[2024-01-24 11:34:54,151] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:54,155] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:54,156] [INFO] DQC Reference Directory: /var/lib/cwl/stg8552e1ec-b19a-4b79-9d02-e25698db50d2/dqc_reference
[2024-01-24 11:34:55,999] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,000] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,001] [INFO] Running command: gunzip -c /var/lib/cwl/stg5998c56e-1da2-4bbb-a3f4-3b44041b46f5/GCF_016925555.1_ASM1692555v1_genomic.fna.gz | prodigal -d GCF_016925555.1_ASM1692555v1_genomic.fna/cds.fna -a GCF_016925555.1_ASM1692555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:57,296] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:57,296] [INFO] Task started: HMMsearch
[2024-01-24 11:34:57,297] [INFO] Running command: hmmsearch --tblout GCF_016925555.1_ASM1692555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8552e1ec-b19a-4b79-9d02-e25698db50d2/dqc_reference/reference_markers.hmm GCF_016925555.1_ASM1692555v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:57,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:57,553] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5998c56e-1da2-4bbb-a3f4-3b44041b46f5/GCF_016925555.1_ASM1692555v1_genomic.fna.gz]
[2024-01-24 11:34:57,566] [INFO] Query marker FASTA was written to GCF_016925555.1_ASM1692555v1_genomic.fna/markers.fasta
[2024-01-24 11:34:57,567] [INFO] Task started: Blastn
[2024-01-24 11:34:57,567] [INFO] Running command: blastn -query GCF_016925555.1_ASM1692555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8552e1ec-b19a-4b79-9d02-e25698db50d2/dqc_reference/reference_markers.fasta -out GCF_016925555.1_ASM1692555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:01,607] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:01,610] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:01,611] [INFO] Target genome list was writen to GCF_016925555.1_ASM1692555v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:01,649] [INFO] Task started: fastANI
[2024-01-24 11:35:01,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg5998c56e-1da2-4bbb-a3f4-3b44041b46f5/GCF_016925555.1_ASM1692555v1_genomic.fna.gz --refList GCF_016925555.1_ASM1692555v1_genomic.fna/target_genomes.txt --output GCF_016925555.1_ASM1692555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:05,112] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:05,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8552e1ec-b19a-4b79-9d02-e25698db50d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:05,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8552e1ec-b19a-4b79-9d02-e25698db50d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:05,123] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:05,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:05,123] [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
Mycoplasma tauri	strain=Zaradi2	GCA_016925555.1	547987	547987	type	True	100.0	254	254	95	conclusive
Mycoplasmopsis primatum	strain=ATCC 25948	GCA_000702785.1	55604	55604	type	True	79.4014	82	254	95	below_threshold
Mycoplasmopsis felifaucium	strain=ATCC 43428	GCA_000687775.1	35768	35768	type	True	79.0166	56	254	95	below_threshold
Mycoplasmopsis maculosa	strain=NCTC10168	GCA_900660665.1	114885	114885	type	True	78.4084	67	254	95	below_threshold
Mycoplasmopsis agalactiae	strain=PG2	GCA_000063605.1	2110	2110	type	True	78.2974	76	254	95	below_threshold
Mycoplasmopsis bovis	strain=PG45	GCA_000183385.1	28903	28903	type	True	78.2709	81	254	95	below_threshold
Mycoplasmopsis lipofaciens	strain=ATCC 35015	GCA_000686585.1	114884	114884	type	True	78.171	51	254	95	below_threshold
Mycoplasmopsis caviae	strain=G122	GCA_024498215.1	55603	55603	type	True	78.1021	50	254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:05,125] [INFO] DFAST Taxonomy check result was written to GCF_016925555.1_ASM1692555v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:05,125] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:05,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:05,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8552e1ec-b19a-4b79-9d02-e25698db50d2/dqc_reference/checkm_data
[2024-01-24 11:35:05,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:05,137] [INFO] Task started: CheckM
[2024-01-24 11:35:05,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016925555.1_ASM1692555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016925555.1_ASM1692555v1_genomic.fna/checkm_input GCF_016925555.1_ASM1692555v1_genomic.fna/checkm_result
[2024-01-24 11:35:22,404] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:22,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:22,428] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:22,428] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:22,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016925555.1_ASM1692555v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:22,429] [INFO] Task started: Blastn
[2024-01-24 11:35:22,430] [INFO] Running command: blastn -query GCF_016925555.1_ASM1692555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8552e1ec-b19a-4b79-9d02-e25698db50d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016925555.1_ASM1692555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:23,759] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:23,762] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:23,762] [INFO] Target genome list was writen to GCF_016925555.1_ASM1692555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:23,800] [INFO] Task started: fastANI
[2024-01-24 11:35:23,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg5998c56e-1da2-4bbb-a3f4-3b44041b46f5/GCF_016925555.1_ASM1692555v1_genomic.fna.gz --refList GCF_016925555.1_ASM1692555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016925555.1_ASM1692555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:26,476] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:26,490] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:26,491] [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_016925555.1	s__Mycoplasmopsis sp016925555	100.0	254	254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000702785.1	s__Mycoplasmopsis primatum	79.4014	82	254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687775.1	s__Mycoplasmopsis felifaucium	79.0166	56	254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660665.1	s__Mycoplasmopsis maculosa	78.5295	65	254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000063605.1	s__Mycoplasmopsis agalactiae	78.2974	76	254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	97.63	95.37	0.95	0.90	5	-
GCF_000183385.1	s__Mycoplasmopsis bovis	78.2709	81	254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	97.97	97.48	0.95	0.85	193	-
GCF_000266865.1	s__Mycoplasmopsis agalactiae_A	78.1899	73	254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005061465.1	s__Mycoplasmopsis bovis_A	78.1117	88	254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:26,492] [INFO] GTDB search result was written to GCF_016925555.1_ASM1692555v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:26,493] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:26,495] [INFO] DFAST_QC result json was written to GCF_016925555.1_ASM1692555v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:26,495] [INFO] DFAST_QC completed!
[2024-01-24 11:35:26,496] [INFO] Total running time: 0h0m32s