[2024-01-24 14:14:20,133] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,143] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,143] [INFO] DQC Reference Directory: /var/lib/cwl/stgd92f4a76-2a63-407f-95d7-1fb5675cafe1/dqc_reference
[2024-01-24 14:14:21,442] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,443] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,443] [INFO] Running command: gunzip -c /var/lib/cwl/stg425bf351-86a2-4e8c-91e2-c7fec31c4be4/GCF_016863555.1_ASM1686355v1_genomic.fna.gz | prodigal -d GCF_016863555.1_ASM1686355v1_genomic.fna/cds.fna -a GCF_016863555.1_ASM1686355v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:41,613] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:41,614] [INFO] Task started: HMMsearch
[2024-01-24 14:14:41,614] [INFO] Running command: hmmsearch --tblout GCF_016863555.1_ASM1686355v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd92f4a76-2a63-407f-95d7-1fb5675cafe1/dqc_reference/reference_markers.hmm GCF_016863555.1_ASM1686355v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:41,931] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:41,933] [INFO] Found 6/6 markers.
[2024-01-24 14:14:41,985] [INFO] Query marker FASTA was written to GCF_016863555.1_ASM1686355v1_genomic.fna/markers.fasta
[2024-01-24 14:14:41,985] [INFO] Task started: Blastn
[2024-01-24 14:14:41,985] [INFO] Running command: blastn -query GCF_016863555.1_ASM1686355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92f4a76-2a63-407f-95d7-1fb5675cafe1/dqc_reference/reference_markers.fasta -out GCF_016863555.1_ASM1686355v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:43,029] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:43,033] [INFO] Selected 19 target genomes.
[2024-01-24 14:14:43,033] [INFO] Target genome list was writen to GCF_016863555.1_ASM1686355v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:43,044] [INFO] Task started: fastANI
[2024-01-24 14:14:43,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg425bf351-86a2-4e8c-91e2-c7fec31c4be4/GCF_016863555.1_ASM1686355v1_genomic.fna.gz --refList GCF_016863555.1_ASM1686355v1_genomic.fna/target_genomes.txt --output GCF_016863555.1_ASM1686355v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:12,597] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:12,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd92f4a76-2a63-407f-95d7-1fb5675cafe1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:12,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd92f4a76-2a63-407f-95d7-1fb5675cafe1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:12,613] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:12,613] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:12,614] [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 craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	87.8122	1283	2154	95	below_threshold
Micromonospora zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	87.1864	1356	2154	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	87.0662	1352	2154	95	below_threshold
Micromonospora phaseoli	strain=CGMCC 4.7038	GCA_900109115.1	1144548	1144548	type	True	86.8971	1387	2154	95	below_threshold
Micromonospora phaseoli	strain=DSM 45730	GCA_003253475.1	1144548	1144548	type	True	86.8934	1385	2154	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	86.8773	1366	2154	95	below_threshold
Micromonospora tarapacensis	strain=Llam7	GCA_019697375.1	2835305	2835305	type	True	86.6414	1352	2154	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	86.5688	1395	2154	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	86.547	1388	2154	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	86.5219	1410	2154	95	below_threshold
Micromonospora gifhornensis	strain=NBRC 16317	GCA_016863515.1	84594	84594	type	True	86.4192	1376	2154	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	86.1203	1269	2154	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_014764405.1	2294034	2294034	type	True	86.1131	1292	2154	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.0301	973	2154	95	below_threshold
Micromonospora endolithica	strain=JCM 12677	GCA_003626595.1	230091	230091	type	True	83.6359	1218	2154	95	below_threshold
Micromonospora endolithica	strain=DSM 44398	GCA_007994185.1	230091	230091	type	True	83.6084	1247	2154	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.4501	1069	2154	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.0182	1205	2154	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	82.9919	1255	2154	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:12,615] [INFO] DFAST Taxonomy check result was written to GCF_016863555.1_ASM1686355v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:12,616] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:12,616] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:12,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd92f4a76-2a63-407f-95d7-1fb5675cafe1/dqc_reference/checkm_data
[2024-01-24 14:15:12,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:12,679] [INFO] Task started: CheckM
[2024-01-24 14:15:12,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863555.1_ASM1686355v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863555.1_ASM1686355v1_genomic.fna/checkm_input GCF_016863555.1_ASM1686355v1_genomic.fna/checkm_result
[2024-01-24 14:16:09,884] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:09,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:09,910] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:09,911] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:09,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863555.1_ASM1686355v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:09,911] [INFO] Task started: Blastn
[2024-01-24 14:16:09,911] [INFO] Running command: blastn -query GCF_016863555.1_ASM1686355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92f4a76-2a63-407f-95d7-1fb5675cafe1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863555.1_ASM1686355v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:11,420] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:11,423] [INFO] Selected 16 target genomes.
[2024-01-24 14:16:11,424] [INFO] Target genome list was writen to GCF_016863555.1_ASM1686355v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:11,460] [INFO] Task started: fastANI
[2024-01-24 14:16:11,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg425bf351-86a2-4e8c-91e2-c7fec31c4be4/GCF_016863555.1_ASM1686355v1_genomic.fna.gz --refList GCF_016863555.1_ASM1686355v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863555.1_ASM1686355v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:38,553] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:38,567] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:38,567] [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_016863555.1	s__Micromonospora qiuiae	100.0	2148	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014646235.1	s__Micromonospora sonchi	93.1701	1619	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236305.1	s__Micromonospora endophytica	88.2924	1254	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.96	99.96	0.99	0.98	3	-
GCF_003236315.1	s__Micromonospora craterilacus	87.862	1277	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005402585.1	s__Micromonospora sp005402585	87.833	1397	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331455.1	s__Micromonospora zingiberis	87.1555	1360	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583405.1	s__Micromonospora radicis	87.0678	1352	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109115.1	s__Micromonospora phaseoli	86.9027	1386	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	3	-
GCF_016863515.1	s__Micromonospora gifhornensis	86.4328	1375	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.77	95.90	0.88	0.87	6	-
GCF_900112325.1	s__Micromonospora sediminimaris	86.2968	1417	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.06	96.13	0.95	0.90	3	-
GCF_016863535.1	s__Micromonospora lutea	86.1398	1325	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364215.1	s__Micromonospora sp004307965	86.1271	1390	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
GCF_014764405.1	s__Micromonospora craniellae	86.0951	1293	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.95	99.95	0.98	0.98	2	-
GCF_009712475.1	s__Micromonospora sp009712475	85.9556	1311	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707425.1	s__Micromonospora sp009707425	83.7057	1149	2154	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	83.3064	1272	2154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:38,569] [INFO] GTDB search result was written to GCF_016863555.1_ASM1686355v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:38,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:38,573] [INFO] DFAST_QC result json was written to GCF_016863555.1_ASM1686355v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:38,573] [INFO] DFAST_QC completed!
[2024-01-24 14:16:38,574] [INFO] Total running time: 0h2m18s