[2024-01-24 12:22:34,051] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg69656ed3-c269-4d9b-a401-3eeef5c1156e/dqc_reference
[2024-01-24 12:22:35,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,716] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,716] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf8c2b42-0693-4bfd-8766-857a43d7b90d/GCF_026013475.1_ASM2601347v1_genomic.fna.gz | prodigal -d GCF_026013475.1_ASM2601347v1_genomic.fna/cds.fna -a GCF_026013475.1_ASM2601347v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:52,701] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:52,702] [INFO] Task started: HMMsearch
[2024-01-24 12:22:52,702] [INFO] Running command: hmmsearch --tblout GCF_026013475.1_ASM2601347v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69656ed3-c269-4d9b-a401-3eeef5c1156e/dqc_reference/reference_markers.hmm GCF_026013475.1_ASM2601347v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:52,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:52,975] [INFO] Found 6/6 markers.
[2024-01-24 12:22:53,031] [INFO] Query marker FASTA was written to GCF_026013475.1_ASM2601347v1_genomic.fna/markers.fasta
[2024-01-24 12:22:53,032] [INFO] Task started: Blastn
[2024-01-24 12:22:53,032] [INFO] Running command: blastn -query GCF_026013475.1_ASM2601347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69656ed3-c269-4d9b-a401-3eeef5c1156e/dqc_reference/reference_markers.fasta -out GCF_026013475.1_ASM2601347v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:54,224] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:54,226] [INFO] Selected 17 target genomes.
[2024-01-24 12:22:54,227] [INFO] Target genome list was writen to GCF_026013475.1_ASM2601347v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:54,234] [INFO] Task started: fastANI
[2024-01-24 12:22:54,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf8c2b42-0693-4bfd-8766-857a43d7b90d/GCF_026013475.1_ASM2601347v1_genomic.fna.gz --refList GCF_026013475.1_ASM2601347v1_genomic.fna/target_genomes.txt --output GCF_026013475.1_ASM2601347v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:25,218] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:25,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69656ed3-c269-4d9b-a401-3eeef5c1156e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:25,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69656ed3-c269-4d9b-a401-3eeef5c1156e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:25,230] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:25,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:25,230] [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 fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	88.8551	1563	2331	95	below_threshold
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	88.7761	1509	2331	95	below_threshold
Micromonospora auratinigra	strain=DSM 44815	GCA_900089595.1	261654	261654	type	True	88.642	1478	2331	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	88.6103	1538	2331	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	88.5076	1545	2331	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	88.4397	1523	2331	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	88.4206	1531	2331	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	88.3985	1535	2331	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	88.3506	1476	2331	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	87.8981	1469	2331	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	87.3028	1447	2331	95	below_threshold
Micromonospora globispora	strain=S2901	GCA_003857015.1	1450148	1450148	type	True	87.2637	1186	2331	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	86.8459	1414	2331	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.4466	1097	2331	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.7048	1233	2331	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.5734	1311	2331	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.4421	1196	2331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:25,232] [INFO] DFAST Taxonomy check result was written to GCF_026013475.1_ASM2601347v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:25,232] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:25,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:25,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69656ed3-c269-4d9b-a401-3eeef5c1156e/dqc_reference/checkm_data
[2024-01-24 12:23:25,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:25,303] [INFO] Task started: CheckM
[2024-01-24 12:23:25,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026013475.1_ASM2601347v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026013475.1_ASM2601347v1_genomic.fna/checkm_input GCF_026013475.1_ASM2601347v1_genomic.fna/checkm_result
[2024-01-24 12:24:25,076] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:25,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:25,091] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:25,091] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:25,092] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026013475.1_ASM2601347v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:25,092] [INFO] Task started: Blastn
[2024-01-24 12:24:25,092] [INFO] Running command: blastn -query GCF_026013475.1_ASM2601347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69656ed3-c269-4d9b-a401-3eeef5c1156e/dqc_reference/reference_markers_gtdb.fasta -out GCF_026013475.1_ASM2601347v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:27,147] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:27,150] [INFO] Selected 14 target genomes.
[2024-01-24 12:24:27,150] [INFO] Target genome list was writen to GCF_026013475.1_ASM2601347v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:27,156] [INFO] Task started: fastANI
[2024-01-24 12:24:27,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf8c2b42-0693-4bfd-8766-857a43d7b90d/GCF_026013475.1_ASM2601347v1_genomic.fna.gz --refList GCF_026013475.1_ASM2601347v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026013475.1_ASM2601347v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:53,632] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:53,641] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:53,641] [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_003725545.1	s__Micromonospora sp003725545	91.0658	1369	2331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_008119785.1	s__Micromonospora sp008119785	89.1143	1749	2331	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	88.8937	1559	2331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_001905095.1	s__Micromonospora sp001905095	88.8636	1739	2331	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	88.7584	1511	2331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091475.1	s__Micromonospora chersina	88.6285	1536	2331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_900089595.1	s__Micromonospora auratinigra	88.6219	1480	2331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008868175.1	s__Micromonospora sp008868175	88.5514	1407	2331	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	88.5282	1513	2331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_900091545.1	s__Micromonospora viridifaciens	88.457	1551	2331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000982955.1	s__Micromonospora sp000982955	88.3933	1405	2331	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	88.3561	1475	2331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003857015.1	s__Micromonospora globispora	87.3215	1181	2331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.52	99.52	0.89	0.89	2	-
GCF_004345505.1	s__Micromonospora sp004345505	84.8888	1337	2331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.85	96.85	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:53,643] [INFO] GTDB search result was written to GCF_026013475.1_ASM2601347v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:53,643] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:53,646] [INFO] DFAST_QC result json was written to GCF_026013475.1_ASM2601347v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:53,647] [INFO] DFAST_QC completed!
[2024-01-24 12:24:53,647] [INFO] Total running time: 0h2m20s