[2024-01-24 14:50:04,646] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:50:04,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:50:04,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c573925-afeb-4493-835a-085124d87413/dqc_reference
[2024-01-24 14:50:08,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:50:08,860] [INFO] Task started: Prodigal
[2024-01-24 14:50:08,861] [INFO] Running command: gunzip -c /var/lib/cwl/stg910ec760-5355-4ca5-9288-2aff193d3227/GCF_002804005.1_ASM280400v1_genomic.fna.gz | prodigal -d GCF_002804005.1_ASM280400v1_genomic.fna/cds.fna -a GCF_002804005.1_ASM280400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:50:10,500] [INFO] Task succeeded: Prodigal
[2024-01-24 14:50:10,500] [INFO] Task started: HMMsearch
[2024-01-24 14:50:10,500] [INFO] Running command: hmmsearch --tblout GCF_002804005.1_ASM280400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c573925-afeb-4493-835a-085124d87413/dqc_reference/reference_markers.hmm GCF_002804005.1_ASM280400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:50:10,777] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:50:10,779] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg910ec760-5355-4ca5-9288-2aff193d3227/GCF_002804005.1_ASM280400v1_genomic.fna.gz]
[2024-01-24 14:50:10,805] [INFO] Query marker FASTA was written to GCF_002804005.1_ASM280400v1_genomic.fna/markers.fasta
[2024-01-24 14:50:10,806] [INFO] Task started: Blastn
[2024-01-24 14:50:10,806] [INFO] Running command: blastn -query GCF_002804005.1_ASM280400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c573925-afeb-4493-835a-085124d87413/dqc_reference/reference_markers.fasta -out GCF_002804005.1_ASM280400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:14,929] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:14,933] [INFO] Selected 17 target genomes.
[2024-01-24 14:50:14,933] [INFO] Target genome list was writen to GCF_002804005.1_ASM280400v1_genomic.fna/target_genomes.txt
[2024-01-24 14:50:15,002] [INFO] Task started: fastANI
[2024-01-24 14:50:15,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg910ec760-5355-4ca5-9288-2aff193d3227/GCF_002804005.1_ASM280400v1_genomic.fna.gz --refList GCF_002804005.1_ASM280400v1_genomic.fna/target_genomes.txt --output GCF_002804005.1_ASM280400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:50:20,133] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:20,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c573925-afeb-4493-835a-085124d87413/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:50:20,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c573925-afeb-4493-835a-085124d87413/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:50:20,191] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:50:20,192] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:50:20,192] [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 somnilux	strain=PYAN-1	GCA_002804005.1	215578	215578	type	True	100.0	289	289	95	conclusive
Williamsoniiplasma somnilux	strain=ATCC 49194	GCA_000526835.1	215578	215578	type	True	99.9869	286	289	95	conclusive
Mesoplasma syrphidae	strain=ATCC 51578	GCA_000686545.1	225999	225999	type	True	78.7425	59	289	95	below_threshold
Mesoplasma syrphidae	strain=YJS	GCA_002843565.1	225999	225999	type	True	78.7068	61	289	95	below_threshold
Mesoplasma seiffertii	strain=ATCC 49495	GCA_000518725.1	28224	28224	type	True	78.4968	73	289	95	below_threshold
Mycoplasma cottewii	strain=VIS	GCA_024918975.1	51364	51364	type	True	77.8732	66	289	95	below_threshold
Mesoplasma chauliocola	strain=CHPA-2	GCA_002290085.1	216427	216427	type	True	77.6912	68	289	95	below_threshold
Mesoplasma chauliocola	strain=ATCC 49578	GCA_000518825.1	216427	216427	type	True	77.653	69	289	95	below_threshold
Entomoplasma melaleucae	strain=M1	GCA_002804105.1	81459	81459	type	True	77.6354	59	289	95	below_threshold
Entomoplasma melaleucae	strain=ATCC 49191	GCA_000685885.1	81459	81459	type	True	77.3625	62	289	95	below_threshold
Spiroplasma cantharicola	strain=CC-1	GCA_001281045.1	362837	362837	type	True	76.7875	53	289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:50:20,194] [INFO] DFAST Taxonomy check result was written to GCF_002804005.1_ASM280400v1_genomic.fna/tc_result.tsv
[2024-01-24 14:50:20,194] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:50:20,195] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:50:20,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c573925-afeb-4493-835a-085124d87413/dqc_reference/checkm_data
[2024-01-24 14:50:20,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:50:20,220] [INFO] Task started: CheckM
[2024-01-24 14:50:20,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002804005.1_ASM280400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002804005.1_ASM280400v1_genomic.fna/checkm_input GCF_002804005.1_ASM280400v1_genomic.fna/checkm_result
[2024-01-24 14:50:41,692] [INFO] Task succeeded: CheckM
[2024-01-24 14:50:41,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:50:41,709] [INFO] ===== Completeness check finished =====
[2024-01-24 14:50:41,710] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:50:41,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002804005.1_ASM280400v1_genomic.fna/markers.fasta)
[2024-01-24 14:50:41,712] [INFO] Task started: Blastn
[2024-01-24 14:50:41,712] [INFO] Running command: blastn -query GCF_002804005.1_ASM280400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c573925-afeb-4493-835a-085124d87413/dqc_reference/reference_markers_gtdb.fasta -out GCF_002804005.1_ASM280400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:42,904] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:42,908] [INFO] Selected 22 target genomes.
[2024-01-24 14:50:42,909] [INFO] Target genome list was writen to GCF_002804005.1_ASM280400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:50:42,928] [INFO] Task started: fastANI
[2024-01-24 14:50:42,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg910ec760-5355-4ca5-9288-2aff193d3227/GCF_002804005.1_ASM280400v1_genomic.fna.gz --refList GCF_002804005.1_ASM280400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002804005.1_ASM280400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:47,344] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:47,381] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:50:47,381] [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_002804005.1	s__Williamsoniiplasma somnilux	100.0	289	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Williamsoniiplasma	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002843565.1	s__Tullyiplasma syrphidae	78.7068	61	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Tullyiplasma	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000518725.1	s__Tullyiplasma seiffertii	78.4968	73	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Tullyiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702725.1	s__Tullyiplasma photuris	78.4466	77	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Tullyiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008305.1	s__Mesoplasma florum	78.2755	72	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.9326	98.30	97.69	0.92	0.91	10	-
GCF_002804245.1	s__Mesoplasma coleopterae	78.1378	69	289	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	78.0894	68	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.9326	98.59	97.19	0.95	0.91	3	-
GCF_002803985.1	s__Williamsoniiplasma luminosum	77.9815	72	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Williamsoniiplasma	95.0	97.66	95.33	0.92	0.84	3	-
GCF_000875755.1	s__Mycoplasma yeatsii	77.7423	66	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	96.62	96.62	0.94	0.94	2	-
GCF_000483165.1	s__Tullyiplasma multilocale	77.7386	74	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Tullyiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002290085.1	s__Mesoplasma chauliocola	77.6912	68	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900489555.1	s__Mycoplasma capri	77.5021	67	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.6652	99.61	97.30	0.99	0.89	26	-
GCF_000012765.1	s__Mycoplasma capricolum	77.3931	69	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	97.30	97.05	0.92	0.90	28	-
GCF_001281045.1	s__Spiroplasma_A cantharicola	76.7875	53	289	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 14:50:47,383] [INFO] GTDB search result was written to GCF_002804005.1_ASM280400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:47,384] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:47,399] [INFO] DFAST_QC result json was written to GCF_002804005.1_ASM280400v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:47,399] [INFO] DFAST_QC completed!
[2024-01-24 14:50:47,400] [INFO] Total running time: 0h0m43s