[2024-01-24 14:38:49,019] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:49,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:49,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg233076e7-16a2-4836-8be7-99729324c3a3/dqc_reference
[2024-01-24 14:38:50,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:50,481] [INFO] Task started: Prodigal
[2024-01-24 14:38:50,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg5986f3de-228e-4025-8d5a-d1a65845ce6b/GCF_014195585.1_ASM1419558v1_genomic.fna.gz | prodigal -d GCF_014195585.1_ASM1419558v1_genomic.fna/cds.fna -a GCF_014195585.1_ASM1419558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:04,964] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:04,964] [INFO] Task started: HMMsearch
[2024-01-24 14:39:04,964] [INFO] Running command: hmmsearch --tblout GCF_014195585.1_ASM1419558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg233076e7-16a2-4836-8be7-99729324c3a3/dqc_reference/reference_markers.hmm GCF_014195585.1_ASM1419558v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:05,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:05,289] [INFO] Found 6/6 markers.
[2024-01-24 14:39:05,315] [INFO] Query marker FASTA was written to GCF_014195585.1_ASM1419558v1_genomic.fna/markers.fasta
[2024-01-24 14:39:05,316] [INFO] Task started: Blastn
[2024-01-24 14:39:05,316] [INFO] Running command: blastn -query GCF_014195585.1_ASM1419558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg233076e7-16a2-4836-8be7-99729324c3a3/dqc_reference/reference_markers.fasta -out GCF_014195585.1_ASM1419558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:05,965] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:05,969] [INFO] Selected 22 target genomes.
[2024-01-24 14:39:05,969] [INFO] Target genome list was writen to GCF_014195585.1_ASM1419558v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:05,978] [INFO] Task started: fastANI
[2024-01-24 14:39:05,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg5986f3de-228e-4025-8d5a-d1a65845ce6b/GCF_014195585.1_ASM1419558v1_genomic.fna.gz --refList GCF_014195585.1_ASM1419558v1_genomic.fna/target_genomes.txt --output GCF_014195585.1_ASM1419558v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:21,570] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:21,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg233076e7-16a2-4836-8be7-99729324c3a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:21,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg233076e7-16a2-4836-8be7-99729324c3a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:21,576] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:21,576] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:21,576] [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
Alloprevotella rava	strain=DSM 22548	GCA_014195585.1	671218	671218	type	True	100.0	837	839	95	conclusive
Alloprevotella tannerae	strain=ATCC 51259	GCA_000159995.1	76122	76122	type	True	79.8372	70	839	95	below_threshold
Prevotellamassilia timonensis	strain=Marseille-P2831	GCA_900106785.1	1852370	1852370	type	True	77.2704	55	839	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:21,578] [INFO] DFAST Taxonomy check result was written to GCF_014195585.1_ASM1419558v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:21,578] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:21,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:21,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg233076e7-16a2-4836-8be7-99729324c3a3/dqc_reference/checkm_data
[2024-01-24 14:39:21,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:21,610] [INFO] Task started: CheckM
[2024-01-24 14:39:21,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014195585.1_ASM1419558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014195585.1_ASM1419558v1_genomic.fna/checkm_input GCF_014195585.1_ASM1419558v1_genomic.fna/checkm_result
[2024-01-24 14:40:05,772] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:05,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:05,792] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:05,792] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:05,792] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014195585.1_ASM1419558v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:05,793] [INFO] Task started: Blastn
[2024-01-24 14:40:05,793] [INFO] Running command: blastn -query GCF_014195585.1_ASM1419558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg233076e7-16a2-4836-8be7-99729324c3a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014195585.1_ASM1419558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:06,917] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:06,923] [INFO] Selected 28 target genomes.
[2024-01-24 14:40:06,923] [INFO] Target genome list was writen to GCF_014195585.1_ASM1419558v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:06,950] [INFO] Task started: fastANI
[2024-01-24 14:40:06,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg5986f3de-228e-4025-8d5a-d1a65845ce6b/GCF_014195585.1_ASM1419558v1_genomic.fna.gz --refList GCF_014195585.1_ASM1419558v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014195585.1_ASM1419558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:22,090] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:22,101] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:22,101] [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_014195585.1	s__Alloprevotella rava	100.0	837	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	96.85	96.85	0.93	0.93	2	conclusive
GCF_000159995.1	s__Alloprevotella tannerae	79.8828	70	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	96.74	96.60	0.92	0.92	3	-
GCA_015259125.1	s__Alloprevotella tannerae_A	77.7584	60	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	97.55	97.55	0.94	0.94	2	-
GCA_900540885.1	s__Alloprevotella sp900540885	77.3876	53	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	97.94	97.84	0.88	0.83	3	-
GCA_000437675.1	s__Alloprevotella sp000437675	76.8584	66	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	99.30	98.80	0.87	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:22,107] [INFO] GTDB search result was written to GCF_014195585.1_ASM1419558v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:22,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:22,112] [INFO] DFAST_QC result json was written to GCF_014195585.1_ASM1419558v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:22,112] [INFO] DFAST_QC completed!
[2024-01-24 14:40:22,112] [INFO] Total running time: 0h1m33s