[2024-01-25 18:51:50,760] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:50,762] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:50,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg9863425a-ab62-4bed-b7cc-e6e93a25d54f/dqc_reference
[2024-01-25 18:51:51,975] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:51,976] [INFO] Task started: Prodigal
[2024-01-25 18:51:51,976] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fd71aa7-1e8d-4ab8-a4c1-24dfc06d0f2b/GCF_002795265.1_ASM279526v1_genomic.fna.gz | prodigal -d GCF_002795265.1_ASM279526v1_genomic.fna/cds.fna -a GCF_002795265.1_ASM279526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:54,450] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:54,450] [INFO] Task started: HMMsearch
[2024-01-25 18:51:54,451] [INFO] Running command: hmmsearch --tblout GCF_002795265.1_ASM279526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9863425a-ab62-4bed-b7cc-e6e93a25d54f/dqc_reference/reference_markers.hmm GCF_002795265.1_ASM279526v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:54,612] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:54,614] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9fd71aa7-1e8d-4ab8-a4c1-24dfc06d0f2b/GCF_002795265.1_ASM279526v1_genomic.fna.gz]
[2024-01-25 18:51:54,632] [INFO] Query marker FASTA was written to GCF_002795265.1_ASM279526v1_genomic.fna/markers.fasta
[2024-01-25 18:51:54,632] [INFO] Task started: Blastn
[2024-01-25 18:51:54,633] [INFO] Running command: blastn -query GCF_002795265.1_ASM279526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9863425a-ab62-4bed-b7cc-e6e93a25d54f/dqc_reference/reference_markers.fasta -out GCF_002795265.1_ASM279526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:55,174] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:55,178] [INFO] Selected 9 target genomes.
[2024-01-25 18:51:55,178] [INFO] Target genome list was writen to GCF_002795265.1_ASM279526v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:55,187] [INFO] Task started: fastANI
[2024-01-25 18:51:55,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fd71aa7-1e8d-4ab8-a4c1-24dfc06d0f2b/GCF_002795265.1_ASM279526v1_genomic.fna.gz --refList GCF_002795265.1_ASM279526v1_genomic.fna/target_genomes.txt --output GCF_002795265.1_ASM279526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:57,644] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:57,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9863425a-ab62-4bed-b7cc-e6e93a25d54f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:57,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9863425a-ab62-4bed-b7cc-e6e93a25d54f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:57,652] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:51:57,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:57,652] [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 clarkii	strain=CN-5	GCA_002795265.1	2139	2139	type	True	100.0	520	520	95	conclusive
Spiroplasma clarkii	strain=CN-5	GCA_002163565.1	2139	2139	type	True	99.9129	519	520	95	conclusive
Spiroplasma chinense	strain=CCH	GCA_008086545.1	216932	216932	type	True	78.6304	124	520	95	below_threshold
Spiroplasma culicicola	strain=AES-1	GCA_000565175.1	216935	216935	type	True	78.4921	122	520	95	below_threshold
Spiroplasma diminutum	strain=CUAS-1	GCA_000439455.1	216936	216936	type	True	78.3896	100	520	95	below_threshold
Spiroplasma floricola	strain=23-6	GCA_002813555.1	216937	216937	type	True	78.0543	111	520	95	below_threshold
Spiroplasma helicoides	strain=TABS-2	GCA_001715535.1	216938	216938	type	True	77.9289	92	520	95	below_threshold
Spiroplasma turonicum	strain=Tab4c	GCA_001262715.1	216946	216946	type	True	77.6339	57	520	95	below_threshold
Spiroplasma turonicum	strain=Tab4c	GCA_001513715.1	216946	216946	type	True	77.6339	57	520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:57,653] [INFO] DFAST Taxonomy check result was written to GCF_002795265.1_ASM279526v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:57,654] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:57,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:57,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9863425a-ab62-4bed-b7cc-e6e93a25d54f/dqc_reference/checkm_data
[2024-01-25 18:51:57,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:57,674] [INFO] Task started: CheckM
[2024-01-25 18:51:57,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002795265.1_ASM279526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002795265.1_ASM279526v1_genomic.fna/checkm_input GCF_002795265.1_ASM279526v1_genomic.fna/checkm_result
[2024-01-25 18:52:11,907] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:11,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:11,925] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:11,926] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:11,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002795265.1_ASM279526v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:11,926] [INFO] Task started: Blastn
[2024-01-25 18:52:11,926] [INFO] Running command: blastn -query GCF_002795265.1_ASM279526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9863425a-ab62-4bed-b7cc-e6e93a25d54f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002795265.1_ASM279526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:12,574] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:12,577] [INFO] Selected 17 target genomes.
[2024-01-25 18:52:12,577] [INFO] Target genome list was writen to GCF_002795265.1_ASM279526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:12,604] [INFO] Task started: fastANI
[2024-01-25 18:52:12,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fd71aa7-1e8d-4ab8-a4c1-24dfc06d0f2b/GCF_002795265.1_ASM279526v1_genomic.fna.gz --refList GCF_002795265.1_ASM279526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002795265.1_ASM279526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:16,723] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:16,730] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:16,731] [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_002795265.1	s__Spiroplasma_A clarkii	100.0	520	520	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	99.91	99.91	1.00	1.00	2	conclusive
GCF_008086545.1	s__Spiroplasma_A chinense	78.6637	123	520	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	78.525	121	520	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	78.4902	89	520	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	78.3896	100	520	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_009730595.1	s__Spiroplasma_A tabanidicola	78.1213	96	520	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	78.0225	112	520	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	77.8942	66	520	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_001715535.1	s__Spiroplasma_A helicoides	77.8908	93	520	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	77.798	58	520	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262715.1	s__Spiroplasma_A turonicum	77.6339	57	520	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:16,732] [INFO] GTDB search result was written to GCF_002795265.1_ASM279526v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:16,732] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:16,734] [INFO] DFAST_QC result json was written to GCF_002795265.1_ASM279526v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:16,735] [INFO] DFAST_QC completed!
[2024-01-25 18:52:16,735] [INFO] Total running time: 0h0m26s