[2024-01-24 11:05:25,332] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,336] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ead8777-5ca8-48cf-aa95-6d2210cb308d/dqc_reference
[2024-01-24 11:05:26,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,747] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ac9bafd-e256-40e7-9c8c-eb2b8d5ae728/GCF_002930145.1_meso03.02_genomic.fna.gz | prodigal -d GCF_002930145.1_meso03.02_genomic.fna/cds.fna -a GCF_002930145.1_meso03.02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:28,085] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:28,085] [INFO] Task started: HMMsearch
[2024-01-24 11:05:28,085] [INFO] Running command: hmmsearch --tblout GCF_002930145.1_meso03.02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ead8777-5ca8-48cf-aa95-6d2210cb308d/dqc_reference/reference_markers.hmm GCF_002930145.1_meso03.02_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:28,315] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:28,316] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2ac9bafd-e256-40e7-9c8c-eb2b8d5ae728/GCF_002930145.1_meso03.02_genomic.fna.gz]
[2024-01-24 11:05:28,328] [INFO] Query marker FASTA was written to GCF_002930145.1_meso03.02_genomic.fna/markers.fasta
[2024-01-24 11:05:28,329] [INFO] Task started: Blastn
[2024-01-24 11:05:28,329] [INFO] Running command: blastn -query GCF_002930145.1_meso03.02_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ead8777-5ca8-48cf-aa95-6d2210cb308d/dqc_reference/reference_markers.fasta -out GCF_002930145.1_meso03.02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:31,593] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:31,596] [INFO] Selected 21 target genomes.
[2024-01-24 11:05:31,597] [INFO] Target genome list was writen to GCF_002930145.1_meso03.02_genomic.fna/target_genomes.txt
[2024-01-24 11:05:31,608] [INFO] Task started: fastANI
[2024-01-24 11:05:31,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ac9bafd-e256-40e7-9c8c-eb2b8d5ae728/GCF_002930145.1_meso03.02_genomic.fna.gz --refList GCF_002930145.1_meso03.02_genomic.fna/target_genomes.txt --output GCF_002930145.1_meso03.02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:36,302] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:36,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ead8777-5ca8-48cf-aa95-6d2210cb308d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:36,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ead8777-5ca8-48cf-aa95-6d2210cb308d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:36,314] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:36,314] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:36,315] [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
Entomoplasma melaleucae	strain=M1	GCA_002804105.1	81459	81459	type	True	79.672	103	278	95	below_threshold
Mesoplasma tabanidae	strain=BARC 857	GCA_002804025.1	219745	219745	type	True	79.5596	99	278	95	below_threshold
Mesoplasma florum	strain=L1; ATCC 33453	GCA_000008305.1	2151	2151	type	True	79.4715	105	278	95	below_threshold
Entomoplasma melaleucae	strain=ATCC 49191	GCA_000685885.1	81459	81459	type	True	79.2699	99	278	95	below_threshold
Mesoplasma chauliocola	strain=CHPA-2	GCA_002290085.1	216427	216427	type	True	78.9633	108	278	95	below_threshold
Mesoplasma coleopterae	strain=BARC 779	GCA_002804245.1	324078	324078	type	True	78.9429	111	278	95	below_threshold
Mesoplasma chauliocola	strain=ATCC 49578	GCA_000518825.1	216427	216427	type	True	78.7354	107	278	95	below_threshold
Mycoplasma cottewii	strain=VIS	GCA_024918975.1	51364	51364	type	True	77.5892	67	278	95	below_threshold
Mycoplasma leachii	strain=PG50	GCA_000183365.1	2105	2105	type	True	77.5205	71	278	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:36,316] [INFO] DFAST Taxonomy check result was written to GCF_002930145.1_meso03.02_genomic.fna/tc_result.tsv
[2024-01-24 11:05:36,317] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:36,317] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:36,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ead8777-5ca8-48cf-aa95-6d2210cb308d/dqc_reference/checkm_data
[2024-01-24 11:05:36,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:36,329] [INFO] Task started: CheckM
[2024-01-24 11:05:36,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002930145.1_meso03.02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002930145.1_meso03.02_genomic.fna/checkm_input GCF_002930145.1_meso03.02_genomic.fna/checkm_result
[2024-01-24 11:05:51,302] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:51,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:51,324] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:51,324] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:51,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002930145.1_meso03.02_genomic.fna/markers.fasta)
[2024-01-24 11:05:51,326] [INFO] Task started: Blastn
[2024-01-24 11:05:51,326] [INFO] Running command: blastn -query GCF_002930145.1_meso03.02_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ead8777-5ca8-48cf-aa95-6d2210cb308d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002930145.1_meso03.02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:52,245] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:52,248] [INFO] Selected 14 target genomes.
[2024-01-24 11:05:52,248] [INFO] Target genome list was writen to GCF_002930145.1_meso03.02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:52,260] [INFO] Task started: fastANI
[2024-01-24 11:05:52,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ac9bafd-e256-40e7-9c8c-eb2b8d5ae728/GCF_002930145.1_meso03.02_genomic.fna.gz --refList GCF_002930145.1_meso03.02_genomic.fna/target_genomes_gtdb.txt --output GCF_002930145.1_meso03.02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:05:55,303] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:55,311] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:05:55,311] [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_002930155.1	s__Entomoplasma ellychniae	97.2369	250	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Entomoplasma	95.0	97.33	97.33	0.90	0.90	2	conclusive
GCF_002804105.1	s__Mesoplasma melaleucae	79.672	103	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002804025.1	s__Mesoplasma tabanidae	79.5596	99	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008305.1	s__Mesoplasma florum	79.3985	107	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.9326	98.30	97.69	0.92	0.91	10	-
GCF_002804125.1	s__Mesoplasma entomophilum	79.0153	111	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	99.01	98.03	0.96	0.92	3	-
GCF_002804245.1	s__Mesoplasma coleopterae	78.9429	111	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	98.88	98.62	0.96	0.96	3	-
GCF_002290085.1	s__Mesoplasma chauliocola	78.9292	110	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000183365.1	s__Mycoplasma leachii	77.5205	71	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	99.23	98.81	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:05:55,313] [INFO] GTDB search result was written to GCF_002930145.1_meso03.02_genomic.fna/result_gtdb.tsv
[2024-01-24 11:05:55,313] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:05:55,316] [INFO] DFAST_QC result json was written to GCF_002930145.1_meso03.02_genomic.fna/dqc_result.json
[2024-01-24 11:05:55,316] [INFO] DFAST_QC completed!
[2024-01-24 11:05:55,316] [INFO] Total running time: 0h0m30s