[2023-06-29 03:21:10,115] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:21:10,117] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:21:10,118] [INFO] DQC Reference Directory: /var/lib/cwl/stg37b904ee-dc48-4481-9cd3-e19fcd44ba72/dqc_reference
[2023-06-29 03:21:11,365] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:21:11,366] [INFO] Task started: Prodigal
[2023-06-29 03:21:11,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dfb3fe9-5e77-40ce-b932-4b19d0a62594/GCA_015264035.1_ASM1526403v1_genomic.fna.gz | prodigal -d GCA_015264035.1_ASM1526403v1_genomic.fna/cds.fna -a GCA_015264035.1_ASM1526403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:21:14,775] [INFO] Task succeeded: Prodigal
[2023-06-29 03:21:14,775] [INFO] Task started: HMMsearch
[2023-06-29 03:21:14,775] [INFO] Running command: hmmsearch --tblout GCA_015264035.1_ASM1526403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37b904ee-dc48-4481-9cd3-e19fcd44ba72/dqc_reference/reference_markers.hmm GCA_015264035.1_ASM1526403v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:21:15,019] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:21:15,021] [INFO] Found 6/6 markers.
[2023-06-29 03:21:15,047] [INFO] Query marker FASTA was written to GCA_015264035.1_ASM1526403v1_genomic.fna/markers.fasta
[2023-06-29 03:21:15,047] [INFO] Task started: Blastn
[2023-06-29 03:21:15,047] [INFO] Running command: blastn -query GCA_015264035.1_ASM1526403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37b904ee-dc48-4481-9cd3-e19fcd44ba72/dqc_reference/reference_markers.fasta -out GCA_015264035.1_ASM1526403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:21:15,631] [INFO] Task succeeded: Blastn
[2023-06-29 03:21:15,640] [INFO] Selected 16 target genomes.
[2023-06-29 03:21:15,641] [INFO] Target genome list was writen to GCA_015264035.1_ASM1526403v1_genomic.fna/target_genomes.txt
[2023-06-29 03:21:15,648] [INFO] Task started: fastANI
[2023-06-29 03:21:15,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dfb3fe9-5e77-40ce-b932-4b19d0a62594/GCA_015264035.1_ASM1526403v1_genomic.fna.gz --refList GCA_015264035.1_ASM1526403v1_genomic.fna/target_genomes.txt --output GCA_015264035.1_ASM1526403v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:21:21,012] [INFO] Task succeeded: fastANI
[2023-06-29 03:21:21,013] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37b904ee-dc48-4481-9cd3-e19fcd44ba72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:21:21,013] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37b904ee-dc48-4481-9cd3-e19fcd44ba72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:21:21,022] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:21:21,022] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 03:21:21,022] [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
Colibacter massiliensis	strain=Marseille-P2911	GCA_900095855.1	1852379	1852379	type	True	77.7808	136	453	95	below_threshold
'Megasphaera vaginalis' Bordigoni et al. 2020	strain=Marseille-P4857	GCA_900240295.1	2045301	2045301	type	True	77.3401	73	453	95	below_threshold
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	77.2158	60	453	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	76.8312	60	453	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	76.7991	62	453	95	below_threshold
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	76.6077	55	453	95	below_threshold
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	76.5636	55	453	95	below_threshold
Megasphaera lornae	strain=UPII 199-6	GCA_000214495.2	1000568	1000568	type	True	76.5138	60	453	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 03:21:21,024] [INFO] DFAST Taxonomy check result was written to GCA_015264035.1_ASM1526403v1_genomic.fna/tc_result.tsv
[2023-06-29 03:21:21,024] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:21:21,025] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:21:21,025] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37b904ee-dc48-4481-9cd3-e19fcd44ba72/dqc_reference/checkm_data
[2023-06-29 03:21:21,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:21:21,050] [INFO] Task started: CheckM
[2023-06-29 03:21:21,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015264035.1_ASM1526403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015264035.1_ASM1526403v1_genomic.fna/checkm_input GCA_015264035.1_ASM1526403v1_genomic.fna/checkm_result
[2023-06-29 03:21:39,464] [INFO] Task succeeded: CheckM
[2023-06-29 03:21:39,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:21:39,488] [INFO] ===== Completeness check finished =====
[2023-06-29 03:21:39,488] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:21:39,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015264035.1_ASM1526403v1_genomic.fna/markers.fasta)
[2023-06-29 03:21:39,489] [INFO] Task started: Blastn
[2023-06-29 03:21:39,489] [INFO] Running command: blastn -query GCA_015264035.1_ASM1526403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37b904ee-dc48-4481-9cd3-e19fcd44ba72/dqc_reference/reference_markers_gtdb.fasta -out GCA_015264035.1_ASM1526403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:21:40,354] [INFO] Task succeeded: Blastn
[2023-06-29 03:21:40,358] [INFO] Selected 18 target genomes.
[2023-06-29 03:21:40,358] [INFO] Target genome list was writen to GCA_015264035.1_ASM1526403v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:21:40,370] [INFO] Task started: fastANI
[2023-06-29 03:21:40,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dfb3fe9-5e77-40ce-b932-4b19d0a62594/GCA_015264035.1_ASM1526403v1_genomic.fna.gz --refList GCA_015264035.1_ASM1526403v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015264035.1_ASM1526403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:21:46,522] [INFO] Task succeeded: fastANI
[2023-06-29 03:21:46,531] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 03:21:46,532] [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_000165735.1	s__Anaeroglobus micronuciformis	98.2361	442	453	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	97.87	97.00	0.95	0.90	14	conclusive
GCF_900095855.1	s__Anaeroglobus massiliensis	77.7808	136	453	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	99.40	98.79	0.98	0.97	3	-
GCF_900240295.1	s__Anaeroglobus vaginalis	77.3616	74	453	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	99.10	99.10	0.91	0.91	2	-
GCA_002319965.1	s__Megasphaera sp002319965	77.2763	53	453	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	98.03	0.89	0.89	4	-
GCF_003367905.1	s__Megasphaera stantonii	76.7991	62	453	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	97.46	96.44	0.91	0.87	8	-
GCA_900752195.1	s__Caecibacter sp900549385	76.7891	50	453	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	99.73	99.52	0.95	0.92	4	-
GCF_003010495.1	s__Megasphaera elsdenii	76.6005	54	453	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.27	97.55	0.90	0.81	29	-
--------------------------------------------------------------------------------
[2023-06-29 03:21:46,534] [INFO] GTDB search result was written to GCA_015264035.1_ASM1526403v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:21:46,535] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:21:46,539] [INFO] DFAST_QC result json was written to GCA_015264035.1_ASM1526403v1_genomic.fna/dqc_result.json
[2023-06-29 03:21:46,539] [INFO] DFAST_QC completed!
[2023-06-29 03:21:46,539] [INFO] Total running time: 0h0m36s