[2024-01-24 14:19:15,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg68378e16-ba94-4791-a92f-1ebff2f41e27/dqc_reference
[2024-01-24 14:19:18,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:18,323] [INFO] Task started: Prodigal
[2024-01-24 14:19:18,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg64b016ef-7a3e-4dfc-81e1-cfa2ebe0e06c/GCF_000428645.1_ASM42864v1_genomic.fna.gz | prodigal -d GCF_000428645.1_ASM42864v1_genomic.fna/cds.fna -a GCF_000428645.1_ASM42864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:19,831] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:19,832] [INFO] Task started: HMMsearch
[2024-01-24 14:19:19,832] [INFO] Running command: hmmsearch --tblout GCF_000428645.1_ASM42864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68378e16-ba94-4791-a92f-1ebff2f41e27/dqc_reference/reference_markers.hmm GCF_000428645.1_ASM42864v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:20,183] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:20,184] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg64b016ef-7a3e-4dfc-81e1-cfa2ebe0e06c/GCF_000428645.1_ASM42864v1_genomic.fna.gz]
[2024-01-24 14:19:20,209] [INFO] Query marker FASTA was written to GCF_000428645.1_ASM42864v1_genomic.fna/markers.fasta
[2024-01-24 14:19:20,210] [INFO] Task started: Blastn
[2024-01-24 14:19:20,210] [INFO] Running command: blastn -query GCF_000428645.1_ASM42864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68378e16-ba94-4791-a92f-1ebff2f41e27/dqc_reference/reference_markers.fasta -out GCF_000428645.1_ASM42864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:24,061] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:24,065] [INFO] Selected 8 target genomes.
[2024-01-24 14:19:24,065] [INFO] Target genome list was writen to GCF_000428645.1_ASM42864v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:24,071] [INFO] Task started: fastANI
[2024-01-24 14:19:24,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg64b016ef-7a3e-4dfc-81e1-cfa2ebe0e06c/GCF_000428645.1_ASM42864v1_genomic.fna.gz --refList GCF_000428645.1_ASM42864v1_genomic.fna/target_genomes.txt --output GCF_000428645.1_ASM42864v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:27,685] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:27,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68378e16-ba94-4791-a92f-1ebff2f41e27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:27,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68378e16-ba94-4791-a92f-1ebff2f41e27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:27,691] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:27,692] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:27,692] [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
Mycoplasmoides gallisepticum	strain=ATCC 19610	GCA_000428645.1	2096	2096	type	True	100.0	288	290	95	conclusive
Mycoplasmoides gallisepticum	strain=NCTC10115	GCA_900476085.1	2096	2096	type	True	99.9765	290	290	95	conclusive
Mycoplasma imitans	strain=ATCC 51306	GCA_000518305.1	29560	29560	type	True	84.3693	237	290	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:27,693] [INFO] DFAST Taxonomy check result was written to GCF_000428645.1_ASM42864v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:27,694] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:27,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:27,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68378e16-ba94-4791-a92f-1ebff2f41e27/dqc_reference/checkm_data
[2024-01-24 14:19:27,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:27,711] [INFO] Task started: CheckM
[2024-01-24 14:19:27,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428645.1_ASM42864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428645.1_ASM42864v1_genomic.fna/checkm_input GCF_000428645.1_ASM42864v1_genomic.fna/checkm_result
[2024-01-24 14:19:48,698] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:48,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:48,735] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:48,735] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:48,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428645.1_ASM42864v1_genomic.fna/markers.fasta)
[2024-01-24 14:19:48,736] [INFO] Task started: Blastn
[2024-01-24 14:19:48,736] [INFO] Running command: blastn -query GCF_000428645.1_ASM42864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68378e16-ba94-4791-a92f-1ebff2f41e27/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428645.1_ASM42864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:50,283] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:50,287] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:50,287] [INFO] Target genome list was writen to GCF_000428645.1_ASM42864v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:50,308] [INFO] Task started: fastANI
[2024-01-24 14:19:50,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg64b016ef-7a3e-4dfc-81e1-cfa2ebe0e06c/GCF_000428645.1_ASM42864v1_genomic.fna.gz --refList GCF_000428645.1_ASM42864v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428645.1_ASM42864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:19:57,452] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:57,541] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:19:57,541] [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_900476085.1	s__Mycoplasmoides gallisepticum	99.9765	290	290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Mycoplasmoides	95.0	98.49	97.87	0.96	0.93	28	conclusive
GCF_014068355.1	s__Mycoplasmoides tullyi	86.9425	235	290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Mycoplasmoides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518305.1	s__Mycoplasmoides imitans	84.383	235	290	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Mycoplasmoides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:19:57,599] [INFO] GTDB search result was written to GCF_000428645.1_ASM42864v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:19:57,601] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:19:57,605] [INFO] DFAST_QC result json was written to GCF_000428645.1_ASM42864v1_genomic.fna/dqc_result.json
[2024-01-24 14:19:57,606] [INFO] DFAST_QC completed!
[2024-01-24 14:19:57,606] [INFO] Total running time: 0h0m42s