[2024-01-24 13:09:33,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:33,927] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:33,927] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7a5b7bf-acfc-48e0-be04-edb5bb49159b/dqc_reference
[2024-01-24 13:09:35,252] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,253] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,253] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8fc11b1-fe14-4d90-89ee-432fdfdb6e5f/GCF_024918975.1_ASM2491897v1_genomic.fna.gz | prodigal -d GCF_024918975.1_ASM2491897v1_genomic.fna/cds.fna -a GCF_024918975.1_ASM2491897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:36,739] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:36,739] [INFO] Task started: HMMsearch
[2024-01-24 13:09:36,739] [INFO] Running command: hmmsearch --tblout GCF_024918975.1_ASM2491897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7a5b7bf-acfc-48e0-be04-edb5bb49159b/dqc_reference/reference_markers.hmm GCF_024918975.1_ASM2491897v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:36,890] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:36,891] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb8fc11b1-fe14-4d90-89ee-432fdfdb6e5f/GCF_024918975.1_ASM2491897v1_genomic.fna.gz]
[2024-01-24 13:09:36,910] [INFO] Query marker FASTA was written to GCF_024918975.1_ASM2491897v1_genomic.fna/markers.fasta
[2024-01-24 13:09:36,911] [INFO] Task started: Blastn
[2024-01-24 13:09:36,911] [INFO] Running command: blastn -query GCF_024918975.1_ASM2491897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7a5b7bf-acfc-48e0-be04-edb5bb49159b/dqc_reference/reference_markers.fasta -out GCF_024918975.1_ASM2491897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:37,410] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:37,415] [INFO] Selected 11 target genomes.
[2024-01-24 13:09:37,415] [INFO] Target genome list was writen to GCF_024918975.1_ASM2491897v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:37,453] [INFO] Task started: fastANI
[2024-01-24 13:09:37,454] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8fc11b1-fe14-4d90-89ee-432fdfdb6e5f/GCF_024918975.1_ASM2491897v1_genomic.fna.gz --refList GCF_024918975.1_ASM2491897v1_genomic.fna/target_genomes.txt --output GCF_024918975.1_ASM2491897v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:39,834] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:39,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7a5b7bf-acfc-48e0-be04-edb5bb49159b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:39,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7a5b7bf-acfc-48e0-be04-edb5bb49159b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:39,843] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:39,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:39,844] [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 cottewii	strain=VIS	GCA_024918975.1	51364	51364	type	True	100.0	338	338	95	conclusive
Mycoplasma putrefaciens	strain=NCTC10155	GCA_900476175.1	2123	2123	type	True	81.5476	182	338	95	below_threshold
Mycoplasma putrefaciens	strain=KS1	GCA_000224105.1	2123	2123	type	True	81.5223	183	338	95	below_threshold
Mycoplasma feriruminatoris	strain=G5847	GCA_000327395.2	1179777	1179777	type	True	80.6051	170	338	95	below_threshold
Mycoplasma capricolum subsp. capripneumoniae	strain=type strain: F38 = NCTC 10192	GCA_000953375.1	40480	2095	type	True	80.374	153	338	95	below_threshold
Mycoplasma mycoides subsp. mycoides	strain=PG1	GCA_000011445.1	2103	2102	type	True	80.2526	170	338	95	below_threshold
Mycoplasma leachii	strain=PG50	GCA_000183365.1	2105	2105	type	True	80.1321	165	338	95	below_threshold
Mycoplasma capricolum subsp. capricolum	strain=ATCC 27343	GCA_000012765.1	40479	2095	type	True	80.0709	165	338	95	below_threshold
Spiroplasma monobiae	strain=MQ-1	GCA_002865545.1	2136	2136	type	True	77.7037	50	338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:39,845] [INFO] DFAST Taxonomy check result was written to GCF_024918975.1_ASM2491897v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:39,846] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:39,846] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:39,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7a5b7bf-acfc-48e0-be04-edb5bb49159b/dqc_reference/checkm_data
[2024-01-24 13:09:39,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:39,860] [INFO] Task started: CheckM
[2024-01-24 13:09:39,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024918975.1_ASM2491897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024918975.1_ASM2491897v1_genomic.fna/checkm_input GCF_024918975.1_ASM2491897v1_genomic.fna/checkm_result
[2024-01-24 13:09:52,865] [INFO] Task succeeded: CheckM
[2024-01-24 13:09:52,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:09:52,882] [INFO] ===== Completeness check finished =====
[2024-01-24 13:09:52,883] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:09:52,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024918975.1_ASM2491897v1_genomic.fna/markers.fasta)
[2024-01-24 13:09:52,883] [INFO] Task started: Blastn
[2024-01-24 13:09:52,883] [INFO] Running command: blastn -query GCF_024918975.1_ASM2491897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7a5b7bf-acfc-48e0-be04-edb5bb49159b/dqc_reference/reference_markers_gtdb.fasta -out GCF_024918975.1_ASM2491897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:53,316] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:53,319] [INFO] Selected 9 target genomes.
[2024-01-24 13:09:53,319] [INFO] Target genome list was writen to GCF_024918975.1_ASM2491897v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:09:53,343] [INFO] Task started: fastANI
[2024-01-24 13:09:53,344] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8fc11b1-fe14-4d90-89ee-432fdfdb6e5f/GCF_024918975.1_ASM2491897v1_genomic.fna.gz --refList GCF_024918975.1_ASM2491897v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024918975.1_ASM2491897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:09:55,491] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:55,498] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:09:55,499] [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_000875755.1	s__Mycoplasma yeatsii	94.0742	266	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	96.62	96.62	0.94	0.94	2	-
GCF_001199495.1	s__Mycoplasma sp001199495	92.4601	250	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	81.5476	182	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	99.58	99.16	0.97	0.94	3	-
GCF_000327395.1	s__Mycoplasma feriruminatoris	80.5679	157	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_900489555.1	s__Mycoplasma capri	80.504	167	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.6652	99.61	97.30	0.99	0.89	26	-
GCA_000011445.1	s__Mycoplasma mycoides	80.3385	171	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_000183365.1	s__Mycoplasma leachii	80.166	164	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	99.23	98.81	0.95	0.93	3	-
GCF_000012765.1	s__Mycoplasma capricolum	80.0801	165	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	97.30	97.05	0.92	0.90	28	-
--------------------------------------------------------------------------------
[2024-01-24 13:09:55,501] [INFO] GTDB search result was written to GCF_024918975.1_ASM2491897v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:09:55,501] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:09:55,504] [INFO] DFAST_QC result json was written to GCF_024918975.1_ASM2491897v1_genomic.fna/dqc_result.json
[2024-01-24 13:09:55,504] [INFO] DFAST_QC completed!
[2024-01-24 13:09:55,505] [INFO] Total running time: 0h0m22s