[2024-01-24 13:24:48,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:48,060] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:48,060] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b14f38b-0f11-4aeb-99c9-204a55c2b004/dqc_reference
[2024-01-24 13:24:49,392] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:49,393] [INFO] Task started: Prodigal
[2024-01-24 13:24:49,394] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f76ef64-e957-4d4c-9a97-0f4dbdc5f6dd/GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/cds.fna -a GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:50,611] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:50,611] [INFO] Task started: HMMsearch
[2024-01-24 13:24:50,611] [INFO] Running command: hmmsearch --tblout GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b14f38b-0f11-4aeb-99c9-204a55c2b004/dqc_reference/reference_markers.hmm GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:50,814] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:50,816] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8f76ef64-e957-4d4c-9a97-0f4dbdc5f6dd/GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna.gz]
[2024-01-24 13:24:50,836] [INFO] Query marker FASTA was written to GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:24:50,836] [INFO] Task started: Blastn
[2024-01-24 13:24:50,836] [INFO] Running command: blastn -query GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b14f38b-0f11-4aeb-99c9-204a55c2b004/dqc_reference/reference_markers.fasta -out GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:51,432] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:51,435] [INFO] Selected 13 target genomes.
[2024-01-24 13:24:51,435] [INFO] Target genome list was writen to GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:24:51,501] [INFO] Task started: fastANI
[2024-01-24 13:24:51,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f76ef64-e957-4d4c-9a97-0f4dbdc5f6dd/GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna.gz --refList GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:54,627] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:54,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b14f38b-0f11-4aeb-99c9-204a55c2b004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:54,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b14f38b-0f11-4aeb-99c9-204a55c2b004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:54,635] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:24:54,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:54,635] [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 verecunda	strain=ATCC 27862	GCA_900167035.1	171291	171291	type	True	100.0	267	267	95	conclusive
Mycoplasmopsis glycophila	strain=ATCC 35277	GCA_000687855.1	171285	171285	type	True	78.3008	57	267	95	below_threshold
Mycoplasmopsis glycophila	strain=NCTC10194	GCA_900660605.1	171285	171285	type	True	78.2868	57	267	95	below_threshold
Mycoplasmopsis columboralis	strain=ATCC 29258	GCA_000701845.1	171282	171282	type	True	77.5259	56	267	95	below_threshold
Mycoplasmopsis citelli	strain=RG-2C	GCA_024498235.1	171281	171281	type	True	76.6786	54	267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:54,637] [INFO] DFAST Taxonomy check result was written to GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:24:54,637] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:54,637] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:54,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b14f38b-0f11-4aeb-99c9-204a55c2b004/dqc_reference/checkm_data
[2024-01-24 13:24:54,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:54,655] [INFO] Task started: CheckM
[2024-01-24 13:24:54,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/checkm_input GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:25:07,761] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:07,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:07,776] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:07,777] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:07,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:25:07,778] [INFO] Task started: Blastn
[2024-01-24 13:25:07,778] [INFO] Running command: blastn -query GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b14f38b-0f11-4aeb-99c9-204a55c2b004/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:08,519] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:08,523] [INFO] Selected 15 target genomes.
[2024-01-24 13:25:08,523] [INFO] Target genome list was writen to GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:08,552] [INFO] Task started: fastANI
[2024-01-24 13:25:08,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f76ef64-e957-4d4c-9a97-0f4dbdc5f6dd/GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna.gz --refList GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:11,653] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:11,664] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:11,664] [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_900167035.1	s__Mycoplasmopsis_A verecundum	100.0	267	267	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_009792315.1	s__Mycoplasmopsis_A sp009792315	78.5322	76	267	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_900660605.1	s__Mycoplasmopsis_A glycophilum	78.424	57	267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013348745.1	s__Mycoplasmopsis_A sp013348745	77.8515	54	267	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_000622205.1	s__Mycoplasmopsis_A leonicaptivi	77.7269	57	267	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_012220205.1	s__Mycoplasmopsis_A gallinacea_A	77.6209	60	267	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	77.5961	54	267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:11,666] [INFO] GTDB search result was written to GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:11,666] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:11,669] [INFO] DFAST_QC result json was written to GCF_900167035.1_IMG-taxon_2582581322_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:25:11,669] [INFO] DFAST_QC completed!
[2024-01-24 13:25:11,669] [INFO] Total running time: 0h0m24s