[2024-01-24 14:22:02,180] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:02,181] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:02,181] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0d43f10-7100-4a5f-9f69-d42c1051ad4b/dqc_reference
[2024-01-24 14:22:03,472] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:03,473] [INFO] Task started: Prodigal
[2024-01-24 14:22:03,473] [INFO] Running command: gunzip -c /var/lib/cwl/stg7dc64f04-da48-4652-983e-677c2ad657c6/GCF_025567065.1_ASM2556706v1_genomic.fna.gz | prodigal -d GCF_025567065.1_ASM2556706v1_genomic.fna/cds.fna -a GCF_025567065.1_ASM2556706v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:10,367] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:10,368] [INFO] Task started: HMMsearch
[2024-01-24 14:22:10,368] [INFO] Running command: hmmsearch --tblout GCF_025567065.1_ASM2556706v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0d43f10-7100-4a5f-9f69-d42c1051ad4b/dqc_reference/reference_markers.hmm GCF_025567065.1_ASM2556706v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:10,649] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:10,650] [INFO] Found 6/6 markers.
[2024-01-24 14:22:10,692] [INFO] Query marker FASTA was written to GCF_025567065.1_ASM2556706v1_genomic.fna/markers.fasta
[2024-01-24 14:22:10,693] [INFO] Task started: Blastn
[2024-01-24 14:22:10,693] [INFO] Running command: blastn -query GCF_025567065.1_ASM2556706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0d43f10-7100-4a5f-9f69-d42c1051ad4b/dqc_reference/reference_markers.fasta -out GCF_025567065.1_ASM2556706v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:11,436] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:11,440] [INFO] Selected 8 target genomes.
[2024-01-24 14:22:11,440] [INFO] Target genome list was writen to GCF_025567065.1_ASM2556706v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:11,456] [INFO] Task started: fastANI
[2024-01-24 14:22:11,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dc64f04-da48-4652-983e-677c2ad657c6/GCF_025567065.1_ASM2556706v1_genomic.fna.gz --refList GCF_025567065.1_ASM2556706v1_genomic.fna/target_genomes.txt --output GCF_025567065.1_ASM2556706v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:16,860] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:16,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0d43f10-7100-4a5f-9f69-d42c1051ad4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:16,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0d43f10-7100-4a5f-9f69-d42c1051ad4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:16,869] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:16,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:16,870] [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
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	97.1673	754	828	95	conclusive
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	97.1592	742	828	95	conclusive
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	79.5551	361	828	95	below_threshold
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	79.4423	366	828	95	below_threshold
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	78.7917	295	828	95	below_threshold
Megasphaera cerevisiae	strain=DSM 20462	GCA_001045675.1	39029	39029	type	True	77.6058	161	828	95	below_threshold
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	76.5096	50	828	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:16,872] [INFO] DFAST Taxonomy check result was written to GCF_025567065.1_ASM2556706v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:16,872] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:16,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:16,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0d43f10-7100-4a5f-9f69-d42c1051ad4b/dqc_reference/checkm_data
[2024-01-24 14:22:16,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:16,908] [INFO] Task started: CheckM
[2024-01-24 14:22:16,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567065.1_ASM2556706v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567065.1_ASM2556706v1_genomic.fna/checkm_input GCF_025567065.1_ASM2556706v1_genomic.fna/checkm_result
[2024-01-24 14:22:43,063] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:43,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:43,086] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:43,087] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:43,087] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567065.1_ASM2556706v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:43,087] [INFO] Task started: Blastn
[2024-01-24 14:22:43,088] [INFO] Running command: blastn -query GCF_025567065.1_ASM2556706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0d43f10-7100-4a5f-9f69-d42c1051ad4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567065.1_ASM2556706v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:44,011] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:44,015] [INFO] Selected 6 target genomes.
[2024-01-24 14:22:44,015] [INFO] Target genome list was writen to GCF_025567065.1_ASM2556706v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:44,021] [INFO] Task started: fastANI
[2024-01-24 14:22:44,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dc64f04-da48-4652-983e-677c2ad657c6/GCF_025567065.1_ASM2556706v1_genomic.fna.gz --refList GCF_025567065.1_ASM2556706v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567065.1_ASM2556706v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:47,185] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:47,191] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:47,192] [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_003367905.1	s__Megasphaera stantonii	97.1571	754	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	97.46	96.44	0.91	0.87	8	conclusive
GCA_900554215.1	s__Megasphaera sp900554215	94.7184	518	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	95.76	95.76	0.83	0.83	2	-
GCF_000417505.1	s__Megasphaera sp000417505	79.7951	354	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.18	97.65	0.90	0.81	11	-
GCA_902388315.1	s__Megasphaera sp902388315	79.5407	259	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.43	99.12	0.87	0.82	3	-
GCF_003010495.1	s__Megasphaera elsdenii	79.4338	366	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.27	97.55	0.90	0.81	29	-
GCA_900548635.1	s__Megasphaera sp900548635	79.273	282	828	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.28	98.56	0.89	0.79	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:47,194] [INFO] GTDB search result was written to GCF_025567065.1_ASM2556706v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:47,194] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:47,197] [INFO] DFAST_QC result json was written to GCF_025567065.1_ASM2556706v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:47,197] [INFO] DFAST_QC completed!
[2024-01-24 14:22:47,197] [INFO] Total running time: 0h0m45s