[2024-01-24 12:29:28,779] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,781] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,781] [INFO] DQC Reference Directory: /var/lib/cwl/stg44a2bcd8-d276-4464-be7e-571e85929cf5/dqc_reference
[2024-01-24 12:29:30,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,177] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,177] [INFO] Running command: gunzip -c /var/lib/cwl/stgb89d9dbe-37d8-4c8e-a469-ff75192d13b4/GCF_002865545.1_ASM286554v1_genomic.fna.gz | prodigal -d GCF_002865545.1_ASM286554v1_genomic.fna/cds.fna -a GCF_002865545.1_ASM286554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:31,764] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:31,765] [INFO] Task started: HMMsearch
[2024-01-24 12:29:31,765] [INFO] Running command: hmmsearch --tblout GCF_002865545.1_ASM286554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44a2bcd8-d276-4464-be7e-571e85929cf5/dqc_reference/reference_markers.hmm GCF_002865545.1_ASM286554v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:31,949] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:31,950] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb89d9dbe-37d8-4c8e-a469-ff75192d13b4/GCF_002865545.1_ASM286554v1_genomic.fna.gz]
[2024-01-24 12:29:31,963] [INFO] Query marker FASTA was written to GCF_002865545.1_ASM286554v1_genomic.fna/markers.fasta
[2024-01-24 12:29:31,964] [INFO] Task started: Blastn
[2024-01-24 12:29:31,964] [INFO] Running command: blastn -query GCF_002865545.1_ASM286554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44a2bcd8-d276-4464-be7e-571e85929cf5/dqc_reference/reference_markers.fasta -out GCF_002865545.1_ASM286554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:33,646] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:33,655] [INFO] Selected 8 target genomes.
[2024-01-24 12:29:33,655] [INFO] Target genome list was writen to GCF_002865545.1_ASM286554v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:33,666] [INFO] Task started: fastANI
[2024-01-24 12:29:33,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgb89d9dbe-37d8-4c8e-a469-ff75192d13b4/GCF_002865545.1_ASM286554v1_genomic.fna.gz --refList GCF_002865545.1_ASM286554v1_genomic.fna/target_genomes.txt --output GCF_002865545.1_ASM286554v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:36,134] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:36,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44a2bcd8-d276-4464-be7e-571e85929cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:36,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44a2bcd8-d276-4464-be7e-571e85929cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:36,142] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:36,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:36,142] [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 monobiae	strain=MQ-1	GCA_002865545.1	2136	2136	type	True	100.0	297	297	95	conclusive
Spiroplasma floricola	strain=23-6	GCA_002813555.1	216937	216937	type	True	82.7905	215	297	95	below_threshold
Spiroplasma diminutum	strain=CUAS-1	GCA_000439455.1	216936	216936	type	True	82.7235	221	297	95	below_threshold
Spiroplasma cantharicola	strain=CC-1	GCA_001281045.1	362837	362837	type	True	81.8755	192	297	95	below_threshold
Spiroplasma taiwanense	strain=CT-1	GCA_000439435.1	2145	2145	type	True	79.123	146	297	95	below_threshold
Spiroplasma gladiatoris	strain=TG-1	GCA_004379335.1	2143	2143	type	True	78.7204	108	297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:36,144] [INFO] DFAST Taxonomy check result was written to GCF_002865545.1_ASM286554v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:36,144] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:36,144] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:36,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44a2bcd8-d276-4464-be7e-571e85929cf5/dqc_reference/checkm_data
[2024-01-24 12:29:36,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:36,162] [INFO] Task started: CheckM
[2024-01-24 12:29:36,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002865545.1_ASM286554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002865545.1_ASM286554v1_genomic.fna/checkm_input GCF_002865545.1_ASM286554v1_genomic.fna/checkm_result
[2024-01-24 12:29:51,449] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:51,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:51,525] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:51,525] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:51,525] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002865545.1_ASM286554v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:51,526] [INFO] Task started: Blastn
[2024-01-24 12:29:51,526] [INFO] Running command: blastn -query GCF_002865545.1_ASM286554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44a2bcd8-d276-4464-be7e-571e85929cf5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002865545.1_ASM286554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:52,375] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:52,384] [INFO] Selected 8 target genomes.
[2024-01-24 12:29:52,384] [INFO] Target genome list was writen to GCF_002865545.1_ASM286554v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:52,398] [INFO] Task started: fastANI
[2024-01-24 12:29:52,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgb89d9dbe-37d8-4c8e-a469-ff75192d13b4/GCF_002865545.1_ASM286554v1_genomic.fna.gz --refList GCF_002865545.1_ASM286554v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002865545.1_ASM286554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:54,765] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:54,772] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:54,772] [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_002865545.1	s__Spiroplasma_A monobiae	100.0	297	297	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_010365805.1	s__Spiroplasma_A sp010365805	84.4245	244	297	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	82.7905	215	297	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	82.7418	220	297	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_001281045.1	s__Spiroplasma_A cantharicola	81.8375	193	297	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	79.1555	145	297	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 12:29:54,774] [INFO] GTDB search result was written to GCF_002865545.1_ASM286554v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:54,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:54,777] [INFO] DFAST_QC result json was written to GCF_002865545.1_ASM286554v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:54,777] [INFO] DFAST_QC completed!
[2024-01-24 12:29:54,777] [INFO] Total running time: 0h0m26s