[2024-01-25 17:37:05,415] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:05,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:05,419] [INFO] DQC Reference Directory: /var/lib/cwl/stgd96bf086-f1e9-4b6d-b961-44ce3d7da523/dqc_reference
[2024-01-25 17:37:06,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:06,549] [INFO] Task started: Prodigal
[2024-01-25 17:37:06,549] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bdefccf-6d5d-4c27-b12b-5744d4ca53b0/GCF_016900955.1_ASM1690095v1_genomic.fna.gz | prodigal -d GCF_016900955.1_ASM1690095v1_genomic.fna/cds.fna -a GCF_016900955.1_ASM1690095v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:24,525] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:24,525] [INFO] Task started: HMMsearch
[2024-01-25 17:37:24,525] [INFO] Running command: hmmsearch --tblout GCF_016900955.1_ASM1690095v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd96bf086-f1e9-4b6d-b961-44ce3d7da523/dqc_reference/reference_markers.hmm GCF_016900955.1_ASM1690095v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:24,813] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:24,814] [INFO] Found 6/6 markers.
[2024-01-25 17:37:24,866] [INFO] Query marker FASTA was written to GCF_016900955.1_ASM1690095v1_genomic.fna/markers.fasta
[2024-01-25 17:37:24,866] [INFO] Task started: Blastn
[2024-01-25 17:37:24,867] [INFO] Running command: blastn -query GCF_016900955.1_ASM1690095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd96bf086-f1e9-4b6d-b961-44ce3d7da523/dqc_reference/reference_markers.fasta -out GCF_016900955.1_ASM1690095v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:25,985] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:25,988] [INFO] Selected 17 target genomes.
[2024-01-25 17:37:25,988] [INFO] Target genome list was writen to GCF_016900955.1_ASM1690095v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:25,992] [INFO] Task started: fastANI
[2024-01-25 17:37:25,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bdefccf-6d5d-4c27-b12b-5744d4ca53b0/GCF_016900955.1_ASM1690095v1_genomic.fna.gz --refList GCF_016900955.1_ASM1690095v1_genomic.fna/target_genomes.txt --output GCF_016900955.1_ASM1690095v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:00,075] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:00,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd96bf086-f1e9-4b6d-b961-44ce3d7da523/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:00,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd96bf086-f1e9-4b6d-b961-44ce3d7da523/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:00,087] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:38:00,087] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:38:00,087] [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 wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	95.3973	1973	2366	95	inconclusive
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	95.2985	2030	2366	95	inconclusive
Micromonospora matsumotoense	strain=DSM 44100	GCA_900091525.1	121616	121616	type	True	92.0044	1940	2366	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	91.664	1899	2366	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	91.6234	1713	2366	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	86.3429	1433	2366	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	85.6869	1621	2366	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	85.6511	1643	2366	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	85.604	1650	2366	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.0538	1041	2366	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.7602	1466	2366	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.4352	1236	2366	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	83.8209	1344	2366	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	83.4937	1333	2366	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	83.3405	1353	2366	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.3303	1310	2366	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	83.3055	1353	2366	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:00,089] [INFO] DFAST Taxonomy check result was written to GCF_016900955.1_ASM1690095v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:00,089] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:00,089] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:00,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd96bf086-f1e9-4b6d-b961-44ce3d7da523/dqc_reference/checkm_data
[2024-01-25 17:38:00,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:00,155] [INFO] Task started: CheckM
[2024-01-25 17:38:00,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016900955.1_ASM1690095v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016900955.1_ASM1690095v1_genomic.fna/checkm_input GCF_016900955.1_ASM1690095v1_genomic.fna/checkm_result
[2024-01-25 17:39:16,411] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:16,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:16,433] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:16,433] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:16,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016900955.1_ASM1690095v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:16,435] [INFO] Task started: Blastn
[2024-01-25 17:39:16,435] [INFO] Running command: blastn -query GCF_016900955.1_ASM1690095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd96bf086-f1e9-4b6d-b961-44ce3d7da523/dqc_reference/reference_markers_gtdb.fasta -out GCF_016900955.1_ASM1690095v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:18,238] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:18,241] [INFO] Selected 15 target genomes.
[2024-01-25 17:39:18,241] [INFO] Target genome list was writen to GCF_016900955.1_ASM1690095v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:18,256] [INFO] Task started: fastANI
[2024-01-25 17:39:18,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bdefccf-6d5d-4c27-b12b-5744d4ca53b0/GCF_016900955.1_ASM1690095v1_genomic.fna.gz --refList GCF_016900955.1_ASM1690095v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016900955.1_ASM1690095v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:51,407] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:51,418] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:39:51,418] [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_002210435.1	s__Micromonospora wenchangensis	95.4361	1969	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	conclusive
GCF_017599305.1	s__Micromonospora sp017599305	92.8164	2011	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091525.1	s__Micromonospora matsumotoense	91.9763	1943	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090265.1	s__Micromonospora rifamycinica	91.6605	1899	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900090245.1	s__Micromonospora halophytica	86.372	1431	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	86.3588	1518	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091595.1	s__Micromonospora haikouensis	85.6613	1626	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_014205165.1	s__Micromonospora carbonacea	85.6182	1638	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_003725545.1	s__Micromonospora sp003725545	85.1146	1295	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_003172935.1	s__Micromonospora sp003172935	85.0515	1249	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.27	99.27	0.87	0.87	2	-
GCF_900091475.1	s__Micromonospora chersina	84.8331	1422	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_018070575.1	s__Micromonospora sp018070575	84.6221	1368	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002926165.1	s__Micromonospora chalcea	84.5618	1413	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_900091585.1	s__Micromonospora nigra	83.8123	1348	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863495.1	s__Micromonospora andamanensis	83.0299	1315	2366	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:39:51,419] [INFO] GTDB search result was written to GCF_016900955.1_ASM1690095v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:51,420] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:51,425] [INFO] DFAST_QC result json was written to GCF_016900955.1_ASM1690095v1_genomic.fna/dqc_result.json
[2024-01-25 17:39:51,425] [INFO] DFAST_QC completed!
[2024-01-25 17:39:51,425] [INFO] Total running time: 0h2m46s