[2024-01-24 13:08:58,421] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,423] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,423] [INFO] DQC Reference Directory: /var/lib/cwl/stg1925df95-02d0-45b4-bc96-f25eb204abf6/dqc_reference
[2024-01-24 13:08:59,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,646] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,646] [INFO] Running command: gunzip -c /var/lib/cwl/stg8aefa1e1-6b04-4662-bf06-db81cbc9ab03/GCF_025144995.1_ASM2514499v1_genomic.fna.gz | prodigal -d GCF_025144995.1_ASM2514499v1_genomic.fna/cds.fna -a GCF_025144995.1_ASM2514499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:15,511] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:15,511] [INFO] Task started: HMMsearch
[2024-01-24 13:09:15,511] [INFO] Running command: hmmsearch --tblout GCF_025144995.1_ASM2514499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1925df95-02d0-45b4-bc96-f25eb204abf6/dqc_reference/reference_markers.hmm GCF_025144995.1_ASM2514499v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:15,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:15,747] [INFO] Found 6/6 markers.
[2024-01-24 13:09:15,774] [INFO] Query marker FASTA was written to GCF_025144995.1_ASM2514499v1_genomic.fna/markers.fasta
[2024-01-24 13:09:15,775] [INFO] Task started: Blastn
[2024-01-24 13:09:15,775] [INFO] Running command: blastn -query GCF_025144995.1_ASM2514499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1925df95-02d0-45b4-bc96-f25eb204abf6/dqc_reference/reference_markers.fasta -out GCF_025144995.1_ASM2514499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:16,392] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:16,396] [INFO] Selected 11 target genomes.
[2024-01-24 13:09:16,396] [INFO] Target genome list was writen to GCF_025144995.1_ASM2514499v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:16,407] [INFO] Task started: fastANI
[2024-01-24 13:09:16,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aefa1e1-6b04-4662-bf06-db81cbc9ab03/GCF_025144995.1_ASM2514499v1_genomic.fna.gz --refList GCF_025144995.1_ASM2514499v1_genomic.fna/target_genomes.txt --output GCF_025144995.1_ASM2514499v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:22,596] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:22,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1925df95-02d0-45b4-bc96-f25eb204abf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:22,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1925df95-02d0-45b4-bc96-f25eb204abf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:22,612] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:09:22,612] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:22,613] [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
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	100.0	951	952	95	conclusive
Alistipes indistinctus	strain=YIT 12060	GCA_000231275.1	626932	626932	type	True	99.9824	948	952	95	conclusive
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	78.2182	238	952	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_000321205.1	1470347	1470347	type	True	77.9893	234	952	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	77.5888	122	952	95	below_threshold
Gallalistipes aquisgranensis	strain=DSM 108975	GCA_014982715.1	2779358	2779358	type	True	77.4041	157	952	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	77.3503	121	952	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	77.1931	115	952	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	77.183	117	952	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	77.1646	120	952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:22,614] [INFO] DFAST Taxonomy check result was written to GCF_025144995.1_ASM2514499v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:22,615] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:22,616] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:22,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1925df95-02d0-45b4-bc96-f25eb204abf6/dqc_reference/checkm_data
[2024-01-24 13:09:22,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:22,647] [INFO] Task started: CheckM
[2024-01-24 13:09:22,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025144995.1_ASM2514499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025144995.1_ASM2514499v1_genomic.fna/checkm_input GCF_025144995.1_ASM2514499v1_genomic.fna/checkm_result
[2024-01-24 13:10:08,461] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:08,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:08,482] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:08,482] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:08,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025144995.1_ASM2514499v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:08,484] [INFO] Task started: Blastn
[2024-01-24 13:10:08,484] [INFO] Running command: blastn -query GCF_025144995.1_ASM2514499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1925df95-02d0-45b4-bc96-f25eb204abf6/dqc_reference/reference_markers_gtdb.fasta -out GCF_025144995.1_ASM2514499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:09,392] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:09,396] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:09,396] [INFO] Target genome list was writen to GCF_025144995.1_ASM2514499v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:10,056] [INFO] Task started: fastANI
[2024-01-24 13:10:10,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aefa1e1-6b04-4662-bf06-db81cbc9ab03/GCF_025144995.1_ASM2514499v1_genomic.fna.gz --refList GCF_025144995.1_ASM2514499v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025144995.1_ASM2514499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:15,961] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:15,975] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:15,975] [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_000231275.1	s__Alistipes_A indistinctus	99.9824	948	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.29	99.01	0.94	0.90	8	conclusive
GCF_009557455.1	s__Alistipes_A pullistercoris	78.3467	233	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.39	98.63	0.95	0.90	13	-
GCA_900545315.1	s__Alistipes_A sp900545315	78.1582	274	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.99	99.98	0.97	0.95	3	-
GCF_000321205.1	s__Alistipes_A ihumii	77.9893	234	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.03	98.23	0.96	0.93	6	-
GCA_900539755.1	s__Alistipes_A sp900539755	77.9561	240	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	98.49	96.99	0.95	0.92	3	-
GCA_017415005.1	s__RGIG1874 sp017415005	77.9066	172	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG1874	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583985.1	s__Alistipes_A sp910583985	77.76	212	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549685.1	s__Alistipes_A sp900549685	77.6296	183	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014982715.1	s__DSM-108975 sp014982715	77.4041	157	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__DSM-108975	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290115.1	s__Alistipes excrementigallinarum	77.1902	93	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.90	98.75	0.93	0.91	6	-
GCA_017935625.1	s__RGIG9113 sp017935625	77.0453	86	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG9113	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116245.1	s__Tidjanibacter faecipullorum	76.6811	89	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214725.1	s__Alistipes sp905214725	76.5579	72	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:15,977] [INFO] GTDB search result was written to GCF_025144995.1_ASM2514499v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:15,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:15,981] [INFO] DFAST_QC result json was written to GCF_025144995.1_ASM2514499v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:15,982] [INFO] DFAST_QC completed!
[2024-01-24 13:10:15,982] [INFO] Total running time: 0h1m18s