[2024-01-24 13:40:34,337] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,338] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,339] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf76519c-6d7c-4212-bca4-0ab7eed6b531/dqc_reference
[2024-01-24 13:40:35,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:35,862] [INFO] Task started: Prodigal
[2024-01-24 13:40:35,862] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0aae086-4bce-433f-90ca-6fa7fe25feb3/GCF_000178375.1_ASM17837v1_genomic.fna.gz | prodigal -d GCF_000178375.1_ASM17837v1_genomic.fna/cds.fna -a GCF_000178375.1_ASM17837v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:37,327] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:37,328] [INFO] Task started: HMMsearch
[2024-01-24 13:40:37,328] [INFO] Running command: hmmsearch --tblout GCF_000178375.1_ASM17837v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf76519c-6d7c-4212-bca4-0ab7eed6b531/dqc_reference/reference_markers.hmm GCF_000178375.1_ASM17837v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:37,511] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:37,512] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb0aae086-4bce-433f-90ca-6fa7fe25feb3/GCF_000178375.1_ASM17837v1_genomic.fna.gz]
[2024-01-24 13:40:37,527] [INFO] Query marker FASTA was written to GCF_000178375.1_ASM17837v1_genomic.fna/markers.fasta
[2024-01-24 13:40:37,527] [INFO] Task started: Blastn
[2024-01-24 13:40:37,527] [INFO] Running command: blastn -query GCF_000178375.1_ASM17837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf76519c-6d7c-4212-bca4-0ab7eed6b531/dqc_reference/reference_markers.fasta -out GCF_000178375.1_ASM17837v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:38,064] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:38,068] [INFO] Selected 10 target genomes.
[2024-01-24 13:40:38,068] [INFO] Target genome list was writen to GCF_000178375.1_ASM17837v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:38,077] [INFO] Task started: fastANI
[2024-01-24 13:40:38,077] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0aae086-4bce-433f-90ca-6fa7fe25feb3/GCF_000178375.1_ASM17837v1_genomic.fna.gz --refList GCF_000178375.1_ASM17837v1_genomic.fna/target_genomes.txt --output GCF_000178375.1_ASM17837v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:40,156] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:40,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf76519c-6d7c-4212-bca4-0ab7eed6b531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:40,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf76519c-6d7c-4212-bca4-0ab7eed6b531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:40,161] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:40:40,162] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:40:40,162] [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
Mycoplasmopsis columboralis	strain=NCTC10179	GCA_900660675.1	171282	171282	type	True	77.8742	52	307	95	below_threshold
Mycoplasma leonicaptivi	strain=ATCC 49890	GCA_000622205.1	36742	36742	type	True	77.625	59	307	95	below_threshold
Mycoplasmopsis citelli	strain=NCTC10181	GCA_900660645.1	171281	171281	type	True	77.0366	51	307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:40,164] [INFO] DFAST Taxonomy check result was written to GCF_000178375.1_ASM17837v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:40,165] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:40,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:40,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf76519c-6d7c-4212-bca4-0ab7eed6b531/dqc_reference/checkm_data
[2024-01-24 13:40:40,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:40,183] [INFO] Task started: CheckM
[2024-01-24 13:40:40,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000178375.1_ASM17837v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000178375.1_ASM17837v1_genomic.fna/checkm_input GCF_000178375.1_ASM17837v1_genomic.fna/checkm_result
[2024-01-24 13:40:53,560] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:53,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:53,592] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:53,593] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:53,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000178375.1_ASM17837v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:53,594] [INFO] Task started: Blastn
[2024-01-24 13:40:53,594] [INFO] Running command: blastn -query GCF_000178375.1_ASM17837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf76519c-6d7c-4212-bca4-0ab7eed6b531/dqc_reference/reference_markers_gtdb.fasta -out GCF_000178375.1_ASM17837v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:54,116] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:54,119] [INFO] Selected 14 target genomes.
[2024-01-24 13:40:54,119] [INFO] Target genome list was writen to GCF_000178375.1_ASM17837v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:54,153] [INFO] Task started: fastANI
[2024-01-24 13:40:54,154] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0aae086-4bce-433f-90ca-6fa7fe25feb3/GCF_000178375.1_ASM17837v1_genomic.fna.gz --refList GCF_000178375.1_ASM17837v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000178375.1_ASM17837v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:57,463] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:57,470] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:57,470] [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_000178375.1	s__Mycoplasmopsis_A alligatoris	100.0	304	307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000025845.1	s__Mycoplasmopsis_A crocodyli	79.3835	128	307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660675.1	s__Mycoplasmopsis_A columborale	77.6607	50	307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000622205.1	s__Mycoplasmopsis_A leonicaptivi	77.6237	59	307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660645.1	s__Mycoplasmopsis_A citelli	77.0366	51	307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:57,472] [INFO] GTDB search result was written to GCF_000178375.1_ASM17837v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:57,472] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:57,475] [INFO] DFAST_QC result json was written to GCF_000178375.1_ASM17837v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:57,475] [INFO] DFAST_QC completed!
[2024-01-24 13:40:57,475] [INFO] Total running time: 0h0m23s