[2024-01-24 14:03:03,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:03,206] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:03,207] [INFO] DQC Reference Directory: /var/lib/cwl/stge8a4f183-3ed9-4b02-a197-5dbf1e973611/dqc_reference
[2024-01-24 14:03:04,419] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:04,420] [INFO] Task started: Prodigal
[2024-01-24 14:03:04,420] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b64f5e9-976f-46fa-b12f-26b39d15dad9/GCF_000686545.1_ASM68654v1_genomic.fna.gz | prodigal -d GCF_000686545.1_ASM68654v1_genomic.fna/cds.fna -a GCF_000686545.1_ASM68654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:06,157] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:06,157] [INFO] Task started: HMMsearch
[2024-01-24 14:03:06,158] [INFO] Running command: hmmsearch --tblout GCF_000686545.1_ASM68654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8a4f183-3ed9-4b02-a197-5dbf1e973611/dqc_reference/reference_markers.hmm GCF_000686545.1_ASM68654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:06,345] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:06,347] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6b64f5e9-976f-46fa-b12f-26b39d15dad9/GCF_000686545.1_ASM68654v1_genomic.fna.gz]
[2024-01-24 14:03:06,364] [INFO] Query marker FASTA was written to GCF_000686545.1_ASM68654v1_genomic.fna/markers.fasta
[2024-01-24 14:03:06,364] [INFO] Task started: Blastn
[2024-01-24 14:03:06,364] [INFO] Running command: blastn -query GCF_000686545.1_ASM68654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8a4f183-3ed9-4b02-a197-5dbf1e973611/dqc_reference/reference_markers.fasta -out GCF_000686545.1_ASM68654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:06,861] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:06,866] [INFO] Selected 9 target genomes.
[2024-01-24 14:03:06,866] [INFO] Target genome list was writen to GCF_000686545.1_ASM68654v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:06,874] [INFO] Task started: fastANI
[2024-01-24 14:03:06,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b64f5e9-976f-46fa-b12f-26b39d15dad9/GCF_000686545.1_ASM68654v1_genomic.fna.gz --refList GCF_000686545.1_ASM68654v1_genomic.fna/target_genomes.txt --output GCF_000686545.1_ASM68654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:08,725] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:08,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8a4f183-3ed9-4b02-a197-5dbf1e973611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:08,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8a4f183-3ed9-4b02-a197-5dbf1e973611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:08,739] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:03:08,739] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:08,739] [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
Mesoplasma syrphidae	strain=ATCC 51578	GCA_000686545.1	225999	225999	type	True	100.0	298	301	95	conclusive
Mesoplasma syrphidae	strain=YJS	GCA_002843565.1	225999	225999	type	True	99.9871	297	301	95	conclusive
Mesoplasma seiffertii	strain=ATCC 49495	GCA_000518725.1	28224	28224	type	True	83.6421	236	301	95	below_threshold
Williamsoniiplasma somnilux	strain=ATCC 49194	GCA_000526835.1	215578	215578	type	True	78.8861	59	301	95	below_threshold
Williamsoniiplasma somnilux	strain=PYAN-1	GCA_002804005.1	215578	215578	type	True	78.8566	59	301	95	below_threshold
Entomoplasma melaleucae	strain=M1	GCA_002804105.1	81459	81459	type	True	78.8566	67	301	95	below_threshold
Entomoplasma melaleucae	strain=ATCC 49191	GCA_000685885.1	81459	81459	type	True	78.1783	66	301	95	below_threshold
Mycoplasma feriruminatoris	strain=G5847	GCA_000327395.2	1179777	1179777	type	True	77.7876	63	301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:08,741] [INFO] DFAST Taxonomy check result was written to GCF_000686545.1_ASM68654v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:08,742] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:08,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:08,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8a4f183-3ed9-4b02-a197-5dbf1e973611/dqc_reference/checkm_data
[2024-01-24 14:03:08,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:08,760] [INFO] Task started: CheckM
[2024-01-24 14:03:08,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000686545.1_ASM68654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000686545.1_ASM68654v1_genomic.fna/checkm_input GCF_000686545.1_ASM68654v1_genomic.fna/checkm_result
[2024-01-24 14:03:22,467] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:22,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:22,486] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:22,487] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:22,487] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000686545.1_ASM68654v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:22,488] [INFO] Task started: Blastn
[2024-01-24 14:03:22,488] [INFO] Running command: blastn -query GCF_000686545.1_ASM68654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8a4f183-3ed9-4b02-a197-5dbf1e973611/dqc_reference/reference_markers_gtdb.fasta -out GCF_000686545.1_ASM68654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:22,968] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:22,972] [INFO] Selected 11 target genomes.
[2024-01-24 14:03:22,972] [INFO] Target genome list was writen to GCF_000686545.1_ASM68654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:03:22,980] [INFO] Task started: fastANI
[2024-01-24 14:03:22,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b64f5e9-976f-46fa-b12f-26b39d15dad9/GCF_000686545.1_ASM68654v1_genomic.fna.gz --refList GCF_000686545.1_ASM68654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000686545.1_ASM68654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:03:25,606] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:25,621] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:03:25,622] [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_002843565.1	s__Tullyiplasma syrphidae	99.9869	298	301	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Tullyiplasma	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000518725.1	s__Tullyiplasma seiffertii	83.6421	236	301	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Tullyiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000483165.1	s__Tullyiplasma multilocale	79.0306	91	301	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Tullyiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002804005.1	s__Williamsoniiplasma somnilux	78.8566	59	301	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Williamsoniiplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002804105.1	s__Mesoplasma melaleucae	78.7939	68	301	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002804245.1	s__Mesoplasma coleopterae	78.7894	68	301	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	98.88	98.62	0.96	0.96	3	-
GCF_000702725.1	s__Tullyiplasma photuris	78.7417	84	301	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Tullyiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900489555.1	s__Mycoplasma capri	78.2137	63	301	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	77.601	60	301	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:03:25,625] [INFO] GTDB search result was written to GCF_000686545.1_ASM68654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:03:25,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:03:25,629] [INFO] DFAST_QC result json was written to GCF_000686545.1_ASM68654v1_genomic.fna/dqc_result.json
[2024-01-24 14:03:25,629] [INFO] DFAST_QC completed!
[2024-01-24 14:03:25,629] [INFO] Total running time: 0h0m22s