[2024-01-24 14:46:57,415] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:57,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:57,418] [INFO] DQC Reference Directory: /var/lib/cwl/stgabdedd31-c62e-4b5c-92e0-392f7482a098/dqc_reference
[2024-01-24 14:46:58,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,713] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,713] [INFO] Running command: gunzip -c /var/lib/cwl/stg214e9197-0cf7-470d-a89c-5daa50bb18c4/GCF_013030945.1_ASM1303094v1_genomic.fna.gz | prodigal -d GCF_013030945.1_ASM1303094v1_genomic.fna/cds.fna -a GCF_013030945.1_ASM1303094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:20,164] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:20,164] [INFO] Task started: HMMsearch
[2024-01-24 14:47:20,164] [INFO] Running command: hmmsearch --tblout GCF_013030945.1_ASM1303094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabdedd31-c62e-4b5c-92e0-392f7482a098/dqc_reference/reference_markers.hmm GCF_013030945.1_ASM1303094v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:20,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:20,535] [INFO] Found 6/6 markers.
[2024-01-24 14:47:20,599] [INFO] Query marker FASTA was written to GCF_013030945.1_ASM1303094v1_genomic.fna/markers.fasta
[2024-01-24 14:47:20,599] [INFO] Task started: Blastn
[2024-01-24 14:47:20,599] [INFO] Running command: blastn -query GCF_013030945.1_ASM1303094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabdedd31-c62e-4b5c-92e0-392f7482a098/dqc_reference/reference_markers.fasta -out GCF_013030945.1_ASM1303094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:22,025] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:22,035] [INFO] Selected 15 target genomes.
[2024-01-24 14:47:22,035] [INFO] Target genome list was writen to GCF_013030945.1_ASM1303094v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:22,051] [INFO] Task started: fastANI
[2024-01-24 14:47:22,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg214e9197-0cf7-470d-a89c-5daa50bb18c4/GCF_013030945.1_ASM1303094v1_genomic.fna.gz --refList GCF_013030945.1_ASM1303094v1_genomic.fna/target_genomes.txt --output GCF_013030945.1_ASM1303094v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:51,502] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:51,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabdedd31-c62e-4b5c-92e0-392f7482a098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:51,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabdedd31-c62e-4b5c-92e0-392f7482a098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:51,516] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:51,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:51,516] [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 morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	100.0	2373	2385	95	conclusive
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	99.9982	2367	2385	95	conclusive
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	85.8371	1337	2385	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	85.2182	1470	2385	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	85.165	1482	2385	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	84.9891	1517	2385	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	84.445	1450	2385	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	84.3791	1465	2385	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	84.3184	1497	2385	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	84.2927	1434	2385	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	83.7265	1324	2385	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	83.6868	1274	2385	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	83.6305	1406	2385	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	81.2772	1259	2385	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	80.8867	1141	2385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:51,518] [INFO] DFAST Taxonomy check result was written to GCF_013030945.1_ASM1303094v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:51,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:51,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:51,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabdedd31-c62e-4b5c-92e0-392f7482a098/dqc_reference/checkm_data
[2024-01-24 14:47:51,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:51,593] [INFO] Task started: CheckM
[2024-01-24 14:47:51,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013030945.1_ASM1303094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013030945.1_ASM1303094v1_genomic.fna/checkm_input GCF_013030945.1_ASM1303094v1_genomic.fna/checkm_result
[2024-01-24 14:49:37,129] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:37,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:37,168] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:37,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:37,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013030945.1_ASM1303094v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:37,169] [INFO] Task started: Blastn
[2024-01-24 14:49:37,169] [INFO] Running command: blastn -query GCF_013030945.1_ASM1303094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabdedd31-c62e-4b5c-92e0-392f7482a098/dqc_reference/reference_markers_gtdb.fasta -out GCF_013030945.1_ASM1303094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:39,561] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:39,565] [INFO] Selected 17 target genomes.
[2024-01-24 14:49:39,566] [INFO] Target genome list was writen to GCF_013030945.1_ASM1303094v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:39,589] [INFO] Task started: fastANI
[2024-01-24 14:49:39,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg214e9197-0cf7-470d-a89c-5daa50bb18c4/GCF_013030945.1_ASM1303094v1_genomic.fna.gz --refList GCF_013030945.1_ASM1303094v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013030945.1_ASM1303094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:11,411] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:11,428] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:50:11,429] [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_013030945.1	s__Streptomyces morookaense	100.0	2373	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_014203555.1	s__Streptomyces olivoverticillatus	85.8544	1335	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650495.1	s__Streptomyces cinnamoneus	85.2527	1486	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655595.1	s__Streptomyces griseocarneus	85.1718	1480	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939475.1	s__Streptomyces cinnamoneus_A	85.0776	1402	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCA_000715685.1	s__Streptomyces lilacinus	85.077	1436	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648775.1	s__Streptomyces abikoensis	84.9944	1516	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.57	96.57	0.89	0.89	2	-
GCF_017349075.1	s__Streptomyces triculaminicus_A	84.9652	1462	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.73	0.98	0.98	3	-
GCF_003011965.1	s__Streptomyces nondiastaticus	84.447	1396	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_014650335.1	s__Streptomyces hiroshimensis	84.4358	1453	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719265.1	s__Streptomyces roseoverticillatus	84.4028	1408	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_003626645.1	s__Streptomyces klenkii	84.3788	1466	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	99.37	0.96	0.96	2	-
GCF_002192455.1	s__Streptomyces albireticuli_B	84.3444	1448	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003391135.1	s__Streptomyces olivoreticuli	84.2246	1519	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003674045.1	s__Streptomyces griseocarneus_A	84.1029	1509	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013055795.1	s__Streptomyces sp013055795	83.6391	1331	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916255.1	s__Streptomyces mobaraensis	83.6345	1405	2385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:50:11,430] [INFO] GTDB search result was written to GCF_013030945.1_ASM1303094v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:11,431] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:11,435] [INFO] DFAST_QC result json was written to GCF_013030945.1_ASM1303094v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:11,435] [INFO] DFAST_QC completed!
[2024-01-24 14:50:11,435] [INFO] Total running time: 0h3m14s