[2024-01-24 15:27:07,443] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:07,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:07,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg3885b078-1f50-4f6e-9d6d-5853d25c88bf/dqc_reference
[2024-01-24 15:27:09,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:09,323] [INFO] Task started: Prodigal
[2024-01-24 15:27:09,323] [INFO] Running command: gunzip -c /var/lib/cwl/stg40b4389d-ef88-48cc-a79d-1dd3c09767bc/GCF_010537335.1_ASM1053733v1_genomic.fna.gz | prodigal -d GCF_010537335.1_ASM1053733v1_genomic.fna/cds.fna -a GCF_010537335.1_ASM1053733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:14,904] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:14,905] [INFO] Task started: HMMsearch
[2024-01-24 15:27:14,905] [INFO] Running command: hmmsearch --tblout GCF_010537335.1_ASM1053733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3885b078-1f50-4f6e-9d6d-5853d25c88bf/dqc_reference/reference_markers.hmm GCF_010537335.1_ASM1053733v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:15,278] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:15,279] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg40b4389d-ef88-48cc-a79d-1dd3c09767bc/GCF_010537335.1_ASM1053733v1_genomic.fna.gz]
[2024-01-24 15:27:15,304] [INFO] Query marker FASTA was written to GCF_010537335.1_ASM1053733v1_genomic.fna/markers.fasta
[2024-01-24 15:27:15,305] [INFO] Task started: Blastn
[2024-01-24 15:27:15,305] [INFO] Running command: blastn -query GCF_010537335.1_ASM1053733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3885b078-1f50-4f6e-9d6d-5853d25c88bf/dqc_reference/reference_markers.fasta -out GCF_010537335.1_ASM1053733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:18,595] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:18,598] [INFO] Selected 18 target genomes.
[2024-01-24 15:27:18,599] [INFO] Target genome list was writen to GCF_010537335.1_ASM1053733v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:18,666] [INFO] Task started: fastANI
[2024-01-24 15:27:18,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg40b4389d-ef88-48cc-a79d-1dd3c09767bc/GCF_010537335.1_ASM1053733v1_genomic.fna.gz --refList GCF_010537335.1_ASM1053733v1_genomic.fna/target_genomes.txt --output GCF_010537335.1_ASM1053733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:29,217] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:29,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3885b078-1f50-4f6e-9d6d-5853d25c88bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:29,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3885b078-1f50-4f6e-9d6d-5853d25c88bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:29,225] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:29,226] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:29,226] [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
Amedibacterium intestinale	strain=9CBEGH2	GCA_010537335.1	2583452	2583452	type	True	100.0	829	829	95	conclusive
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	79.2927	62	829	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	79.0439	64	829	95	below_threshold
Amedibacillus dolichus	strain=DSM 3991	GCA_000154285.1	31971	31971	type	True	78.7351	112	829	95	below_threshold
Longicatena caecimuris	strain=DSM 29481	GCA_004341945.1	1796635	1796635	type	True	78.4837	168	829	95	below_threshold
Longicatena caecimuris	strain=DSM 29481	GCA_024622185.1	1796635	1796635	type	True	78.4398	168	829	95	below_threshold
Holdemanella porci	strain=LKV-472-APC-3	GCA_009696075.1	2652276	2652276	suspected-type	True	77.1284	69	829	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:29,227] [INFO] DFAST Taxonomy check result was written to GCF_010537335.1_ASM1053733v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:29,228] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:29,228] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:29,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3885b078-1f50-4f6e-9d6d-5853d25c88bf/dqc_reference/checkm_data
[2024-01-24 15:27:29,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:29,260] [INFO] Task started: CheckM
[2024-01-24 15:27:29,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010537335.1_ASM1053733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010537335.1_ASM1053733v1_genomic.fna/checkm_input GCF_010537335.1_ASM1053733v1_genomic.fna/checkm_result
[2024-01-24 15:27:53,854] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:53,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:53,880] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:53,880] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:53,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010537335.1_ASM1053733v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:53,881] [INFO] Task started: Blastn
[2024-01-24 15:27:53,881] [INFO] Running command: blastn -query GCF_010537335.1_ASM1053733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3885b078-1f50-4f6e-9d6d-5853d25c88bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_010537335.1_ASM1053733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:54,748] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:54,751] [INFO] Selected 17 target genomes.
[2024-01-24 15:27:54,752] [INFO] Target genome list was writen to GCF_010537335.1_ASM1053733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:54,764] [INFO] Task started: fastANI
[2024-01-24 15:27:54,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg40b4389d-ef88-48cc-a79d-1dd3c09767bc/GCF_010537335.1_ASM1053733v1_genomic.fna.gz --refList GCF_010537335.1_ASM1053733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010537335.1_ASM1053733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:02,192] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:02,200] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:02,200] [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_010537335.1	s__Amedibacterium intestinale	100.0	829	829	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	98.96	98.46	0.86	0.72	14	conclusive
GCF_014337235.1	s__NSJ-61 sp003433845	79.8305	173	829	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__NSJ-61	95.0	99.54	98.10	0.85	0.77	12	-
GCA_017161075.1	s__Clostridium_AQ sp000165065	79.3621	111	829	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	97.84	97.80	0.84	0.80	7	-
GCA_900552125.1	s__Clostridium_AQ sp900552125	78.7816	214	829	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	99.93	99.93	0.86	0.86	2	-
GCF_000154285.1	s__Amedibacillus dolichus	78.7312	112	829	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacillus	95.0	99.06	98.73	0.91	0.85	7	-
GCF_004341945.1	s__Longicatena caecimuris	78.501	169	829	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Longicatena	95.0	98.56	98.14	0.91	0.88	21	-
GCA_904395785.1	s__Amedibacterium sp904395785	78.4811	156	829	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003458715.1	s__Holdemanella sp003458715	77.0806	76	829	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.81	97.17	0.85	0.77	7	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:02,202] [INFO] GTDB search result was written to GCF_010537335.1_ASM1053733v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:02,203] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:02,205] [INFO] DFAST_QC result json was written to GCF_010537335.1_ASM1053733v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:02,206] [INFO] DFAST_QC completed!
[2024-01-24 15:28:02,206] [INFO] Total running time: 0h0m55s