[2024-01-24 10:47:06,596] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,601] [INFO] DQC Reference Directory: /var/lib/cwl/stge9f84b5e-a8ea-4f8e-a5cd-b4888eaf5697/dqc_reference
[2024-01-24 10:47:12,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,829] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,830] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd0b3aae-45bf-45ea-874d-01cd66234403/GCF_002093975.1_ASM209397v1_genomic.fna.gz | prodigal -d GCF_002093975.1_ASM209397v1_genomic.fna/cds.fna -a GCF_002093975.1_ASM209397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:35,439] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:35,439] [INFO] Task started: HMMsearch
[2024-01-24 10:47:35,439] [INFO] Running command: hmmsearch --tblout GCF_002093975.1_ASM209397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9f84b5e-a8ea-4f8e-a5cd-b4888eaf5697/dqc_reference/reference_markers.hmm GCF_002093975.1_ASM209397v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:35,870] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:35,871] [INFO] Found 6/6 markers.
[2024-01-24 10:47:35,936] [INFO] Query marker FASTA was written to GCF_002093975.1_ASM209397v1_genomic.fna/markers.fasta
[2024-01-24 10:47:35,937] [INFO] Task started: Blastn
[2024-01-24 10:47:35,937] [INFO] Running command: blastn -query GCF_002093975.1_ASM209397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9f84b5e-a8ea-4f8e-a5cd-b4888eaf5697/dqc_reference/reference_markers.fasta -out GCF_002093975.1_ASM209397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:37,378] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:37,387] [INFO] Selected 29 target genomes.
[2024-01-24 10:47:37,387] [INFO] Target genome list was writen to GCF_002093975.1_ASM209397v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:37,928] [INFO] Task started: fastANI
[2024-01-24 10:47:37,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd0b3aae-45bf-45ea-874d-01cd66234403/GCF_002093975.1_ASM209397v1_genomic.fna.gz --refList GCF_002093975.1_ASM209397v1_genomic.fna/target_genomes.txt --output GCF_002093975.1_ASM209397v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:40,688] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:40,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9f84b5e-a8ea-4f8e-a5cd-b4888eaf5697/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:40,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9f84b5e-a8ea-4f8e-a5cd-b4888eaf5697/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:40,709] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:40,709] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:40,709] [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 muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	82.1491	1565	2687	95	below_threshold
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	82.0694	1187	2687	95	below_threshold
Nonomuraea africana	strain=DSM 43748	GCA_014873535.1	46171	46171	type	True	82.0152	1579	2687	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	81.966	1564	2687	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	81.9507	1519	2687	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	81.9148	1604	2687	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	81.8594	1084	2687	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	81.819	1514	2687	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	81.8173	1574	2687	95	below_threshold
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	81.755	1542	2687	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	81.683	1533	2687	95	below_threshold
Nonomuraea dietziae	strain=DSM 44320	GCA_014195505.1	65515	65515	type	True	81.6497	1640	2687	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	81.6158	1420	2687	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	81.605	1529	2687	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	81.5989	1419	2687	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	81.5153	1520	2687	95	below_threshold
Nonomuraea terrae	strain=CH32	GCA_004348995.1	2530383	2530383	type	True	81.4877	1422	2687	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	81.468	1599	2687	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	81.3937	1561	2687	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	81.3384	1584	2687	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	81.302	1597	2687	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	81.198	1620	2687	95	below_threshold
Nonomuraea glycinis	strain=NEAU-BB2C19	GCA_020215885.1	2047744	2047744	type	True	81.1306	1475	2687	95	below_threshold
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	81.0698	1390	2687	95	below_threshold
Streptosporangium becharense	strain=CECT 8961	GCA_014191075.1	1816182	1816182	type	True	80.361	1172	2687	95	below_threshold
Streptosporangium becharense	strain=DSM 46887	GCA_014204985.1	1816182	1816182	type	True	80.3092	1191	2687	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	79.7327	1164	2687	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	79.5165	1258	2687	95	below_threshold
Herbidospora sakaeratensis	strain=NBRC 102641	GCA_001570525.1	564415	564415	type	True	79.35	1179	2687	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:40,711] [INFO] DFAST Taxonomy check result was written to GCF_002093975.1_ASM209397v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:40,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:40,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:40,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9f84b5e-a8ea-4f8e-a5cd-b4888eaf5697/dqc_reference/checkm_data
[2024-01-24 10:48:40,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:40,789] [INFO] Task started: CheckM
[2024-01-24 10:48:40,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002093975.1_ASM209397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002093975.1_ASM209397v1_genomic.fna/checkm_input GCF_002093975.1_ASM209397v1_genomic.fna/checkm_result
[2024-01-24 10:49:53,899] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:53,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.67%
Strain heterogeneity: 28.57%
--------------------------------------------------------------------------------
[2024-01-24 10:49:53,929] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:53,930] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:53,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002093975.1_ASM209397v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:53,930] [INFO] Task started: Blastn
[2024-01-24 10:49:53,931] [INFO] Running command: blastn -query GCF_002093975.1_ASM209397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9f84b5e-a8ea-4f8e-a5cd-b4888eaf5697/dqc_reference/reference_markers_gtdb.fasta -out GCF_002093975.1_ASM209397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:56,152] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:56,157] [INFO] Selected 23 target genomes.
[2024-01-24 10:49:56,158] [INFO] Target genome list was writen to GCF_002093975.1_ASM209397v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:56,180] [INFO] Task started: fastANI
[2024-01-24 10:49:56,181] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd0b3aae-45bf-45ea-874d-01cd66234403/GCF_002093975.1_ASM209397v1_genomic.fna.gz --refList GCF_002093975.1_ASM209397v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002093975.1_ASM209397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:47,899] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:47,920] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:47,921] [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_002093975.1	s__Nonomuraea rubra_A	100.0	2680	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013761175.1	s__Nonomuraea soli	82.6371	1736	2687	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	82.139	1567	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873535.1	s__Nonomuraea africana	82.007	1579	2687	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	81.9594	1517	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725485.1	s__Nonomuraea candida	81.8232	1571	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111685.1	s__Nonomuraea wenchangensis	81.7407	1545	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195505.1	s__Nonomuraea dietziae	81.6855	1633	2687	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	81.6793	1569	2687	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	81.632	1554	2687	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	81.5955	1425	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531495.1	s__Nonomuraea sp018531495	81.5873	1637	2687	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	81.5206	1655	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760925.1	s__Nonomuraea typhae	81.5154	1589	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109355.1	s__Nonomuraea pusilla	81.4992	1524	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	-
GCF_003001935.1	s__Nonomuraea fuscirosea	81.2914	1601	2687	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	81.1705	1609	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646515.1	s__Nonomuraea glycinis	81.0985	1480	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645445.1	s__Nonomuraea cypriaca	81.0527	1392	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204985.1	s__Streptosporangium becharense	80.3452	1186	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016863395.1	s__Sphaerisporangium rufum	79.7247	1166	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570525.1	s__Herbidospora sakaeratensis	79.3483	1183	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092645.1	s__Thermobispora bispora	79.1253	766	2687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobispora	95.0	99.72	99.67	0.98	0.98	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:47,922] [INFO] GTDB search result was written to GCF_002093975.1_ASM209397v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:47,923] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:47,928] [INFO] DFAST_QC result json was written to GCF_002093975.1_ASM209397v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:47,928] [INFO] DFAST_QC completed!
[2024-01-24 10:50:47,928] [INFO] Total running time: 0h3m41s