[2024-01-25 19:00:20,579] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:20,581] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:20,581] [INFO] DQC Reference Directory: /var/lib/cwl/stge0319ca7-cbe3-47db-a548-29c0101cd898/dqc_reference
[2024-01-25 19:00:21,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:21,787] [INFO] Task started: Prodigal
[2024-01-25 19:00:21,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg595bb49a-18e3-4670-bf91-59f946f3c278/GCF_027922005.1_ASM2792200v1_genomic.fna.gz | prodigal -d GCF_027922005.1_ASM2792200v1_genomic.fna/cds.fna -a GCF_027922005.1_ASM2792200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:45,365] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:45,366] [INFO] Task started: HMMsearch
[2024-01-25 19:00:45,366] [INFO] Running command: hmmsearch --tblout GCF_027922005.1_ASM2792200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0319ca7-cbe3-47db-a548-29c0101cd898/dqc_reference/reference_markers.hmm GCF_027922005.1_ASM2792200v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:45,714] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:45,715] [INFO] Found 6/6 markers.
[2024-01-25 19:00:45,789] [INFO] Query marker FASTA was written to GCF_027922005.1_ASM2792200v1_genomic.fna/markers.fasta
[2024-01-25 19:00:45,790] [INFO] Task started: Blastn
[2024-01-25 19:00:45,790] [INFO] Running command: blastn -query GCF_027922005.1_ASM2792200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0319ca7-cbe3-47db-a548-29c0101cd898/dqc_reference/reference_markers.fasta -out GCF_027922005.1_ASM2792200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:47,131] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:47,135] [INFO] Selected 29 target genomes.
[2024-01-25 19:00:47,135] [INFO] Target genome list was writen to GCF_027922005.1_ASM2792200v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:47,155] [INFO] Task started: fastANI
[2024-01-25 19:00:47,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg595bb49a-18e3-4670-bf91-59f946f3c278/GCF_027922005.1_ASM2792200v1_genomic.fna.gz --refList GCF_027922005.1_ASM2792200v1_genomic.fna/target_genomes.txt --output GCF_027922005.1_ASM2792200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:44,595] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:44,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0319ca7-cbe3-47db-a548-29c0101cd898/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:44,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0319ca7-cbe3-47db-a548-29c0101cd898/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:44,613] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:01:44,613] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:01:44,613] [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
Streptosporangium saharense	strain=CECT 8840	GCA_014203715.1	1706840	1706840	type	True	86.549	1983	3218	95	below_threshold
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	85.6284	1854	3218	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	85.5772	1769	3218	95	below_threshold
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	85.5486	1984	3218	95	below_threshold
Streptosporangium violaceochromogenes	strain=JCM 3281	GCA_014654615.1	46188	46188	type	True	85.0994	1419	3218	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	84.6963	1593	3218	95	below_threshold
Streptosporangium becharense	strain=CECT 8961	GCA_014191075.1	1816182	1816182	type	True	83.5052	1535	3218	95	below_threshold
Streptosporangium becharense	strain=DSM 46887	GCA_014204985.1	1816182	1816182	type	True	83.461	1551	3218	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	83.429	1624	3218	95	below_threshold
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	83.4186	1650	3218	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	83.2749	1669	3218	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	83.1428	1609	3218	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	83.0094	1528	3218	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	82.9224	1645	3218	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.1636	905	3218	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.9357	1396	3218	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	79.9197	1525	3218	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	79.5928	1341	3218	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	79.5667	1374	3218	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.5455	1405	3218	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	77.1338	541	3218	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	76.8011	668	3218	95	below_threshold
Kitasatospora herbaricolor	strain=JCM 4138	GCA_014648975.1	68217	68217	type	True	76.7494	810	3218	95	below_threshold
Streptomyces fagopyri	strain=QMT-28	GCA_009498275.1	2662397	2662397	type	True	76.7201	624	3218	95	below_threshold
Wenjunlia vitaminophila	strain=ATCC 31673	GCA_001445835.1	76728	76728	type	True	76.6927	542	3218	95	below_threshold
Wenjunlia vitaminophila	strain=DSM 41686	GCA_000380165.1	76728	76728	type	True	76.6855	536	3218	95	below_threshold
Streptomyces murinus	strain=NRRL B-2286	GCA_002154555.1	33900	33900	type	True	76.5412	604	3218	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	76.4918	641	3218	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	76.3337	605	3218	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:44,614] [INFO] DFAST Taxonomy check result was written to GCF_027922005.1_ASM2792200v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:44,615] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:44,615] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:44,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0319ca7-cbe3-47db-a548-29c0101cd898/dqc_reference/checkm_data
[2024-01-25 19:01:44,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:44,706] [INFO] Task started: CheckM
[2024-01-25 19:01:44,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027922005.1_ASM2792200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027922005.1_ASM2792200v1_genomic.fna/checkm_input GCF_027922005.1_ASM2792200v1_genomic.fna/checkm_result
[2024-01-25 19:03:13,608] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:13,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 18.17%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2024-01-25 19:03:13,635] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:13,635] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:13,636] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027922005.1_ASM2792200v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:13,636] [INFO] Task started: Blastn
[2024-01-25 19:03:13,636] [INFO] Running command: blastn -query GCF_027922005.1_ASM2792200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0319ca7-cbe3-47db-a548-29c0101cd898/dqc_reference/reference_markers_gtdb.fasta -out GCF_027922005.1_ASM2792200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:15,828] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:15,832] [INFO] Selected 21 target genomes.
[2024-01-25 19:03:15,833] [INFO] Target genome list was writen to GCF_027922005.1_ASM2792200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:15,848] [INFO] Task started: fastANI
[2024-01-25 19:03:15,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg595bb49a-18e3-4670-bf91-59f946f3c278/GCF_027922005.1_ASM2792200v1_genomic.fna.gz --refList GCF_027922005.1_ASM2792200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027922005.1_ASM2792200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:54,979] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:54,992] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:03:54,992] [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_014203715.1	s__Streptosporangium saharense	86.5385	1985	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149035.1	s__Streptosporangium minutum	85.6143	1763	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	85.5819	1861	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_000024865.1	s__Streptosporangium roseum	85.5377	1986	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654615.1	s__Streptosporangium violaceochromogenes	85.104	1420	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	84.7075	1591	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188345.1	s__Streptosporangium subroseum	83.8548	1730	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	95.81	95.81	0.87	0.87	2	-
GCF_015711605.1	s__Planomonospora_A sp015711605	83.4956	1565	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204985.1	s__Streptosporangium becharense	83.4763	1548	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013409935.1	s__Streptosporangium sandarakinum	83.4507	1618	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_000721075.1	s__Streptosporangium amethystogenes	83.4394	1648	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	83.3136	1662	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_016863195.1	s__Planobispora takensis	83.1454	1606	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	82.9259	1644	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_008704515.1	s__Streptomyces viridosporus	76.7984	680	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.12	0.96	0.94	4	-
GCF_001906585.1	s__Streptomyces kebangsaanensis	76.7795	648	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	76.772	700	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364155.1	s__Streptomyces sp013364155	76.6023	655	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154555.1	s__Streptomyces murinus	76.5214	609	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	97.0065	97.48	97.10	0.91	0.89	7	-
GCA_009930425.1	s__UBA1383 sp009930425	76.2047	135	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__UBA1383	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882825.1	s__JAFGBM01 sp017882825	75.439	105	3218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__JAFGBM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:54,993] [INFO] GTDB search result was written to GCF_027922005.1_ASM2792200v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:54,994] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:54,998] [INFO] DFAST_QC result json was written to GCF_027922005.1_ASM2792200v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:54,999] [INFO] DFAST_QC completed!
[2024-01-25 19:03:54,999] [INFO] Total running time: 0h3m34s