[2024-01-24 11:05:34,627] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg13fda809-4a18-4a05-8910-72f414c94b44/dqc_reference
[2024-01-24 11:05:35,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:35,847] [INFO] Task started: Prodigal
[2024-01-24 11:05:35,847] [INFO] Running command: gunzip -c /var/lib/cwl/stgb89d813b-f793-4d70-9680-76624dc29965/GCF_011170145.1_ASM1117014v1_genomic.fna.gz | prodigal -d GCF_011170145.1_ASM1117014v1_genomic.fna/cds.fna -a GCF_011170145.1_ASM1117014v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:54,779] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:54,779] [INFO] Task started: HMMsearch
[2024-01-24 11:05:54,779] [INFO] Running command: hmmsearch --tblout GCF_011170145.1_ASM1117014v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13fda809-4a18-4a05-8910-72f414c94b44/dqc_reference/reference_markers.hmm GCF_011170145.1_ASM1117014v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:55,168] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:55,170] [INFO] Found 6/6 markers.
[2024-01-24 11:05:55,228] [INFO] Query marker FASTA was written to GCF_011170145.1_ASM1117014v1_genomic.fna/markers.fasta
[2024-01-24 11:05:55,229] [INFO] Task started: Blastn
[2024-01-24 11:05:55,229] [INFO] Running command: blastn -query GCF_011170145.1_ASM1117014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13fda809-4a18-4a05-8910-72f414c94b44/dqc_reference/reference_markers.fasta -out GCF_011170145.1_ASM1117014v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:56,556] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:56,561] [INFO] Selected 10 target genomes.
[2024-01-24 11:05:56,561] [INFO] Target genome list was writen to GCF_011170145.1_ASM1117014v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:56,567] [INFO] Task started: fastANI
[2024-01-24 11:05:56,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgb89d813b-f793-4d70-9680-76624dc29965/GCF_011170145.1_ASM1117014v1_genomic.fna.gz --refList GCF_011170145.1_ASM1117014v1_genomic.fna/target_genomes.txt --output GCF_011170145.1_ASM1117014v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:16,729] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:16,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13fda809-4a18-4a05-8910-72f414c94b44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:16,730] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13fda809-4a18-4a05-8910-72f414c94b44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:16,744] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:06:16,744] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:06:16,745] [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 gougerotii	strain=NBRC 13043	GCA_011170145.1	53448	53448	suspected-type	True	100.0	2324	2376	95	inconclusive
Streptomyces gougerotii	strain=JCM 4136	GCA_014648955.1	53448	53448	suspected-type	True	99.9732	2149	2376	95	inconclusive
Streptomyces diastaticus subsp. diastaticus	strain=NBRC 13412	GCA_011170125.1	68040	1956	suspected-type	True	99.5884	2123	2376	95	inconclusive
Streptomyces diastaticus subsp. diastaticus	strain=JCM 4128	GCA_014648935.1	68040	1956	suspected-type	True	99.5551	2092	2376	95	inconclusive
Streptomyces albidoflavus	strain=DSM 40455	GCA_004195735.1	1886	1886	type	True	92.1578	1815	2376	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.7581	1238	2376	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.5861	1026	2376	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	81.4784	1212	2376	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.4443	1069	2376	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.1828	1222	2376	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:16,746] [INFO] DFAST Taxonomy check result was written to GCF_011170145.1_ASM1117014v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:16,747] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:16,747] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:16,747] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13fda809-4a18-4a05-8910-72f414c94b44/dqc_reference/checkm_data
[2024-01-24 11:06:16,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:16,814] [INFO] Task started: CheckM
[2024-01-24 11:06:16,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011170145.1_ASM1117014v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011170145.1_ASM1117014v1_genomic.fna/checkm_input GCF_011170145.1_ASM1117014v1_genomic.fna/checkm_result
[2024-01-24 11:08:01,121] [INFO] Task succeeded: CheckM
[2024-01-24 11:08:01,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 11:08:01,161] [INFO] ===== Completeness check finished =====
[2024-01-24 11:08:01,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:08:01,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011170145.1_ASM1117014v1_genomic.fna/markers.fasta)
[2024-01-24 11:08:01,163] [INFO] Task started: Blastn
[2024-01-24 11:08:01,163] [INFO] Running command: blastn -query GCF_011170145.1_ASM1117014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13fda809-4a18-4a05-8910-72f414c94b44/dqc_reference/reference_markers_gtdb.fasta -out GCF_011170145.1_ASM1117014v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:08:03,349] [INFO] Task succeeded: Blastn
[2024-01-24 11:08:03,352] [INFO] Selected 23 target genomes.
[2024-01-24 11:08:03,352] [INFO] Target genome list was writen to GCF_011170145.1_ASM1117014v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:08:03,389] [INFO] Task started: fastANI
[2024-01-24 11:08:03,389] [INFO] Running command: fastANI --query /var/lib/cwl/stgb89d813b-f793-4d70-9680-76624dc29965/GCF_011170145.1_ASM1117014v1_genomic.fna.gz --refList GCF_011170145.1_ASM1117014v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011170145.1_ASM1117014v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:46,093] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:46,114] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:46,114] [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_011170125.1	s__Streptomyces diastaticus	99.5875	2123	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.51	98.72	0.93	0.90	11	conclusive
GCF_000719955.1	s__Streptomyces albidoflavus	92.1003	1830	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	95.93	0.92	0.84	100	-
GCF_018069565.1	s__Streptomyces sp018069565	82.0393	1264	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010548465.1	s__Streptomyces sp010548465	81.9198	1051	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003268675.1	s__Streptomyces bacillaris	81.8632	1328	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.84	95.80	0.88	0.83	37	-
GCF_014655295.1	s__Streptomyces fumanus	81.8326	1323	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091845.1	s__Streptomyces sp900091845	81.8059	1300	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014648855.1	s__Streptomyces parvulus	81.7777	1305	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.93	0.93	0.87	4	-
GCF_004784465.1	s__Streptomyces griseoluteus	81.7705	1155	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	97.39	95.67	0.90	0.82	4	-
GCF_003112555.1	s__Streptomyces coelicoflavus	81.7598	1361	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_004127445.1	s__Streptomyces alfalfae	81.73	1301	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	-
GCF_003671715.1	s__Streptomyces sp003671715	81.701	1237	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCF_014656095.1	s__Streptomyces longispororuber	81.6688	1288	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090105.1	s__Streptomyces sp019090105	81.6075	1181	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018982965.1	s__Streptomyces sp018982965	81.51	1269	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649335.1	s__Streptomyces roseolilacinus	81.4689	1188	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905885.1	s__Streptomyces sp001905885	81.4104	1228	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	96.05	0.87	0.87	2	-
GCF_000720835.1	s__Streptomyces achromogenes	81.3991	1244	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	N/A	N/A	N/A	N/A	1	-
GCF_007679425.1	s__Streptomyces incarnatus_A	81.2429	1247	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.00	0.97	0.94	3	-
GCF_014649115.1	s__Streptomyces eurythermus	81.2394	1325	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_013364195.1	s__Streptomyces sp013364195	81.2144	1166	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155905.1	s__Streptomyces tricolor	81.1729	1105	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_008974245.1	s__Streptomyces abyssomicinicus	81.1552	1219	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:46,116] [INFO] GTDB search result was written to GCF_011170145.1_ASM1117014v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:46,117] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:46,120] [INFO] DFAST_QC result json was written to GCF_011170145.1_ASM1117014v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:46,121] [INFO] DFAST_QC completed!
[2024-01-24 11:08:46,121] [INFO] Total running time: 0h3m11s