GCF_000585355.1_ASM58535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5db2d65-5c28-4da4-ad40-1396730cdd31/dqc_reference/reference_markers_gtdb.fasta -out GCF_000585355.1_ASM58535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:09,158] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:09,163] [INFO] Selected 28 target genomes.
[2024-01-25 19:40:09,163] [INFO] Target genome list was writen to GCF_000585355.1_ASM58535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:09,201] [INFO] Task started: fastANI
[2024-01-25 19:40:09,201] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8979fc1-12d7-40b4-a470-60a4394ab96e/GCF_000585355.1_ASM58535v1_genomic.fna.gz --refList GCF_000585355.1_ASM58535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000585355.1_ASM58535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:25,852] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:25,858] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:25,858] [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_000585355.1	s__Prevotella oryzae	100.0	1094	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.65	97.65	0.80	0.80	2	conclusive
GCF_017347605.1	s__Prevotella sp017347605	79.4728	178	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003043925.1	s__Prevotella sp003043925	78.4737	51	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_018054505.1	s__Prevotella sp018054505	77.2095	78	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.05	98.05	0.52	0.52	2	-
GCA_000436695.1	s__Prevotella sp000436695	77.0048	72	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.24	0.85	0.83	3	-
GCF_002251435.1	s__Prevotella sp002251435	76.9516	53	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004535825.1	s__Prevotella hominis	76.5664	69	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.52	95.16	0.76	0.66	13	-
GCA_017410365.1	s__Prevotella sp017410365	76.4552	66	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.93	96.60	0.79	0.74	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:25,860] [INFO] GTDB search result was written to GCF_000585355.1_ASM58535v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:25,860] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:25,865] [INFO] DFAST_QC result json was written to GCF_000585355.1_ASM58535v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:25,865] [INFO] DFAST_QC completed!
[2024-01-25 19:40:25,865] [INFO] Total running time: 0h1m20s