[2024-01-24 12:40:07,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,961] [INFO] DQC Reference Directory: /var/lib/cwl/stge3894f7a-db2a-428b-89af-ff7f4db2797b/dqc_reference
[2024-01-24 12:40:09,362] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,364] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,365] [INFO] Running command: gunzip -c /var/lib/cwl/stgefc5a84f-27ce-41b4-a608-dfc43bd942fa/GCF_000712175.1_ASM71217v1_genomic.fna.gz | prodigal -d GCF_000712175.1_ASM71217v1_genomic.fna/cds.fna -a GCF_000712175.1_ASM71217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:10,582] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:10,582] [INFO] Task started: HMMsearch
[2024-01-24 12:40:10,583] [INFO] Running command: hmmsearch --tblout GCF_000712175.1_ASM71217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3894f7a-db2a-428b-89af-ff7f4db2797b/dqc_reference/reference_markers.hmm GCF_000712175.1_ASM71217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:10,761] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:10,762] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgefc5a84f-27ce-41b4-a608-dfc43bd942fa/GCF_000712175.1_ASM71217v1_genomic.fna.gz]
[2024-01-24 12:40:10,774] [INFO] Query marker FASTA was written to GCF_000712175.1_ASM71217v1_genomic.fna/markers.fasta
[2024-01-24 12:40:10,774] [INFO] Task started: Blastn
[2024-01-24 12:40:10,774] [INFO] Running command: blastn -query GCF_000712175.1_ASM71217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3894f7a-db2a-428b-89af-ff7f4db2797b/dqc_reference/reference_markers.fasta -out GCF_000712175.1_ASM71217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:11,287] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:11,291] [INFO] Selected 9 target genomes.
[2024-01-24 12:40:11,291] [INFO] Target genome list was writen to GCF_000712175.1_ASM71217v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:11,295] [INFO] Task started: fastANI
[2024-01-24 12:40:11,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgefc5a84f-27ce-41b4-a608-dfc43bd942fa/GCF_000712175.1_ASM71217v1_genomic.fna.gz --refList GCF_000712175.1_ASM71217v1_genomic.fna/target_genomes.txt --output GCF_000712175.1_ASM71217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:13,259] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:13,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3894f7a-db2a-428b-89af-ff7f4db2797b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:13,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3894f7a-db2a-428b-89af-ff7f4db2797b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:13,268] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:13,268] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:13,268] [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
Mycoplasmopsis columbina	strain=ATCC 29257	GCA_000712175.1	114881	114881	type	True	100.0	249	249	95	conclusive
Mycoplasmopsis columbina	strain=NCTC10178	GCA_900660685.1	114881	114881	type	True	99.9956	249	249	95	conclusive
Mycoplasmopsis gallinarum	strain=DSM 19816	GCA_000621085.1	29557	29557	type	True	78.3125	82	249	95	below_threshold
Mycoplasmopsis meleagridis	strain=NCTC10153	GCA_900660695.1	29561	29561	type	True	77.9423	66	249	95	below_threshold
Mycoplasmopsis meleagridis	strain=ATCC 25294	GCA_000969625.1	29561	29561	type	True	77.747	64	249	95	below_threshold
Mycoplasmopsis fermentans	strain=PG18	GCA_000209735.1	2115	2115	type	True	77.4168	65	249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:13,273] [INFO] DFAST Taxonomy check result was written to GCF_000712175.1_ASM71217v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:13,274] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:13,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:13,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3894f7a-db2a-428b-89af-ff7f4db2797b/dqc_reference/checkm_data
[2024-01-24 12:40:13,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:13,289] [INFO] Task started: CheckM
[2024-01-24 12:40:13,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000712175.1_ASM71217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000712175.1_ASM71217v1_genomic.fna/checkm_input GCF_000712175.1_ASM71217v1_genomic.fna/checkm_result
[2024-01-24 12:40:26,187] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:26,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:26,208] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:26,209] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:26,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000712175.1_ASM71217v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:26,209] [INFO] Task started: Blastn
[2024-01-24 12:40:26,210] [INFO] Running command: blastn -query GCF_000712175.1_ASM71217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3894f7a-db2a-428b-89af-ff7f4db2797b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000712175.1_ASM71217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:26,723] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:26,727] [INFO] Selected 12 target genomes.
[2024-01-24 12:40:26,727] [INFO] Target genome list was writen to GCF_000712175.1_ASM71217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:26,754] [INFO] Task started: fastANI
[2024-01-24 12:40:26,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgefc5a84f-27ce-41b4-a608-dfc43bd942fa/GCF_000712175.1_ASM71217v1_genomic.fna.gz --refList GCF_000712175.1_ASM71217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000712175.1_ASM71217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:29,081] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:29,091] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:29,091] [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_900660685.1	s__Mycoplasmopsis columbina	99.9956	249	249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.36	98.73	0.99	0.99	3	conclusive
GCF_000701805.1	s__Mycoplasmopsis iners	78.4033	105	249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621085.1	s__Mycoplasmopsis gallinarum	78.3162	83	249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	96.67	96.67	0.95	0.95	2	-
GCF_900660695.1	s__Mycoplasmopsis meleagridis	77.9423	66	249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.56	98.69	0.99	0.98	4	-
GCF_900660665.1	s__Mycoplasmopsis maculosa	77.7629	53	249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000209735.1	s__Mycoplasmopsis fermentans	77.3153	63	249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.32	98.97	0.96	0.92	5	-
GCF_017084445.1	s__Mycoplasmopsis sp017084445	77.1358	50	249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:29,095] [INFO] GTDB search result was written to GCF_000712175.1_ASM71217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:29,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:29,102] [INFO] DFAST_QC result json was written to GCF_000712175.1_ASM71217v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:29,103] [INFO] DFAST_QC completed!
[2024-01-24 12:40:29,103] [INFO] Total running time: 0h0m21s