[2024-01-24 11:12:28,145] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:28,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:28,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bc04f38-78c5-40a7-9ca1-3f266dd423b3/dqc_reference
[2024-01-24 11:12:29,489] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,490] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,491] [INFO] Running command: gunzip -c /var/lib/cwl/stgd21ccb7a-0aad-4ae8-a981-8b51b74d9a54/GCF_900660495.1_50648_F01-3_genomic.fna.gz | prodigal -d GCF_900660495.1_50648_F01-3_genomic.fna/cds.fna -a GCF_900660495.1_50648_F01-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:31,341] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:31,341] [INFO] Task started: HMMsearch
[2024-01-24 11:12:31,341] [INFO] Running command: hmmsearch --tblout GCF_900660495.1_50648_F01-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bc04f38-78c5-40a7-9ca1-3f266dd423b3/dqc_reference/reference_markers.hmm GCF_900660495.1_50648_F01-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:31,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:31,518] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd21ccb7a-0aad-4ae8-a981-8b51b74d9a54/GCF_900660495.1_50648_F01-3_genomic.fna.gz]
[2024-01-24 11:12:31,535] [INFO] Query marker FASTA was written to GCF_900660495.1_50648_F01-3_genomic.fna/markers.fasta
[2024-01-24 11:12:31,535] [INFO] Task started: Blastn
[2024-01-24 11:12:31,535] [INFO] Running command: blastn -query GCF_900660495.1_50648_F01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bc04f38-78c5-40a7-9ca1-3f266dd423b3/dqc_reference/reference_markers.fasta -out GCF_900660495.1_50648_F01-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:33,413] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:33,416] [INFO] Selected 17 target genomes.
[2024-01-24 11:12:33,417] [INFO] Target genome list was writen to GCF_900660495.1_50648_F01-3_genomic.fna/target_genomes.txt
[2024-01-24 11:12:33,478] [INFO] Task started: fastANI
[2024-01-24 11:12:33,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgd21ccb7a-0aad-4ae8-a981-8b51b74d9a54/GCF_900660495.1_50648_F01-3_genomic.fna.gz --refList GCF_900660495.1_50648_F01-3_genomic.fna/target_genomes.txt --output GCF_900660495.1_50648_F01-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:37,940] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:37,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bc04f38-78c5-40a7-9ca1-3f266dd423b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:37,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bc04f38-78c5-40a7-9ca1-3f266dd423b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:37,949] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:37,949] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:37,950] [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 gallinacea	strain=NCTC10183	GCA_900660495.1	29556	29556	type	True	100.0	354	358	95	conclusive
Mycoplasmopsis columboralis	strain=NCTC10179	GCA_900660675.1	171282	171282	type	True	79.9366	67	358	95	below_threshold
Mycoplasmopsis columboralis	strain=ATCC 29258	GCA_000701845.1	171282	171282	type	True	79.2353	65	358	95	below_threshold
Mycoplasmopsis edwardii	strain=NCTC10132	GCA_900476105.1	53558	53558	type	True	78.8801	79	358	95	below_threshold
Mycoplasmopsis bovirhinis	strain=NCTC10118	GCA_900660515.1	29553	29553	type	True	78.861	56	358	95	below_threshold
Mycoplasmopsis cynos	strain=NCTC10142	GCA_900660545.1	171284	171284	type	True	78.2856	55	358	95	below_threshold
Mycoplasmopsis citelli	strain=RG-2C	GCA_024498235.1	171281	171281	type	True	78.1016	76	358	95	below_threshold
Mycoplasmopsis citelli	strain=NCTC10181	GCA_900660645.1	171281	171281	type	True	77.933	74	358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:37,952] [INFO] DFAST Taxonomy check result was written to GCF_900660495.1_50648_F01-3_genomic.fna/tc_result.tsv
[2024-01-24 11:12:37,952] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:37,952] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:37,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bc04f38-78c5-40a7-9ca1-3f266dd423b3/dqc_reference/checkm_data
[2024-01-24 11:12:37,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:37,983] [INFO] Task started: CheckM
[2024-01-24 11:12:37,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660495.1_50648_F01-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660495.1_50648_F01-3_genomic.fna/checkm_input GCF_900660495.1_50648_F01-3_genomic.fna/checkm_result
[2024-01-24 11:12:52,720] [INFO] Task succeeded: CheckM
[2024-01-24 11:12:52,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:12:52,749] [INFO] ===== Completeness check finished =====
[2024-01-24 11:12:52,750] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:12:52,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660495.1_50648_F01-3_genomic.fna/markers.fasta)
[2024-01-24 11:12:52,750] [INFO] Task started: Blastn
[2024-01-24 11:12:52,750] [INFO] Running command: blastn -query GCF_900660495.1_50648_F01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bc04f38-78c5-40a7-9ca1-3f266dd423b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660495.1_50648_F01-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:53,679] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:53,689] [INFO] Selected 15 target genomes.
[2024-01-24 11:12:53,689] [INFO] Target genome list was writen to GCF_900660495.1_50648_F01-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:12:53,720] [INFO] Task started: fastANI
[2024-01-24 11:12:53,720] [INFO] Running command: fastANI --query /var/lib/cwl/stgd21ccb7a-0aad-4ae8-a981-8b51b74d9a54/GCF_900660495.1_50648_F01-3_genomic.fna.gz --refList GCF_900660495.1_50648_F01-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660495.1_50648_F01-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:12:57,505] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:57,516] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:12:57,516] [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_900660495.1	s__Mycoplasmopsis_A gallinaceum	100.0	353	358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	96.30	96.30	0.91	0.91	2	conclusive
GCF_012220205.1	s__Mycoplasmopsis_A gallinacea_A	94.6884	294	358	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	82.8281	116	358	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_900660675.1	s__Mycoplasmopsis_A columborale	79.893	68	358	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_009792315.1	s__Mycoplasmopsis_A sp009792315	79.0106	83	358	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_014352955.1	s__Mycoplasmopsis_A sp014352955	78.9276	75	358	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_900476105.1	s__Mycoplasmopsis_A edwardii	78.8801	79	358	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_900660515.1	s__Mycoplasmopsis_A bovirhinis	78.861	56	358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	98.45	97.89	0.93	0.90	3	-
GCF_900660545.1	s__Mycoplasmopsis_A cynos	78.2813	55	358	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.10	98.35	0.95	0.90	3	-
GCF_900660645.1	s__Mycoplasmopsis_A citelli	78.1553	74	358	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_007858495.1	s__Mycoplasmopsis_A anserisalpingitidis_A	78.0124	58	358	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 11:12:57,518] [INFO] GTDB search result was written to GCF_900660495.1_50648_F01-3_genomic.fna/result_gtdb.tsv
[2024-01-24 11:12:57,518] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:12:57,522] [INFO] DFAST_QC result json was written to GCF_900660495.1_50648_F01-3_genomic.fna/dqc_result.json
[2024-01-24 11:12:57,522] [INFO] DFAST_QC completed!
[2024-01-24 11:12:57,522] [INFO] Total running time: 0h0m29s