[2024-01-24 13:13:37,322] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:37,324] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:37,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg2344d5b6-a7ea-4cfa-89ec-724276e3f81c/dqc_reference
[2024-01-24 13:13:38,593] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:38,595] [INFO] Task started: Prodigal
[2024-01-24 13:13:38,595] [INFO] Running command: gunzip -c /var/lib/cwl/stgbab86b25-72a3-42be-a359-59fba283f2ff/GCF_003363775.1_ASM336377v1_genomic.fna.gz | prodigal -d GCF_003363775.1_ASM336377v1_genomic.fna/cds.fna -a GCF_003363775.1_ASM336377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:40,945] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:40,945] [INFO] Task started: HMMsearch
[2024-01-24 13:13:40,945] [INFO] Running command: hmmsearch --tblout GCF_003363775.1_ASM336377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2344d5b6-a7ea-4cfa-89ec-724276e3f81c/dqc_reference/reference_markers.hmm GCF_003363775.1_ASM336377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:41,124] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:41,125] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbab86b25-72a3-42be-a359-59fba283f2ff/GCF_003363775.1_ASM336377v1_genomic.fna.gz]
[2024-01-24 13:13:41,144] [INFO] Query marker FASTA was written to GCF_003363775.1_ASM336377v1_genomic.fna/markers.fasta
[2024-01-24 13:13:41,145] [INFO] Task started: Blastn
[2024-01-24 13:13:41,145] [INFO] Running command: blastn -query GCF_003363775.1_ASM336377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2344d5b6-a7ea-4cfa-89ec-724276e3f81c/dqc_reference/reference_markers.fasta -out GCF_003363775.1_ASM336377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:41,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:41,786] [INFO] Selected 13 target genomes.
[2024-01-24 13:13:41,787] [INFO] Target genome list was writen to GCF_003363775.1_ASM336377v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:41,804] [INFO] Task started: fastANI
[2024-01-24 13:13:41,805] [INFO] Running command: fastANI --query /var/lib/cwl/stgbab86b25-72a3-42be-a359-59fba283f2ff/GCF_003363775.1_ASM336377v1_genomic.fna.gz --refList GCF_003363775.1_ASM336377v1_genomic.fna/target_genomes.txt --output GCF_003363775.1_ASM336377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:45,101] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:45,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2344d5b6-a7ea-4cfa-89ec-724276e3f81c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:45,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2344d5b6-a7ea-4cfa-89ec-724276e3f81c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:45,109] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:45,109] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:45,110] [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 alleghenense	strain=PLHS-1	GCA_003363775.1	216931	216931	type	True	100.0	444	445	95	conclusive
Spiroplasma sabaudiense	strain=Ar-1343	GCA_000565215.1	216944	216944	type	True	79.6366	160	445	95	below_threshold
Spiroplasma chinense	strain=CCH	GCA_008086545.1	216932	216932	type	True	78.1476	57	445	95	below_threshold
Spiroplasma clarkii	strain=CN-5	GCA_002795265.1	2139	2139	type	True	77.879	53	445	95	below_threshold
Spiroplasma gladiatoris	strain=TG-1	GCA_004379335.1	2143	2143	type	True	77.2645	60	445	95	below_threshold
Spiroplasma culicicola	strain=AES-1	GCA_000565175.1	216935	216935	type	True	77.1814	73	445	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:45,111] [INFO] DFAST Taxonomy check result was written to GCF_003363775.1_ASM336377v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:45,112] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:45,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:45,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2344d5b6-a7ea-4cfa-89ec-724276e3f81c/dqc_reference/checkm_data
[2024-01-24 13:13:45,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:45,129] [INFO] Task started: CheckM
[2024-01-24 13:13:45,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003363775.1_ASM336377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003363775.1_ASM336377v1_genomic.fna/checkm_input GCF_003363775.1_ASM336377v1_genomic.fna/checkm_result
[2024-01-24 13:14:00,726] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:00,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:00,744] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:00,744] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:00,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003363775.1_ASM336377v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:00,745] [INFO] Task started: Blastn
[2024-01-24 13:14:00,745] [INFO] Running command: blastn -query GCF_003363775.1_ASM336377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2344d5b6-a7ea-4cfa-89ec-724276e3f81c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003363775.1_ASM336377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:01,496] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:01,500] [INFO] Selected 16 target genomes.
[2024-01-24 13:14:01,501] [INFO] Target genome list was writen to GCF_003363775.1_ASM336377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:01,541] [INFO] Task started: fastANI
[2024-01-24 13:14:01,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgbab86b25-72a3-42be-a359-59fba283f2ff/GCF_003363775.1_ASM336377v1_genomic.fna.gz --refList GCF_003363775.1_ASM336377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003363775.1_ASM336377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:04,721] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:04,730] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:04,730] [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_003363775.1	s__Spiroplasma_B alleghenense	100.0	445	445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000565215.1	s__Spiroplasma_B sabaudiense	79.6231	160	445	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_008086545.1	s__Spiroplasma_A chinense	78.5188	60	445	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_002795265.1	s__Spiroplasma_A clarkii	77.7626	52	445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	99.91	99.91	1.00	1.00	2	-
GCF_010365805.1	s__Spiroplasma_A sp010365805	77.7023	59	445	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	77.6751	60	445	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_004379335.1	s__Spiroplasma_A gladiatoris	77.2208	61	445	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	77.1814	73	445	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	77.1102	58	445	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 13:14:04,732] [INFO] GTDB search result was written to GCF_003363775.1_ASM336377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:04,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:04,735] [INFO] DFAST_QC result json was written to GCF_003363775.1_ASM336377v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:04,736] [INFO] DFAST_QC completed!
[2024-01-24 13:14:04,736] [INFO] Total running time: 0h0m27s