[2024-01-24 12:40:35,616] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:35,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:35,618] [INFO] DQC Reference Directory: /var/lib/cwl/stga49bd82a-1380-40f2-a6d4-cc119eba2e2d/dqc_reference
[2024-01-24 12:40:36,844] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:36,844] [INFO] Task started: Prodigal
[2024-01-24 12:40:36,845] [INFO] Running command: gunzip -c /var/lib/cwl/stgbab43c60-6e8c-48a7-b71e-a6f12e3ca393/GCF_000701845.1_ASM70184v1_genomic.fna.gz | prodigal -d GCF_000701845.1_ASM70184v1_genomic.fna/cds.fna -a GCF_000701845.1_ASM70184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:38,297] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:38,297] [INFO] Task started: HMMsearch
[2024-01-24 12:40:38,297] [INFO] Running command: hmmsearch --tblout GCF_000701845.1_ASM70184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga49bd82a-1380-40f2-a6d4-cc119eba2e2d/dqc_reference/reference_markers.hmm GCF_000701845.1_ASM70184v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:38,471] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:38,474] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbab43c60-6e8c-48a7-b71e-a6f12e3ca393/GCF_000701845.1_ASM70184v1_genomic.fna.gz]
[2024-01-24 12:40:38,489] [INFO] Query marker FASTA was written to GCF_000701845.1_ASM70184v1_genomic.fna/markers.fasta
[2024-01-24 12:40:38,490] [INFO] Task started: Blastn
[2024-01-24 12:40:38,490] [INFO] Running command: blastn -query GCF_000701845.1_ASM70184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga49bd82a-1380-40f2-a6d4-cc119eba2e2d/dqc_reference/reference_markers.fasta -out GCF_000701845.1_ASM70184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:39,036] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:39,041] [INFO] Selected 9 target genomes.
[2024-01-24 12:40:39,041] [INFO] Target genome list was writen to GCF_000701845.1_ASM70184v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:39,045] [INFO] Task started: fastANI
[2024-01-24 12:40:39,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgbab43c60-6e8c-48a7-b71e-a6f12e3ca393/GCF_000701845.1_ASM70184v1_genomic.fna.gz --refList GCF_000701845.1_ASM70184v1_genomic.fna/target_genomes.txt --output GCF_000701845.1_ASM70184v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:41,344] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:41,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga49bd82a-1380-40f2-a6d4-cc119eba2e2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:41,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga49bd82a-1380-40f2-a6d4-cc119eba2e2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:41,356] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:41,356] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:41,356] [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 columboralis	strain=ATCC 29258	GCA_000701845.1	171282	171282	type	True	100.0	284	288	95	conclusive
Mycoplasmopsis columboralis	strain=NCTC10179	GCA_900660675.1	171282	171282	type	True	99.9756	286	288	95	conclusive
Mycoplasmopsis citelli	strain=RG-2C	GCA_024498235.1	171281	171281	type	True	79.8611	137	288	95	below_threshold
Mycoplasmopsis citelli	strain=NCTC10181	GCA_900660645.1	171281	171281	type	True	79.8107	138	288	95	below_threshold
Mycoplasmopsis sturni	strain=DSM 22021	GCA_000701485.1	39047	39047	type	True	79.3909	80	288	95	below_threshold
Mycoplasmopsis gallopavonis	strain=NCTC10186	GCA_900660635.1	76629	76629	type	True	78.8978	59	288	95	below_threshold
Mycoplasmopsis cricetuli	strain=ATCC 35279	GCA_000526955.1	171283	171283	type	True	78.1477	93	288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:41,358] [INFO] DFAST Taxonomy check result was written to GCF_000701845.1_ASM70184v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:41,358] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:41,359] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:41,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga49bd82a-1380-40f2-a6d4-cc119eba2e2d/dqc_reference/checkm_data
[2024-01-24 12:40:41,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:41,376] [INFO] Task started: CheckM
[2024-01-24 12:40:41,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000701845.1_ASM70184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000701845.1_ASM70184v1_genomic.fna/checkm_input GCF_000701845.1_ASM70184v1_genomic.fna/checkm_result
[2024-01-24 12:40:54,082] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:54,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:54,101] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:54,101] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:54,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000701845.1_ASM70184v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:54,102] [INFO] Task started: Blastn
[2024-01-24 12:40:54,103] [INFO] Running command: blastn -query GCF_000701845.1_ASM70184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga49bd82a-1380-40f2-a6d4-cc119eba2e2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000701845.1_ASM70184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:54,780] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:54,784] [INFO] Selected 17 target genomes.
[2024-01-24 12:40:54,785] [INFO] Target genome list was writen to GCF_000701845.1_ASM70184v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:54,798] [INFO] Task started: fastANI
[2024-01-24 12:40:54,799] [INFO] Running command: fastANI --query /var/lib/cwl/stgbab43c60-6e8c-48a7-b71e-a6f12e3ca393/GCF_000701845.1_ASM70184v1_genomic.fna.gz --refList GCF_000701845.1_ASM70184v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000701845.1_ASM70184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:58,257] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:58,268] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:58,268] [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_900660675.1	s__Mycoplasmopsis_A columborale	99.9756	286	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_900660645.1	s__Mycoplasmopsis_A citelli	79.795	140	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701485.1	s__Mycoplasmopsis_A sturni	79.2743	82	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660495.1	s__Mycoplasmopsis_A gallinaceum	78.9339	68	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	96.30	96.30	0.91	0.91	2	-
GCF_900660635.1	s__Mycoplasmopsis_A gallopavonis	78.933	59	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.97	99.97	1.00	1.00	2	-
GCF_009792315.1	s__Mycoplasmopsis_A sp009792315	78.7504	71	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526955.1	s__Mycoplasmopsis_A cricetuli	78.1477	93	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733865.1	s__Mycoplasmopsis_A buteonis	77.8741	60	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167035.1	s__Mycoplasmopsis_A verecundum	77.7189	52	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:58,270] [INFO] GTDB search result was written to GCF_000701845.1_ASM70184v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:58,271] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:58,274] [INFO] DFAST_QC result json was written to GCF_000701845.1_ASM70184v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:58,274] [INFO] DFAST_QC completed!
[2024-01-24 12:40:58,274] [INFO] Total running time: 0h0m23s