[2024-01-24 12:13:26,523] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:26,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:26,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg8db53d14-3cf8-48a9-acf5-f6a158335e9b/dqc_reference
[2024-01-24 12:13:27,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:27,762] [INFO] Task started: Prodigal
[2024-01-24 12:13:27,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg95929a3a-5737-4b10-91c7-040a4ebb6306/GCF_000159995.1_ASM15999v1_genomic.fna.gz | prodigal -d GCF_000159995.1_ASM15999v1_genomic.fna/cds.fna -a GCF_000159995.1_ASM15999v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:40,991] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:40,991] [INFO] Task started: HMMsearch
[2024-01-24 12:13:40,991] [INFO] Running command: hmmsearch --tblout GCF_000159995.1_ASM15999v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8db53d14-3cf8-48a9-acf5-f6a158335e9b/dqc_reference/reference_markers.hmm GCF_000159995.1_ASM15999v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:41,305] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:41,307] [INFO] Found 6/6 markers.
[2024-01-24 12:13:41,327] [INFO] Query marker FASTA was written to GCF_000159995.1_ASM15999v1_genomic.fna/markers.fasta
[2024-01-24 12:13:41,328] [INFO] Task started: Blastn
[2024-01-24 12:13:41,328] [INFO] Running command: blastn -query GCF_000159995.1_ASM15999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8db53d14-3cf8-48a9-acf5-f6a158335e9b/dqc_reference/reference_markers.fasta -out GCF_000159995.1_ASM15999v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:41,921] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:41,924] [INFO] Selected 24 target genomes.
[2024-01-24 12:13:41,924] [INFO] Target genome list was writen to GCF_000159995.1_ASM15999v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:41,933] [INFO] Task started: fastANI
[2024-01-24 12:13:41,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg95929a3a-5737-4b10-91c7-040a4ebb6306/GCF_000159995.1_ASM15999v1_genomic.fna.gz --refList GCF_000159995.1_ASM15999v1_genomic.fna/target_genomes.txt --output GCF_000159995.1_ASM15999v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:55,719] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:55,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8db53d14-3cf8-48a9-acf5-f6a158335e9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:55,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8db53d14-3cf8-48a9-acf5-f6a158335e9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:55,726] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:55,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:55,726] [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 tannerae	strain=ATCC 51259	GCA_000159995.1	76122	76122	type	True	100.0	860	860	95	conclusive
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_002998435.1	28119	28119	type	True	82.7623	63	860	95	below_threshold
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	82.4697	70	860	95	below_threshold
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_007830715.1	28119	28119	type	True	82.242	58	860	95	below_threshold
Prevotellamassilia timonensis	strain=Marseille-P2831	GCA_900106785.1	1852370	1852370	type	True	81.9131	55	860	95	below_threshold
Alloprevotella rava	strain=DSM 22548	GCA_014195585.1	671218	671218	type	True	80.095	86	860	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:55,732] [INFO] DFAST Taxonomy check result was written to GCF_000159995.1_ASM15999v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:55,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:55,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:55,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8db53d14-3cf8-48a9-acf5-f6a158335e9b/dqc_reference/checkm_data
[2024-01-24 12:13:55,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:55,771] [INFO] Task started: CheckM
[2024-01-24 12:13:55,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000159995.1_ASM15999v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000159995.1_ASM15999v1_genomic.fna/checkm_input GCF_000159995.1_ASM15999v1_genomic.fna/checkm_result
[2024-01-24 12:14:37,821] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:37,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:37,841] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:37,841] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:37,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000159995.1_ASM15999v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:37,842] [INFO] Task started: Blastn
[2024-01-24 12:14:37,842] [INFO] Running command: blastn -query GCF_000159995.1_ASM15999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8db53d14-3cf8-48a9-acf5-f6a158335e9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000159995.1_ASM15999v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:38,896] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:38,901] [INFO] Selected 16 target genomes.
[2024-01-24 12:14:38,901] [INFO] Target genome list was writen to GCF_000159995.1_ASM15999v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:38,958] [INFO] Task started: fastANI
[2024-01-24 12:14:38,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg95929a3a-5737-4b10-91c7-040a4ebb6306/GCF_000159995.1_ASM15999v1_genomic.fna.gz --refList GCF_000159995.1_ASM15999v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000159995.1_ASM15999v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:47,236] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:47,241] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:47,242] [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_000159995.1	s__Alloprevotella tannerae	100.0	860	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	96.74	96.60	0.92	0.92	3	conclusive
GCA_015259125.1	s__Alloprevotella tannerae_A	94.4788	665	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	97.55	97.55	0.94	0.94	2	-
GCA_015259305.1	s__Alloprevotella tannerae_B	93.3368	453	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539625.1	s__Alloprevotella sp900539625	79.2613	55	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.08	97.36	0.88	0.77	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:47,243] [INFO] GTDB search result was written to GCF_000159995.1_ASM15999v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:47,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:47,246] [INFO] DFAST_QC result json was written to GCF_000159995.1_ASM15999v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:47,246] [INFO] DFAST_QC completed!
[2024-01-24 12:14:47,246] [INFO] Total running time: 0h1m21s