[2024-01-24 15:10:54,436] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:54,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:54,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg042427c3-cfd0-42cb-abd5-dadd8b13984d/dqc_reference
[2024-01-24 15:10:56,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,633] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg89f82d7d-7614-4f2f-9223-6258e777cfca/GCF_002803985.1_ASM280398v1_genomic.fna.gz | prodigal -d GCF_002803985.1_ASM280398v1_genomic.fna/cds.fna -a GCF_002803985.1_ASM280398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:58,644] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:58,645] [INFO] Task started: HMMsearch
[2024-01-24 15:10:58,645] [INFO] Running command: hmmsearch --tblout GCF_002803985.1_ASM280398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg042427c3-cfd0-42cb-abd5-dadd8b13984d/dqc_reference/reference_markers.hmm GCF_002803985.1_ASM280398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:58,954] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:58,956] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg89f82d7d-7614-4f2f-9223-6258e777cfca/GCF_002803985.1_ASM280398v1_genomic.fna.gz]
[2024-01-24 15:10:58,976] [INFO] Query marker FASTA was written to GCF_002803985.1_ASM280398v1_genomic.fna/markers.fasta
[2024-01-24 15:10:58,982] [INFO] Task started: Blastn
[2024-01-24 15:10:58,982] [INFO] Running command: blastn -query GCF_002803985.1_ASM280398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg042427c3-cfd0-42cb-abd5-dadd8b13984d/dqc_reference/reference_markers.fasta -out GCF_002803985.1_ASM280398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:02,418] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:02,421] [INFO] Selected 10 target genomes.
[2024-01-24 15:11:02,421] [INFO] Target genome list was writen to GCF_002803985.1_ASM280398v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:02,455] [INFO] Task started: fastANI
[2024-01-24 15:11:02,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg89f82d7d-7614-4f2f-9223-6258e777cfca/GCF_002803985.1_ASM280398v1_genomic.fna.gz --refList GCF_002803985.1_ASM280398v1_genomic.fna/target_genomes.txt --output GCF_002803985.1_ASM280398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:05,004] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:05,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg042427c3-cfd0-42cb-abd5-dadd8b13984d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:05,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg042427c3-cfd0-42cb-abd5-dadd8b13984d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:05,013] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:11:05,013] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:05,013] [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
Williamsoniiplasma luminosum	strain=PIMN-1	GCA_002803985.1	214888	214888	type	True	100.0	343	343	95	conclusive
Williamsoniiplasma luminosum	strain=ATCC 49195	GCA_000526855.1	214888	214888	type	True	99.9058	318	343	95	conclusive
Williamsoniiplasma lucivorax	strain=ATCC 49196	GCA_000518285.1	209274	209274	type	True	80.6707	209	343	95	below_threshold
Williamsoniiplasma lucivorax	strain=PIPN-2	GCA_002930185.1	209274	209274	type	True	80.5962	213	343	95	below_threshold
Mesoplasma florum	strain=L1; ATCC 33453	GCA_000008305.1	2151	2151	type	True	77.6424	59	343	95	below_threshold
Mycoplasma leachii	strain=PG50	GCA_000183365.1	2105	2105	type	True	77.1868	59	343	95	below_threshold
Mycoplasma mycoides subsp. mycoides	strain=PG1	GCA_000011445.1	2103	2102	type	True	77.0952	63	343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:05,015] [INFO] DFAST Taxonomy check result was written to GCF_002803985.1_ASM280398v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:05,015] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:05,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:05,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg042427c3-cfd0-42cb-abd5-dadd8b13984d/dqc_reference/checkm_data
[2024-01-24 15:11:05,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:05,034] [INFO] Task started: CheckM
[2024-01-24 15:11:05,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002803985.1_ASM280398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002803985.1_ASM280398v1_genomic.fna/checkm_input GCF_002803985.1_ASM280398v1_genomic.fna/checkm_result
[2024-01-24 15:11:23,566] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:23,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:23,585] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:23,585] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:23,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002803985.1_ASM280398v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:23,586] [INFO] Task started: Blastn
[2024-01-24 15:11:23,586] [INFO] Running command: blastn -query GCF_002803985.1_ASM280398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg042427c3-cfd0-42cb-abd5-dadd8b13984d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002803985.1_ASM280398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:24,377] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:24,381] [INFO] Selected 23 target genomes.
[2024-01-24 15:11:24,381] [INFO] Target genome list was writen to GCF_002803985.1_ASM280398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:24,428] [INFO] Task started: fastANI
[2024-01-24 15:11:24,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg89f82d7d-7614-4f2f-9223-6258e777cfca/GCF_002803985.1_ASM280398v1_genomic.fna.gz --refList GCF_002803985.1_ASM280398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002803985.1_ASM280398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:30,841] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:30,852] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:30,852] [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_002803985.1	s__Williamsoniiplasma luminosum	100.0	343	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Williamsoniiplasma	95.0	97.66	95.33	0.92	0.84	3	conclusive
GCF_000518285.1	s__Williamsoniiplasma lucivorax	80.7069	209	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Williamsoniiplasma	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002804105.1	s__Mesoplasma melaleucae	77.8866	57	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002804005.1	s__Williamsoniiplasma somnilux	77.833	66	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Williamsoniiplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002804245.1	s__Mesoplasma coleopterae	77.8266	55	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	98.88	98.62	0.96	0.96	3	-
GCF_000701525.1	s__Mesoplasma grammopterae	77.7921	55	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.9326	98.59	97.19	0.95	0.91	3	-
GCF_000008305.1	s__Mesoplasma florum	77.6061	59	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.9326	98.30	97.69	0.92	0.91	10	-
GCF_002804025.1	s__Mesoplasma tabanidae	77.4118	57	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000565175.1	s__Spiroplasma_A culicicola	77.2741	51	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183365.1	s__Mycoplasma leachii	77.1868	59	343	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	77.0952	63	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.6652	99.80	97.85	0.98	0.96	21	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:30,854] [INFO] GTDB search result was written to GCF_002803985.1_ASM280398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:30,854] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:30,858] [INFO] DFAST_QC result json was written to GCF_002803985.1_ASM280398v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:30,858] [INFO] DFAST_QC completed!
[2024-01-24 15:11:30,858] [INFO] Total running time: 0h0m36s