[2024-01-24 13:51:12,482] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:51:12,484] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:51:12,484] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf2de5e6-9750-469c-bc7a-9de142b3b914/dqc_reference
[2024-01-24 13:51:13,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:51:13,823] [INFO] Task started: Prodigal
[2024-01-24 13:51:13,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d64a100-9889-44db-ac6c-de2a21e05fa7/GCF_003419945.1_ASM341994v1_genomic.fna.gz | prodigal -d GCF_003419945.1_ASM341994v1_genomic.fna/cds.fna -a GCF_003419945.1_ASM341994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:35,544] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:35,544] [INFO] Task started: HMMsearch
[2024-01-24 13:51:35,544] [INFO] Running command: hmmsearch --tblout GCF_003419945.1_ASM341994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf2de5e6-9750-469c-bc7a-9de142b3b914/dqc_reference/reference_markers.hmm GCF_003419945.1_ASM341994v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:35,884] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:35,886] [INFO] Found 6/6 markers.
[2024-01-24 13:51:35,944] [INFO] Query marker FASTA was written to GCF_003419945.1_ASM341994v1_genomic.fna/markers.fasta
[2024-01-24 13:51:35,944] [INFO] Task started: Blastn
[2024-01-24 13:51:35,944] [INFO] Running command: blastn -query GCF_003419945.1_ASM341994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf2de5e6-9750-469c-bc7a-9de142b3b914/dqc_reference/reference_markers.fasta -out GCF_003419945.1_ASM341994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:37,074] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:37,077] [INFO] Selected 18 target genomes.
[2024-01-24 13:51:37,077] [INFO] Target genome list was writen to GCF_003419945.1_ASM341994v1_genomic.fna/target_genomes.txt
[2024-01-24 13:51:37,084] [INFO] Task started: fastANI
[2024-01-24 13:51:37,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d64a100-9889-44db-ac6c-de2a21e05fa7/GCF_003419945.1_ASM341994v1_genomic.fna.gz --refList GCF_003419945.1_ASM341994v1_genomic.fna/target_genomes.txt --output GCF_003419945.1_ASM341994v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:06,239] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:06,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf2de5e6-9750-469c-bc7a-9de142b3b914/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:06,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf2de5e6-9750-469c-bc7a-9de142b3b914/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:06,263] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:52:06,263] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:06,263] [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 craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	100.0	2132	2136	95	conclusive
Micromonospora craniellae	strain=LHW63014	GCA_014764405.1	2294034	2294034	type	True	99.9515	2093	2136	95	conclusive
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	87.4318	1240	2136	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	87.1108	1315	2136	95	below_threshold
Micromonospora zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	86.9947	1307	2136	95	below_threshold
Micromonospora phaseoli	strain=CGMCC 4.7038	GCA_900109115.1	1144548	1144548	type	True	86.9614	1394	2136	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	86.9068	1370	2136	95	below_threshold
Micromonospora tarapacensis	strain=Llam7	GCA_019697375.1	2835305	2835305	type	True	86.5715	1372	2136	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	86.33	1384	2136	95	below_threshold
Micromonospora gifhornensis	strain=NBRC 16317	GCA_016863515.1	84594	84594	type	True	86.1301	1369	2136	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	86.1267	1394	2136	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.4416	945	2136	95	below_threshold
Micromonospora peucetia	strain=DSM 43363	GCA_900091625.1	47871	47871	type	True	83.9483	1201	2136	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.755	1058	2136	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.4653	1238	2136	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.3948	1214	2136	95	below_threshold
Micromonospora sagamiensis	strain=JCM 3310	GCA_014680085.1	47875	47875	type	True	82.9877	1170	2136	95	below_threshold
Micromonospora sagamiensis	strain=DSM 43912	GCA_007829995.1	47875	47875	type	True	82.9774	1179	2136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:06,265] [INFO] DFAST Taxonomy check result was written to GCF_003419945.1_ASM341994v1_genomic.fna/tc_result.tsv
[2024-01-24 13:52:06,265] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:06,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:06,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf2de5e6-9750-469c-bc7a-9de142b3b914/dqc_reference/checkm_data
[2024-01-24 13:52:06,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:06,331] [INFO] Task started: CheckM
[2024-01-24 13:52:06,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003419945.1_ASM341994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003419945.1_ASM341994v1_genomic.fna/checkm_input GCF_003419945.1_ASM341994v1_genomic.fna/checkm_result
[2024-01-24 13:53:17,530] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:17,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:17,560] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:17,560] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:17,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003419945.1_ASM341994v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:17,561] [INFO] Task started: Blastn
[2024-01-24 13:53:17,561] [INFO] Running command: blastn -query GCF_003419945.1_ASM341994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf2de5e6-9750-469c-bc7a-9de142b3b914/dqc_reference/reference_markers_gtdb.fasta -out GCF_003419945.1_ASM341994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:19,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:19,339] [INFO] Selected 17 target genomes.
[2024-01-24 13:53:19,339] [INFO] Target genome list was writen to GCF_003419945.1_ASM341994v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:19,352] [INFO] Task started: fastANI
[2024-01-24 13:53:19,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d64a100-9889-44db-ac6c-de2a21e05fa7/GCF_003419945.1_ASM341994v1_genomic.fna.gz --refList GCF_003419945.1_ASM341994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003419945.1_ASM341994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:46,998] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:47,060] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:47,060] [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_014764405.1	s__Micromonospora craniellae	99.9443	2094	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.95	99.95	0.98	0.98	2	conclusive
GCF_013364215.1	s__Micromonospora sp004307965	92.7771	1629	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
GCF_003236315.1	s__Micromonospora craterilacus	87.4177	1241	2136	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	87.1304	1396	2136	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	87.0858	1317	2136	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	86.9958	1307	2136	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	86.9487	1396	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014646235.1	s__Micromonospora sonchi	86.4707	1274	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010560025.1	s__Micromonospora sp010560025	86.3404	1315	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
GCF_003236305.1	s__Micromonospora endophytica	86.2791	1152	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.96	99.96	0.99	0.98	3	-
GCF_016863555.1	s__Micromonospora qiuiae	86.1095	1267	2136	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	86.0779	1346	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_009712475.1	s__Micromonospora sp009712475	86.0332	1304	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863535.1	s__Micromonospora lutea	85.8515	1296	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091625.1	s__Micromonospora peucetia	83.9475	1201	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091455.1	s__Micromonospora coriariae	83.6555	1181	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070045.1	s__Micromonospora sp018070045	83.4526	1216	2136	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 13:53:47,062] [INFO] GTDB search result was written to GCF_003419945.1_ASM341994v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:47,062] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:47,066] [INFO] DFAST_QC result json was written to GCF_003419945.1_ASM341994v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:47,067] [INFO] DFAST_QC completed!
[2024-01-24 13:53:47,067] [INFO] Total running time: 0h2m35s