[2024-01-24 13:22:10,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c4cff97-b956-4968-8378-22752f84a374/dqc_reference
[2024-01-24 13:22:11,499] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:11,500] [INFO] Task started: Prodigal
[2024-01-24 13:22:11,500] [INFO] Running command: gunzip -c /var/lib/cwl/stg3afce73e-d5c8-46f0-a08f-c4e3682b7a80/GCF_003367905.1_ASM336790v1_genomic.fna.gz | prodigal -d GCF_003367905.1_ASM336790v1_genomic.fna/cds.fna -a GCF_003367905.1_ASM336790v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:18,427] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:18,427] [INFO] Task started: HMMsearch
[2024-01-24 13:22:18,427] [INFO] Running command: hmmsearch --tblout GCF_003367905.1_ASM336790v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c4cff97-b956-4968-8378-22752f84a374/dqc_reference/reference_markers.hmm GCF_003367905.1_ASM336790v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:18,699] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:18,701] [INFO] Found 6/6 markers.
[2024-01-24 13:22:18,728] [INFO] Query marker FASTA was written to GCF_003367905.1_ASM336790v1_genomic.fna/markers.fasta
[2024-01-24 13:22:18,729] [INFO] Task started: Blastn
[2024-01-24 13:22:18,729] [INFO] Running command: blastn -query GCF_003367905.1_ASM336790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c4cff97-b956-4968-8378-22752f84a374/dqc_reference/reference_markers.fasta -out GCF_003367905.1_ASM336790v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:19,346] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:19,349] [INFO] Selected 10 target genomes.
[2024-01-24 13:22:19,349] [INFO] Target genome list was writen to GCF_003367905.1_ASM336790v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:19,378] [INFO] Task started: fastANI
[2024-01-24 13:22:19,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg3afce73e-d5c8-46f0-a08f-c4e3682b7a80/GCF_003367905.1_ASM336790v1_genomic.fna.gz --refList GCF_003367905.1_ASM336790v1_genomic.fna/target_genomes.txt --output GCF_003367905.1_ASM336790v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:25,689] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:25,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c4cff97-b956-4968-8378-22752f84a374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:25,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c4cff97-b956-4968-8378-22752f84a374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:25,697] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:25,697] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:25,697] [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	100.0	884	884	95	conclusive
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	99.9432	827	884	95	conclusive
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	79.9768	348	884	95	below_threshold
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	79.9533	344	884	95	below_threshold
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	78.8644	287	884	95	below_threshold
Megasphaera cerevisiae	strain=DSM 20462	GCA_001045675.1	39029	39029	type	True	77.5802	166	884	95	below_threshold
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	76.7232	51	884	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:25,699] [INFO] DFAST Taxonomy check result was written to GCF_003367905.1_ASM336790v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:25,699] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:25,700] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:25,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c4cff97-b956-4968-8378-22752f84a374/dqc_reference/checkm_data
[2024-01-24 13:22:25,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:25,727] [INFO] Task started: CheckM
[2024-01-24 13:22:25,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003367905.1_ASM336790v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003367905.1_ASM336790v1_genomic.fna/checkm_input GCF_003367905.1_ASM336790v1_genomic.fna/checkm_result
[2024-01-24 13:22:51,584] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:51,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:51,605] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:51,606] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:51,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003367905.1_ASM336790v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:51,607] [INFO] Task started: Blastn
[2024-01-24 13:22:51,607] [INFO] Running command: blastn -query GCF_003367905.1_ASM336790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c4cff97-b956-4968-8378-22752f84a374/dqc_reference/reference_markers_gtdb.fasta -out GCF_003367905.1_ASM336790v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:52,493] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:52,497] [INFO] Selected 7 target genomes.
[2024-01-24 13:22:52,497] [INFO] Target genome list was writen to GCF_003367905.1_ASM336790v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:52,542] [INFO] Task started: fastANI
[2024-01-24 13:22:52,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg3afce73e-d5c8-46f0-a08f-c4e3682b7a80/GCF_003367905.1_ASM336790v1_genomic.fna.gz --refList GCF_003367905.1_ASM336790v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003367905.1_ASM336790v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:56,034] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:56,044] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:56,044] [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	100.0	884	884	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	94.7466	538	884	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	80.0646	356	884	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.18	97.65	0.90	0.81	11	-
GCF_003010495.1	s__Megasphaera elsdenii	79.8746	343	884	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_902388315.1	s__Megasphaera sp902388315	79.7006	257	884	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.43	99.12	0.87	0.82	3	-
GCA_900548635.1	s__Megasphaera sp900548635	79.5649	269	884	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	79.03	290	884	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.96	99.94	0.97	0.94	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:56,046] [INFO] GTDB search result was written to GCF_003367905.1_ASM336790v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:56,046] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:56,053] [INFO] DFAST_QC result json was written to GCF_003367905.1_ASM336790v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:56,053] [INFO] DFAST_QC completed!
[2024-01-24 13:22:56,053] [INFO] Total running time: 0h0m46s