[2024-01-24 12:13:28,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ab34c63-4750-4b73-ab9a-af65fd560ed4/dqc_reference
[2024-01-24 12:13:29,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:29,723] [INFO] Task started: Prodigal
[2024-01-24 12:13:29,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f5766dd-683d-401f-9067-97b4e3e4e8b3/GCF_032108445.1_ASM3210844v1_genomic.fna.gz | prodigal -d GCF_032108445.1_ASM3210844v1_genomic.fna/cds.fna -a GCF_032108445.1_ASM3210844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:49,724] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:49,724] [INFO] Task started: HMMsearch
[2024-01-24 12:13:49,724] [INFO] Running command: hmmsearch --tblout GCF_032108445.1_ASM3210844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ab34c63-4750-4b73-ab9a-af65fd560ed4/dqc_reference/reference_markers.hmm GCF_032108445.1_ASM3210844v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:50,114] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:50,116] [INFO] Found 6/6 markers.
[2024-01-24 12:13:50,186] [INFO] Query marker FASTA was written to GCF_032108445.1_ASM3210844v1_genomic.fna/markers.fasta
[2024-01-24 12:13:50,187] [INFO] Task started: Blastn
[2024-01-24 12:13:50,187] [INFO] Running command: blastn -query GCF_032108445.1_ASM3210844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ab34c63-4750-4b73-ab9a-af65fd560ed4/dqc_reference/reference_markers.fasta -out GCF_032108445.1_ASM3210844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:51,769] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:51,773] [INFO] Selected 12 target genomes.
[2024-01-24 12:13:51,773] [INFO] Target genome list was writen to GCF_032108445.1_ASM3210844v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:51,779] [INFO] Task started: fastANI
[2024-01-24 12:13:51,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f5766dd-683d-401f-9067-97b4e3e4e8b3/GCF_032108445.1_ASM3210844v1_genomic.fna.gz --refList GCF_032108445.1_ASM3210844v1_genomic.fna/target_genomes.txt --output GCF_032108445.1_ASM3210844v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:17,174] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:17,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ab34c63-4750-4b73-ab9a-af65fd560ed4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:17,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ab34c63-4750-4b73-ab9a-af65fd560ed4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:17,185] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:17,186] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:17,186] [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
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	93.2695	1907	2318	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	93.0446	1896	2318	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	93.0294	1868	2318	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	92.9892	1890	2318	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	92.6691	1861	2318	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	88.2615	1609	2318	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	88.0416	1534	2318	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	86.6715	1607	2318	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.8378	1216	2318	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	85.1361	1389	2318	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	85.0641	1394	2318	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.5113	1301	2318	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:17,188] [INFO] DFAST Taxonomy check result was written to GCF_032108445.1_ASM3210844v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:17,188] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:17,188] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:17,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ab34c63-4750-4b73-ab9a-af65fd560ed4/dqc_reference/checkm_data
[2024-01-24 12:14:17,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:17,256] [INFO] Task started: CheckM
[2024-01-24 12:14:17,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_032108445.1_ASM3210844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_032108445.1_ASM3210844v1_genomic.fna/checkm_input GCF_032108445.1_ASM3210844v1_genomic.fna/checkm_result
[2024-01-24 12:15:45,869] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:45,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:45,961] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:45,962] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:45,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_032108445.1_ASM3210844v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:45,963] [INFO] Task started: Blastn
[2024-01-24 12:15:45,963] [INFO] Running command: blastn -query GCF_032108445.1_ASM3210844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ab34c63-4750-4b73-ab9a-af65fd560ed4/dqc_reference/reference_markers_gtdb.fasta -out GCF_032108445.1_ASM3210844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:48,305] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:48,311] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:48,311] [INFO] Target genome list was writen to GCF_032108445.1_ASM3210844v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:48,319] [INFO] Task started: fastANI
[2024-01-24 12:15:48,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f5766dd-683d-401f-9067-97b4e3e4e8b3/GCF_032108445.1_ASM3210844v1_genomic.fna.gz --refList GCF_032108445.1_ASM3210844v1_genomic.fna/target_genomes_gtdb.txt --output GCF_032108445.1_ASM3210844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:10,220] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:10,235] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:16:10,235] [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_008868175.1	s__Micromonospora sp008868175	94.5079	1761	2318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	93.2823	1906	2318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_014648395.1	s__Micromonospora fulviviridis	93.035	1897	2318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_900091475.1	s__Micromonospora chersina	92.666	1861	2318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_003725545.1	s__Micromonospora sp003725545	88.8463	1432	2318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_000982955.1	s__Micromonospora sp000982955	88.6245	1556	2318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008119785.1	s__Micromonospora sp008119785	88.4639	1704	2318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090105.1	s__Micromonospora humi	88.1871	1597	2318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905095.1	s__Micromonospora sp001905095	88.172	1697	2318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090225.1	s__Micromonospora eburnea	87.681	1535	2318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:10,237] [INFO] GTDB search result was written to GCF_032108445.1_ASM3210844v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:10,237] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:10,240] [INFO] DFAST_QC result json was written to GCF_032108445.1_ASM3210844v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:10,241] [INFO] DFAST_QC completed!
[2024-01-24 12:16:10,241] [INFO] Total running time: 0h2m42s