[2024-01-25 19:49:06,028] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:06,030] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:06,030] [INFO] DQC Reference Directory: /var/lib/cwl/stg755e2682-f603-43f9-87ea-d69e4c7f9581/dqc_reference
[2024-01-25 19:49:07,171] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:07,172] [INFO] Task started: Prodigal
[2024-01-25 19:49:07,172] [INFO] Running command: gunzip -c /var/lib/cwl/stge478aa02-c5cf-4677-bb16-dc7d4c69a8e0/GCF_003030445.1_ASM303044v1_genomic.fna.gz | prodigal -d GCF_003030445.1_ASM303044v1_genomic.fna/cds.fna -a GCF_003030445.1_ASM303044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:13,740] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:13,740] [INFO] Task started: HMMsearch
[2024-01-25 19:49:13,740] [INFO] Running command: hmmsearch --tblout GCF_003030445.1_ASM303044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg755e2682-f603-43f9-87ea-d69e4c7f9581/dqc_reference/reference_markers.hmm GCF_003030445.1_ASM303044v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:13,948] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:13,950] [INFO] Found 6/6 markers.
[2024-01-25 19:49:13,973] [INFO] Query marker FASTA was written to GCF_003030445.1_ASM303044v1_genomic.fna/markers.fasta
[2024-01-25 19:49:13,973] [INFO] Task started: Blastn
[2024-01-25 19:49:13,973] [INFO] Running command: blastn -query GCF_003030445.1_ASM303044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg755e2682-f603-43f9-87ea-d69e4c7f9581/dqc_reference/reference_markers.fasta -out GCF_003030445.1_ASM303044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:14,543] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:14,545] [INFO] Selected 10 target genomes.
[2024-01-25 19:49:14,546] [INFO] Target genome list was writen to GCF_003030445.1_ASM303044v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:14,560] [INFO] Task started: fastANI
[2024-01-25 19:49:14,560] [INFO] Running command: fastANI --query /var/lib/cwl/stge478aa02-c5cf-4677-bb16-dc7d4c69a8e0/GCF_003030445.1_ASM303044v1_genomic.fna.gz --refList GCF_003030445.1_ASM303044v1_genomic.fna/target_genomes.txt --output GCF_003030445.1_ASM303044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:20,393] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:20,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg755e2682-f603-43f9-87ea-d69e4c7f9581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:20,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg755e2682-f603-43f9-87ea-d69e4c7f9581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:20,399] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:49:20,399] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:20,399] [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_003030445.1	2144175	2144175	type	True	100.0	830	835	95	conclusive
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	99.9888	830	835	95	conclusive
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	79.6726	327	835	95	below_threshold
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	79.546	343	835	95	below_threshold
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	78.9656	280	835	95	below_threshold
Megasphaera cerevisiae	strain=DSM 20462	GCA_001045675.1	39029	39029	type	True	77.6575	166	835	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:20,401] [INFO] DFAST Taxonomy check result was written to GCF_003030445.1_ASM303044v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:20,401] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:20,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:20,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg755e2682-f603-43f9-87ea-d69e4c7f9581/dqc_reference/checkm_data
[2024-01-25 19:49:20,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:20,441] [INFO] Task started: CheckM
[2024-01-25 19:49:20,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003030445.1_ASM303044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003030445.1_ASM303044v1_genomic.fna/checkm_input GCF_003030445.1_ASM303044v1_genomic.fna/checkm_result
[2024-01-25 19:49:44,515] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:44,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.32%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:44,544] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:44,544] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:44,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003030445.1_ASM303044v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:44,545] [INFO] Task started: Blastn
[2024-01-25 19:49:44,545] [INFO] Running command: blastn -query GCF_003030445.1_ASM303044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg755e2682-f603-43f9-87ea-d69e4c7f9581/dqc_reference/reference_markers_gtdb.fasta -out GCF_003030445.1_ASM303044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:45,398] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:45,401] [INFO] Selected 7 target genomes.
[2024-01-25 19:49:45,401] [INFO] Target genome list was writen to GCF_003030445.1_ASM303044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:45,406] [INFO] Task started: fastANI
[2024-01-25 19:49:45,406] [INFO] Running command: fastANI --query /var/lib/cwl/stge478aa02-c5cf-4677-bb16-dc7d4c69a8e0/GCF_003030445.1_ASM303044v1_genomic.fna.gz --refList GCF_003030445.1_ASM303044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003030445.1_ASM303044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:48,869] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:48,875] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:48,875] [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	99.9888	830	835	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	94.9381	524	835	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	79.8704	350	835	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	79.577	261	835	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	79.538	346	835	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	79.5244	263	835	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.28	98.56	0.89	0.79	3	-
GCF_001546855.1	s__Megasphaera sp001546855	79.1066	283	835	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.96	99.94	0.97	0.94	9	-
--------------------------------------------------------------------------------
[2024-01-25 19:49:48,877] [INFO] GTDB search result was written to GCF_003030445.1_ASM303044v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:48,877] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:48,879] [INFO] DFAST_QC result json was written to GCF_003030445.1_ASM303044v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:48,880] [INFO] DFAST_QC completed!
[2024-01-25 19:49:48,880] [INFO] Total running time: 0h0m43s