[2024-01-24 11:26:27,572] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:27,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:27,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e7b13b7-b390-4647-a9aa-8484eba0e6ea/dqc_reference
[2024-01-24 11:26:29,051] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,052] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,052] [INFO] Running command: gunzip -c /var/lib/cwl/stg39f10353-bdae-495e-a4e3-338a3241f2bb/GCF_024172185.1_ASM2417218v1_genomic.fna.gz | prodigal -d GCF_024172185.1_ASM2417218v1_genomic.fna/cds.fna -a GCF_024172185.1_ASM2417218v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:56,291] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:56,292] [INFO] Task started: HMMsearch
[2024-01-24 11:26:56,292] [INFO] Running command: hmmsearch --tblout GCF_024172185.1_ASM2417218v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e7b13b7-b390-4647-a9aa-8484eba0e6ea/dqc_reference/reference_markers.hmm GCF_024172185.1_ASM2417218v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:56,784] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:56,785] [INFO] Found 6/6 markers.
[2024-01-24 11:26:56,858] [INFO] Query marker FASTA was written to GCF_024172185.1_ASM2417218v1_genomic.fna/markers.fasta
[2024-01-24 11:26:56,859] [INFO] Task started: Blastn
[2024-01-24 11:26:56,859] [INFO] Running command: blastn -query GCF_024172185.1_ASM2417218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e7b13b7-b390-4647-a9aa-8484eba0e6ea/dqc_reference/reference_markers.fasta -out GCF_024172185.1_ASM2417218v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:58,250] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:58,254] [INFO] Selected 19 target genomes.
[2024-01-24 11:26:58,254] [INFO] Target genome list was writen to GCF_024172185.1_ASM2417218v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:58,263] [INFO] Task started: fastANI
[2024-01-24 11:26:58,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg39f10353-bdae-495e-a4e3-338a3241f2bb/GCF_024172185.1_ASM2417218v1_genomic.fna.gz --refList GCF_024172185.1_ASM2417218v1_genomic.fna/target_genomes.txt --output GCF_024172185.1_ASM2417218v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:51,605] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:51,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e7b13b7-b390-4647-a9aa-8484eba0e6ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:51,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e7b13b7-b390-4647-a9aa-8484eba0e6ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:51,629] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:51,629] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:51,630] [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
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	100.0	3248	3250	95	conclusive
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	94.5298	2752	3250	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	85.3495	2043	3250	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	85.2339	1933	3250	95	below_threshold
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	84.8983	1426	3250	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	84.129	1680	3250	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	84.034	1241	3250	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	84.0191	1711	3250	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.6082	2098	3250	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	83.4741	2143	3250	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	83.4519	2149	3250	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	83.3214	2139	3250	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	83.2004	1945	3250	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	83.1581	1769	3250	95	below_threshold
Nonomuraea terrae	strain=CH32	GCA_004348995.1	2530383	2530383	type	True	83.0473	1688	3250	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	82.8739	1946	3250	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	82.8139	1760	3250	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	82.7511	1843	3250	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	81.7966	1819	3250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:51,631] [INFO] DFAST Taxonomy check result was written to GCF_024172185.1_ASM2417218v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:51,632] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:51,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:51,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e7b13b7-b390-4647-a9aa-8484eba0e6ea/dqc_reference/checkm_data
[2024-01-24 11:27:51,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:51,722] [INFO] Task started: CheckM
[2024-01-24 11:27:51,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024172185.1_ASM2417218v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024172185.1_ASM2417218v1_genomic.fna/checkm_input GCF_024172185.1_ASM2417218v1_genomic.fna/checkm_result
[2024-01-24 11:29:45,841] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:45,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.52%
Strain heterogeneity: 71.43%
--------------------------------------------------------------------------------
[2024-01-24 11:29:45,873] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:45,874] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:45,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024172185.1_ASM2417218v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:45,874] [INFO] Task started: Blastn
[2024-01-24 11:29:45,875] [INFO] Running command: blastn -query GCF_024172185.1_ASM2417218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e7b13b7-b390-4647-a9aa-8484eba0e6ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_024172185.1_ASM2417218v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:48,100] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:48,105] [INFO] Selected 15 target genomes.
[2024-01-24 11:29:48,105] [INFO] Target genome list was writen to GCF_024172185.1_ASM2417218v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:48,117] [INFO] Task started: fastANI
[2024-01-24 11:29:48,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg39f10353-bdae-495e-a4e3-338a3241f2bb/GCF_024172185.1_ASM2417218v1_genomic.fna.gz --refList GCF_024172185.1_ASM2417218v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024172185.1_ASM2417218v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:30:29,447] [INFO] Task succeeded: fastANI
[2024-01-24 11:30:29,471] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:30:29,472] [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_013363975.1	s__Nonomuraea montanisoli	94.5251	2752	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363995.1	s__Nonomuraea rhodomycinica	94.4824	2704	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207745.1	s__Nonomuraea muscovyensis	85.3742	2039	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850745.1	s__Nonomuraea indica	85.1537	1946	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646355.1	s__Nonomuraea cavernae	84.1381	1681	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873145.1	s__Nonomuraea angiospora	83.4805	2139	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204795.1	s__Nonomuraea jabiensis	83.4733	2145	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603905.1	s__Nonomuraea sp018603905	83.3403	2093	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017515.1	s__Nonomuraea sp008017515	83.1628	1827	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006334985.2	s__Nonomuraea phyllanthi	83.1471	1958	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.34	99.34	0.97	0.97	2	-
GCF_004348995.1	s__Nonomuraea terrae	83.0146	1696	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	82.899	1943	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889735.1	s__Nonomuraea turkmeniaca	82.8454	1754	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065375.1	s__Nonomuraea sp008065375	82.8019	1984	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283785.1	s__Nonomuraea sp013283785	82.7572	1841	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:30:29,473] [INFO] GTDB search result was written to GCF_024172185.1_ASM2417218v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:30:29,474] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:30:29,478] [INFO] DFAST_QC result json was written to GCF_024172185.1_ASM2417218v1_genomic.fna/dqc_result.json
[2024-01-24 11:30:29,479] [INFO] DFAST_QC completed!
[2024-01-24 11:30:29,479] [INFO] Total running time: 0h4m2s