[2024-01-25 20:07:20,439] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:20,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:20,441] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc5f2c37-04a1-45f9-9dae-4438e6d7bd92/dqc_reference
[2024-01-25 20:07:21,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:21,601] [INFO] Task started: Prodigal
[2024-01-25 20:07:21,601] [INFO] Running command: gunzip -c /var/lib/cwl/stgb44fb586-632a-4695-8fbd-73c4ab7118f3/GCF_020532625.1_ASM2053262v1_genomic.fna.gz | prodigal -d GCF_020532625.1_ASM2053262v1_genomic.fna/cds.fna -a GCF_020532625.1_ASM2053262v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:36,147] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:36,148] [INFO] Task started: HMMsearch
[2024-01-25 20:07:36,148] [INFO] Running command: hmmsearch --tblout GCF_020532625.1_ASM2053262v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc5f2c37-04a1-45f9-9dae-4438e6d7bd92/dqc_reference/reference_markers.hmm GCF_020532625.1_ASM2053262v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:36,485] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:36,486] [INFO] Found 6/6 markers.
[2024-01-25 20:07:36,537] [INFO] Query marker FASTA was written to GCF_020532625.1_ASM2053262v1_genomic.fna/markers.fasta
[2024-01-25 20:07:36,537] [INFO] Task started: Blastn
[2024-01-25 20:07:36,537] [INFO] Running command: blastn -query GCF_020532625.1_ASM2053262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc5f2c37-04a1-45f9-9dae-4438e6d7bd92/dqc_reference/reference_markers.fasta -out GCF_020532625.1_ASM2053262v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:37,804] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:37,808] [INFO] Selected 20 target genomes.
[2024-01-25 20:07:37,809] [INFO] Target genome list was writen to GCF_020532625.1_ASM2053262v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:37,829] [INFO] Task started: fastANI
[2024-01-25 20:07:37,829] [INFO] Running command: fastANI --query /var/lib/cwl/stgb44fb586-632a-4695-8fbd-73c4ab7118f3/GCF_020532625.1_ASM2053262v1_genomic.fna.gz --refList GCF_020532625.1_ASM2053262v1_genomic.fna/target_genomes.txt --output GCF_020532625.1_ASM2053262v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:13,600] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:13,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc5f2c37-04a1-45f9-9dae-4438e6d7bd92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:13,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc5f2c37-04a1-45f9-9dae-4438e6d7bd92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:13,613] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:08:13,613] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:08:13,613] [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
Streptomyces katrae	strain=NRRL ISP-5550	GCA_000966975.1	68223	68223	type	True	85.6912	1192	2042	95	below_threshold
Streptomyces vinaceus	strain=ATCC 27476	GCA_008704935.1	1960	1960	type	True	85.6209	1496	2042	95	below_threshold
Streptomyces vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	85.5619	1495	2042	95	below_threshold
Streptomyces amritsarensis	strain=MTCC 11845	GCA_001953875.1	681158	681158	type	True	85.5485	1453	2042	95	below_threshold
Streptomyces yangpuensis	strain=fd2-tb	GCA_001005295.1	1648182	1648182	type	True	85.5439	1501	2042	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	85.5025	1505	2042	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	85.4932	1490	2042	95	below_threshold
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	85.4767	1479	2042	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	85.4167	1507	2042	95	below_threshold
Streptomyces nojiriensis	strain=NBRC 13794	GCA_016755855.1	66374	66374	type	True	85.4029	1510	2042	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	85.387	1504	2042	95	below_threshold
Streptomyces subrutilus	strain=JCM 4834	GCA_014650935.1	36818	36818	type	True	85.2144	1422	2042	95	below_threshold
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	85.1934	1447	2042	95	below_threshold
Streptomyces toxytricini	strain=JCM 4421	GCA_014649915.1	67369	67369	type	True	85.1607	1445	2042	95	below_threshold
Streptomyces bambusae	strain=T110	GCA_020532645.1	1550616	1550616	type	True	84.9033	1408	2042	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	82.494	1270	2042	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	82.0178	1206	2042	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	81.9904	1200	2042	95	below_threshold
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	81.9568	1181	2042	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	81.923	1203	2042	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:13,614] [INFO] DFAST Taxonomy check result was written to GCF_020532625.1_ASM2053262v1_genomic.fna/tc_result.tsv
[2024-01-25 20:08:13,615] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:13,615] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:13,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc5f2c37-04a1-45f9-9dae-4438e6d7bd92/dqc_reference/checkm_data
[2024-01-25 20:08:13,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:13,676] [INFO] Task started: CheckM
[2024-01-25 20:08:13,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020532625.1_ASM2053262v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020532625.1_ASM2053262v1_genomic.fna/checkm_input GCF_020532625.1_ASM2053262v1_genomic.fna/checkm_result
[2024-01-25 20:09:29,798] [INFO] Task succeeded: CheckM
[2024-01-25 20:09:29,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:09:29,817] [INFO] ===== Completeness check finished =====
[2024-01-25 20:09:29,818] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:09:29,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020532625.1_ASM2053262v1_genomic.fna/markers.fasta)
[2024-01-25 20:09:29,819] [INFO] Task started: Blastn
[2024-01-25 20:09:29,819] [INFO] Running command: blastn -query GCF_020532625.1_ASM2053262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc5f2c37-04a1-45f9-9dae-4438e6d7bd92/dqc_reference/reference_markers_gtdb.fasta -out GCF_020532625.1_ASM2053262v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:09:31,722] [INFO] Task succeeded: Blastn
[2024-01-25 20:09:31,725] [INFO] Selected 18 target genomes.
[2024-01-25 20:09:31,725] [INFO] Target genome list was writen to GCF_020532625.1_ASM2053262v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:09:31,754] [INFO] Task started: fastANI
[2024-01-25 20:09:31,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgb44fb586-632a-4695-8fbd-73c4ab7118f3/GCF_020532625.1_ASM2053262v1_genomic.fna.gz --refList GCF_020532625.1_ASM2053262v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020532625.1_ASM2053262v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:10:04,249] [INFO] Task succeeded: fastANI
[2024-01-25 20:10:04,260] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:10:04,260] [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_003949795.1	s__Streptomyces sp003949795	91.0058	1509	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642295.1	s__Streptomyces venezuelae_C	85.6835	1484	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704935.1	s__Streptomyces vinaceus	85.6269	1495	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	97.63	0.95	0.92	5	-
GCF_000720115.1	s__Streptomyces sp000720115	85.607	1495	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002028425.1	s__Streptomyces katrae_A	85.5457	1505	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.44	0.97	0.94	4	-
GCF_001044425.1	s__Streptomyces roseus	85.5331	1438	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650555.1	s__Streptomyces goshikiensis	85.529	1472	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	96.91	0.89	0.81	10	-
GCA_001298555.1	s__Streptomyces sp001298555	85.425	1497	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017639205.1	s__Streptomyces nojiriensis	85.3982	1503	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013401435.1	s__Streptomyces sp013401435	85.3834	1347	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803845.1	s__Streptomyces lavendulae_C	85.3801	1524	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.97	0.99	0.99	3	-
GCF_014649915.1	s__Streptomyces toxytricini	85.1579	1445	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003325375.1	s__Streptomyces globosus	85.1241	1445	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.29	95.29	0.89	0.89	2	-
GCF_000612545.1	s__Streptomyces sp000612545	85.0159	1450	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719335.1	s__Streptomyces sp000719335	84.7106	1402	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353505.1	s__Streptomyces sp004353505	82.6428	1247	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.86	0.97	0.92	4	-
GCA_003268675.1	s__Streptomyces bacillaris	81.8807	1217	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.84	95.80	0.88	0.83	37	-
GCF_018619185.1	s__Streptomyces sp018619185	81.8073	1129	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:10:04,262] [INFO] GTDB search result was written to GCF_020532625.1_ASM2053262v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:10:04,262] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:10:04,265] [INFO] DFAST_QC result json was written to GCF_020532625.1_ASM2053262v1_genomic.fna/dqc_result.json
[2024-01-25 20:10:04,265] [INFO] DFAST_QC completed!
[2024-01-25 20:10:04,265] [INFO] Total running time: 0h2m44s