[2024-01-24 13:31:44,286] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,288] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,288] [INFO] DQC Reference Directory: /var/lib/cwl/stg3babb535-c249-4c7e-b783-6da5b18bd06e/dqc_reference
[2024-01-24 13:31:45,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,481] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg8945e257-b329-4e0b-a26f-673695683c84/GCF_009671205.1_ASM967120v1_genomic.fna.gz | prodigal -d GCF_009671205.1_ASM967120v1_genomic.fna/cds.fna -a GCF_009671205.1_ASM967120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:04,933] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:04,933] [INFO] Task started: HMMsearch
[2024-01-24 13:32:04,933] [INFO] Running command: hmmsearch --tblout GCF_009671205.1_ASM967120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3babb535-c249-4c7e-b783-6da5b18bd06e/dqc_reference/reference_markers.hmm GCF_009671205.1_ASM967120v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:05,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:05,295] [INFO] Found 6/6 markers.
[2024-01-24 13:32:05,355] [INFO] Query marker FASTA was written to GCF_009671205.1_ASM967120v1_genomic.fna/markers.fasta
[2024-01-24 13:32:05,355] [INFO] Task started: Blastn
[2024-01-24 13:32:05,356] [INFO] Running command: blastn -query GCF_009671205.1_ASM967120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3babb535-c249-4c7e-b783-6da5b18bd06e/dqc_reference/reference_markers.fasta -out GCF_009671205.1_ASM967120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:06,941] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:06,945] [INFO] Selected 10 target genomes.
[2024-01-24 13:32:06,946] [INFO] Target genome list was writen to GCF_009671205.1_ASM967120v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:06,952] [INFO] Task started: fastANI
[2024-01-24 13:32:06,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg8945e257-b329-4e0b-a26f-673695683c84/GCF_009671205.1_ASM967120v1_genomic.fna.gz --refList GCF_009671205.1_ASM967120v1_genomic.fna/target_genomes.txt --output GCF_009671205.1_ASM967120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:29,864] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:29,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3babb535-c249-4c7e-b783-6da5b18bd06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:29,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3babb535-c249-4c7e-b783-6da5b18bd06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:29,875] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:32:29,876] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:32:29,876] [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 terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	100.0	2244	2247	95	inconclusive
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	99.9932	2211	2247	95	inconclusive
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	95.1915	1931	2247	95	inconclusive
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	92.6693	1872	2247	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	92.5963	1856	2247	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	88.1586	1563	2247	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.7741	1200	2247	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	85.0237	1378	2247	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	85.0178	1341	2247	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.4316	1287	2247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:29,877] [INFO] DFAST Taxonomy check result was written to GCF_009671205.1_ASM967120v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:29,878] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:29,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:29,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3babb535-c249-4c7e-b783-6da5b18bd06e/dqc_reference/checkm_data
[2024-01-24 13:32:29,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:29,946] [INFO] Task started: CheckM
[2024-01-24 13:32:29,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009671205.1_ASM967120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009671205.1_ASM967120v1_genomic.fna/checkm_input GCF_009671205.1_ASM967120v1_genomic.fna/checkm_result
[2024-01-24 13:34:21,465] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:21,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:21,489] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:21,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:21,490] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009671205.1_ASM967120v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:21,490] [INFO] Task started: Blastn
[2024-01-24 13:34:21,490] [INFO] Running command: blastn -query GCF_009671205.1_ASM967120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3babb535-c249-4c7e-b783-6da5b18bd06e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009671205.1_ASM967120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:23,887] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:23,895] [INFO] Selected 11 target genomes.
[2024-01-24 13:34:23,896] [INFO] Target genome list was writen to GCF_009671205.1_ASM967120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:23,906] [INFO] Task started: fastANI
[2024-01-24 13:34:23,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg8945e257-b329-4e0b-a26f-673695683c84/GCF_009671205.1_ASM967120v1_genomic.fna.gz --refList GCF_009671205.1_ASM967120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009671205.1_ASM967120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:47,346] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:47,366] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:47,367] [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_900091435.1	s__Micromonospora chaiyaphumensis	95.1807	1932	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	conclusive
GCF_008868175.1	s__Micromonospora sp008868175	93.1197	1682	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648395.1	s__Micromonospora fulviviridis	92.6514	1874	2247	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	92.565	1859	2247	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	88.9611	1406	2247	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	88.4986	1554	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089585.1	s__Micromonospora sediminicola	88.4305	1639	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.55	97.81	0.94	0.92	3	-
GCF_008119785.1	s__Micromonospora sp008119785	88.359	1650	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089595.1	s__Micromonospora auratinigra	88.2546	1616	2247	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	88.1251	1657	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089605.1	s__Micromonospora narathiwatensis	88.1008	1520	2247	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 13:34:47,369] [INFO] GTDB search result was written to GCF_009671205.1_ASM967120v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:47,369] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:47,372] [INFO] DFAST_QC result json was written to GCF_009671205.1_ASM967120v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:47,372] [INFO] DFAST_QC completed!
[2024-01-24 13:34:47,373] [INFO] Total running time: 0h3m3s