[2024-01-25 19:52:05,765] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:05,766] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:05,766] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfb7702f-7b37-4c8e-9973-5eeb1be6b82e/dqc_reference
[2024-01-25 19:52:06,939] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:06,940] [INFO] Task started: Prodigal
[2024-01-25 19:52:06,940] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8a95460-9f36-4650-b917-22d6f883a283/GCF_000953375.1_F38.1_genomic.fna.gz | prodigal -d GCF_000953375.1_F38.1_genomic.fna/cds.fna -a GCF_000953375.1_F38.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:08,113] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:08,113] [INFO] Task started: HMMsearch
[2024-01-25 19:52:08,113] [INFO] Running command: hmmsearch --tblout GCF_000953375.1_F38.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfb7702f-7b37-4c8e-9973-5eeb1be6b82e/dqc_reference/reference_markers.hmm GCF_000953375.1_F38.1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:08,247] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:08,256] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd8a95460-9f36-4650-b917-22d6f883a283/GCF_000953375.1_F38.1_genomic.fna.gz]
[2024-01-25 19:52:08,275] [INFO] Query marker FASTA was written to GCF_000953375.1_F38.1_genomic.fna/markers.fasta
[2024-01-25 19:52:08,275] [INFO] Task started: Blastn
[2024-01-25 19:52:08,275] [INFO] Running command: blastn -query GCF_000953375.1_F38.1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfb7702f-7b37-4c8e-9973-5eeb1be6b82e/dqc_reference/reference_markers.fasta -out GCF_000953375.1_F38.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:08,796] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:08,799] [INFO] Selected 12 target genomes.
[2024-01-25 19:52:08,799] [INFO] Target genome list was writen to GCF_000953375.1_F38.1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:08,816] [INFO] Task started: fastANI
[2024-01-25 19:52:08,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8a95460-9f36-4650-b917-22d6f883a283/GCF_000953375.1_F38.1_genomic.fna.gz --refList GCF_000953375.1_F38.1_genomic.fna/target_genomes.txt --output GCF_000953375.1_F38.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:12,735] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:12,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfb7702f-7b37-4c8e-9973-5eeb1be6b82e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:12,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfb7702f-7b37-4c8e-9973-5eeb1be6b82e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:12,745] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:52:12,745] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:12,746] [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 capricolum subsp. capripneumoniae	strain=type strain: F38 = NCTC 10192	GCA_000953375.1	40480	2095	type	True	100.0	338	338	95	conclusive
Mycoplasma capricolum subsp. capricolum	strain=ATCC 27343	GCA_000012765.1	40479	2095	type	True	97.0067	309	338	95	conclusive
Mycoplasma leachii	strain=PG50	GCA_000183365.1	2105	2105	type	True	94.286	289	338	95	below_threshold
Mycoplasma mycoides subsp. mycoides	strain=PG1	GCA_000011445.1	2103	2102	type	True	90.4807	280	338	95	below_threshold
Mycoplasma mycoides subsp. capri	strain=PG3	GCA_000590435.1	40477	2102	type	True	90.417	267	338	95	below_threshold
Mycoplasma mycoides subsp. capri	strain=PG3	GCA_000339035.1	40477	2102	type	True	90.1353	277	338	95	below_threshold
Mycoplasma feriruminatoris	strain=G5847	GCA_000327395.2	1179777	1179777	type	True	88.009	279	338	95	below_threshold
Mycoplasma putrefaciens	strain=NCTC10155	GCA_900476175.1	2123	2123	type	True	80.01	136	338	95	below_threshold
Mycoplasma cottewii	strain=VIS	GCA_024918975.1	51364	51364	type	True	79.9943	153	338	95	below_threshold
Mycoplasma putrefaciens	strain=KS1	GCA_000224105.1	2123	2123	type	True	79.9019	135	338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:12,747] [INFO] DFAST Taxonomy check result was written to GCF_000953375.1_F38.1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:12,748] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:12,748] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:12,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfb7702f-7b37-4c8e-9973-5eeb1be6b82e/dqc_reference/checkm_data
[2024-01-25 19:52:12,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:12,762] [INFO] Task started: CheckM
[2024-01-25 19:52:12,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000953375.1_F38.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000953375.1_F38.1_genomic.fna/checkm_input GCF_000953375.1_F38.1_genomic.fna/checkm_result
[2024-01-25 19:52:24,002] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:24,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:24,023] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:24,024] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:24,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000953375.1_F38.1_genomic.fna/markers.fasta)
[2024-01-25 19:52:24,024] [INFO] Task started: Blastn
[2024-01-25 19:52:24,024] [INFO] Running command: blastn -query GCF_000953375.1_F38.1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfb7702f-7b37-4c8e-9973-5eeb1be6b82e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000953375.1_F38.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:24,718] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:24,720] [INFO] Selected 6 target genomes.
[2024-01-25 19:52:24,721] [INFO] Target genome list was writen to GCF_000953375.1_F38.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:24,729] [INFO] Task started: fastANI
[2024-01-25 19:52:24,730] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8a95460-9f36-4650-b917-22d6f883a283/GCF_000953375.1_F38.1_genomic.fna.gz --refList GCF_000953375.1_F38.1_genomic.fna/target_genomes_gtdb.txt --output GCF_000953375.1_F38.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:26,275] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:26,281] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:26,281] [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_000012765.1	s__Mycoplasma capricolum	96.9686	310	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	97.30	97.05	0.92	0.90	28	conclusive
GCF_000183365.1	s__Mycoplasma leachii	94.286	289	338	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	90.5773	278	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.6652	99.80	97.85	0.98	0.96	21	-
GCF_900489555.1	s__Mycoplasma capri	90.4915	262	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.6652	99.61	97.30	0.99	0.89	26	-
GCF_000327395.1	s__Mycoplasma feriruminatoris	87.9475	261	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224105.1	s__Mycoplasma putrefaciens	79.9413	134	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	99.58	99.16	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:26,282] [INFO] GTDB search result was written to GCF_000953375.1_F38.1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:26,283] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:26,285] [INFO] DFAST_QC result json was written to GCF_000953375.1_F38.1_genomic.fna/dqc_result.json
[2024-01-25 19:52:26,285] [INFO] DFAST_QC completed!
[2024-01-25 19:52:26,286] [INFO] Total running time: 0h0m21s