[2024-01-24 14:28:17,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:17,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:17,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg4941d96f-31c7-46fa-af56-acfcb8b170a3/dqc_reference
[2024-01-24 14:28:20,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,484] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a990039-2f58-4cbf-93b5-6c3508d63449/GCF_900476175.1_50648_D01_genomic.fna.gz | prodigal -d GCF_900476175.1_50648_D01_genomic.fna/cds.fna -a GCF_900476175.1_50648_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:21,810] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:21,811] [INFO] Task started: HMMsearch
[2024-01-24 14:28:21,811] [INFO] Running command: hmmsearch --tblout GCF_900476175.1_50648_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4941d96f-31c7-46fa-af56-acfcb8b170a3/dqc_reference/reference_markers.hmm GCF_900476175.1_50648_D01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:22,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:22,108] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3a990039-2f58-4cbf-93b5-6c3508d63449/GCF_900476175.1_50648_D01_genomic.fna.gz]
[2024-01-24 14:28:22,122] [INFO] Query marker FASTA was written to GCF_900476175.1_50648_D01_genomic.fna/markers.fasta
[2024-01-24 14:28:22,122] [INFO] Task started: Blastn
[2024-01-24 14:28:22,122] [INFO] Running command: blastn -query GCF_900476175.1_50648_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg4941d96f-31c7-46fa-af56-acfcb8b170a3/dqc_reference/reference_markers.fasta -out GCF_900476175.1_50648_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:26,469] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:26,479] [INFO] Selected 12 target genomes.
[2024-01-24 14:28:26,479] [INFO] Target genome list was writen to GCF_900476175.1_50648_D01_genomic.fna/target_genomes.txt
[2024-01-24 14:28:26,490] [INFO] Task started: fastANI
[2024-01-24 14:28:26,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a990039-2f58-4cbf-93b5-6c3508d63449/GCF_900476175.1_50648_D01_genomic.fna.gz --refList GCF_900476175.1_50648_D01_genomic.fna/target_genomes.txt --output GCF_900476175.1_50648_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:29,539] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:29,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4941d96f-31c7-46fa-af56-acfcb8b170a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:29,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4941d96f-31c7-46fa-af56-acfcb8b170a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:29,548] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:29,548] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:29,548] [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 putrefaciens	strain=NCTC10155	GCA_900476175.1	2123	2123	type	True	100.0	277	277	95	conclusive
Mycoplasma putrefaciens	strain=KS1	GCA_000224105.1	2123	2123	type	True	99.9984	277	277	95	conclusive
Mycoplasma cottewii	strain=VIS	GCA_024918975.1	51364	51364	type	True	81.1605	191	277	95	below_threshold
Mycoplasma capricolum subsp. capricolum	strain=ATCC 27343	GCA_000012765.1	40479	2095	type	True	79.9107	146	277	95	below_threshold
Mycoplasma feriruminatoris	strain=G5847	GCA_000327395.2	1179777	1179777	type	True	79.8965	148	277	95	below_threshold
Mycoplasma capricolum subsp. capripneumoniae	strain=type strain: F38 = NCTC 10192	GCA_000953375.1	40480	2095	type	True	79.7245	148	277	95	below_threshold
Mycoplasma leachii	strain=PG50	GCA_000183365.1	2105	2105	type	True	79.399	140	277	95	below_threshold
Mycoplasma mycoides subsp. capri	strain=PG3	GCA_000590435.1	40477	2102	type	True	79.3592	157	277	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:29,550] [INFO] DFAST Taxonomy check result was written to GCF_900476175.1_50648_D01_genomic.fna/tc_result.tsv
[2024-01-24 14:28:29,551] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:29,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:29,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4941d96f-31c7-46fa-af56-acfcb8b170a3/dqc_reference/checkm_data
[2024-01-24 14:28:29,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:29,563] [INFO] Task started: CheckM
[2024-01-24 14:28:29,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900476175.1_50648_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900476175.1_50648_D01_genomic.fna/checkm_input GCF_900476175.1_50648_D01_genomic.fna/checkm_result
[2024-01-24 14:28:47,897] [INFO] Task succeeded: CheckM
[2024-01-24 14:28:47,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:28:47,913] [INFO] ===== Completeness check finished =====
[2024-01-24 14:28:47,914] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:28:47,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900476175.1_50648_D01_genomic.fna/markers.fasta)
[2024-01-24 14:28:47,915] [INFO] Task started: Blastn
[2024-01-24 14:28:47,915] [INFO] Running command: blastn -query GCF_900476175.1_50648_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg4941d96f-31c7-46fa-af56-acfcb8b170a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900476175.1_50648_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:48,748] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:48,753] [INFO] Selected 14 target genomes.
[2024-01-24 14:28:48,753] [INFO] Target genome list was writen to GCF_900476175.1_50648_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:28:48,768] [INFO] Task started: fastANI
[2024-01-24 14:28:48,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a990039-2f58-4cbf-93b5-6c3508d63449/GCF_900476175.1_50648_D01_genomic.fna.gz --refList GCF_900476175.1_50648_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900476175.1_50648_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:28:51,805] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:51,823] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:28:51,823] [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_000224105.1	s__Mycoplasma putrefaciens	99.9984	277	277	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	99.58	99.16	0.97	0.94	3	conclusive
GCF_001199495.1	s__Mycoplasma sp001199495	81.4293	170	277	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000875755.1	s__Mycoplasma yeatsii	81.3915	181	277	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	96.62	96.62	0.94	0.94	2	-
GCF_000327395.1	s__Mycoplasma feriruminatoris	79.8126	142	277	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012765.1	s__Mycoplasma capricolum	79.8112	149	277	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	97.30	97.05	0.92	0.90	28	-
GCF_000183365.1	s__Mycoplasma leachii	79.399	140	277	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	99.23	98.81	0.95	0.93	3	-
GCA_000011445.1	s__Mycoplasma mycoides	79.3727	151	277	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.6652	99.80	97.85	0.98	0.96	21	-
GCF_002804105.1	s__Mesoplasma melaleucae	78.25	68	277	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002813555.1	s__Spiroplasma_A floricola	76.7615	50	277	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:28:51,826] [INFO] GTDB search result was written to GCF_900476175.1_50648_D01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:28:51,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:28:51,831] [INFO] DFAST_QC result json was written to GCF_900476175.1_50648_D01_genomic.fna/dqc_result.json
[2024-01-24 14:28:51,831] [INFO] DFAST_QC completed!
[2024-01-24 14:28:51,831] [INFO] Total running time: 0h0m34s