[2024-01-24 14:54:56,441] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,443] [INFO] DQC Reference Directory: /var/lib/cwl/stgecf61ae2-7821-4487-b8a4-04ac613f0fde/dqc_reference
[2024-01-24 14:54:57,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,943] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,944] [INFO] Running command: gunzip -c /var/lib/cwl/stg3513b11e-9ea1-4d7d-97f1-13314293810f/GCF_004379335.1_ASM437933v1_genomic.fna.gz | prodigal -d GCF_004379335.1_ASM437933v1_genomic.fna/cds.fna -a GCF_004379335.1_ASM437933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:59,675] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:59,676] [INFO] Task started: HMMsearch
[2024-01-24 14:54:59,676] [INFO] Running command: hmmsearch --tblout GCF_004379335.1_ASM437933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecf61ae2-7821-4487-b8a4-04ac613f0fde/dqc_reference/reference_markers.hmm GCF_004379335.1_ASM437933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:59,851] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:59,852] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3513b11e-9ea1-4d7d-97f1-13314293810f/GCF_004379335.1_ASM437933v1_genomic.fna.gz]
[2024-01-24 14:54:59,871] [INFO] Query marker FASTA was written to GCF_004379335.1_ASM437933v1_genomic.fna/markers.fasta
[2024-01-24 14:54:59,871] [INFO] Task started: Blastn
[2024-01-24 14:54:59,871] [INFO] Running command: blastn -query GCF_004379335.1_ASM437933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecf61ae2-7821-4487-b8a4-04ac613f0fde/dqc_reference/reference_markers.fasta -out GCF_004379335.1_ASM437933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:00,431] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:00,436] [INFO] Selected 19 target genomes.
[2024-01-24 14:55:00,437] [INFO] Target genome list was writen to GCF_004379335.1_ASM437933v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:00,548] [INFO] Task started: fastANI
[2024-01-24 14:55:00,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg3513b11e-9ea1-4d7d-97f1-13314293810f/GCF_004379335.1_ASM437933v1_genomic.fna.gz --refList GCF_004379335.1_ASM437933v1_genomic.fna/target_genomes.txt --output GCF_004379335.1_ASM437933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:06,467] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:06,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecf61ae2-7821-4487-b8a4-04ac613f0fde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:06,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecf61ae2-7821-4487-b8a4-04ac613f0fde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:06,478] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:06,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:06,478] [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
Spiroplasma gladiatoris	strain=TG-1	GCA_004379335.1	2143	2143	type	True	100.0	388	388	95	conclusive
Spiroplasma tabanidicola	strain=TAUS-1	GCA_009730595.1	324079	324079	type	True	82.0684	241	388	95	below_threshold
Spiroplasma culicicola	strain=AES-1	GCA_000565175.1	216935	216935	type	True	78.9086	159	388	95	below_threshold
Spiroplasma monobiae	strain=MQ-1	GCA_002865545.1	2136	2136	type	True	78.8843	104	388	95	below_threshold
Spiroplasma chinense	strain=CCH	GCA_008086545.1	216932	216932	type	True	78.8128	147	388	95	below_threshold
Spiroplasma diminutum	strain=CUAS-1	GCA_000439455.1	216936	216936	type	True	78.6218	125	388	95	below_threshold
Spiroplasma floricola	strain=23-6	GCA_002813555.1	216937	216937	type	True	78.4268	140	388	95	below_threshold
Spiroplasma taiwanense	strain=CT-1	GCA_000439435.1	2145	2145	type	True	78.4266	129	388	95	below_threshold
Spiroplasma apis	strain=B31	GCA_000500935.1	2137	2137	type	True	78.2147	81	388	95	below_threshold
Spiroplasma litorale	strain=TN-1	GCA_001267155.1	216942	216942	type	True	77.8733	116	388	95	below_threshold
Spiroplasma alleghenense	strain=PLHS-1	GCA_003363775.1	216931	216931	type	True	77.2521	65	388	95	below_threshold
Mycoplasma mycoides subsp. mycoides	strain=PG1	GCA_000011445.1	2103	2102	type	True	76.7122	65	388	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:06,480] [INFO] DFAST Taxonomy check result was written to GCF_004379335.1_ASM437933v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:06,480] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:06,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:06,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecf61ae2-7821-4487-b8a4-04ac613f0fde/dqc_reference/checkm_data
[2024-01-24 14:55:06,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:06,499] [INFO] Task started: CheckM
[2024-01-24 14:55:06,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004379335.1_ASM437933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004379335.1_ASM437933v1_genomic.fna/checkm_input GCF_004379335.1_ASM437933v1_genomic.fna/checkm_result
[2024-01-24 14:55:20,847] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:20,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:20,865] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:20,865] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:20,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004379335.1_ASM437933v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:20,865] [INFO] Task started: Blastn
[2024-01-24 14:55:20,866] [INFO] Running command: blastn -query GCF_004379335.1_ASM437933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecf61ae2-7821-4487-b8a4-04ac613f0fde/dqc_reference/reference_markers_gtdb.fasta -out GCF_004379335.1_ASM437933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:21,615] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:21,618] [INFO] Selected 15 target genomes.
[2024-01-24 14:55:21,618] [INFO] Target genome list was writen to GCF_004379335.1_ASM437933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:21,646] [INFO] Task started: fastANI
[2024-01-24 14:55:21,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg3513b11e-9ea1-4d7d-97f1-13314293810f/GCF_004379335.1_ASM437933v1_genomic.fna.gz --refList GCF_004379335.1_ASM437933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004379335.1_ASM437933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:25,913] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:25,924] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:25,925] [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_004379335.1	s__Spiroplasma_A gladiatoris	100.0	388	388	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009730595.1	s__Spiroplasma_A tabanidicola	82.1014	240	388	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_000565175.1	s__Spiroplasma_A culicicola	78.9344	158	388	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_008086545.1	s__Spiroplasma_A chinense	78.9134	146	388	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_002865545.1	s__Spiroplasma_A monobiae	78.8843	104	388	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_010365805.1	s__Spiroplasma_A sp010365805	78.7726	109	388	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_000439455.1	s__Spiroplasma_A diminutum	78.623	126	388	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_000439435.1	s__Spiroplasma_A taiwanense	78.4466	127	388	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_002813555.1	s__Spiroplasma_A floricola	78.4268	140	388	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_000500935.1	s__Spiroplasma_A apis	78.2204	83	388	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_001267155.1	s__Spiroplasma_A litorale	77.8541	118	388	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_003363775.1	s__Spiroplasma_B alleghenense	77.2521	65	388	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:25,926] [INFO] GTDB search result was written to GCF_004379335.1_ASM437933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:25,927] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:25,932] [INFO] DFAST_QC result json was written to GCF_004379335.1_ASM437933v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:25,932] [INFO] DFAST_QC completed!
[2024-01-24 14:55:25,932] [INFO] Total running time: 0h0m29s