[2024-01-24 11:59:09,149] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:09,152] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:09,152] [INFO] DQC Reference Directory: /var/lib/cwl/stgffe0c15a-2763-466d-bc7a-d806fe2cae1f/dqc_reference
[2024-01-24 11:59:10,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:10,424] [INFO] Task started: Prodigal
[2024-01-24 11:59:10,424] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4c611e9-fa21-47c5-af46-be4c8988bcf2/GCF_014651015.1_ASM1465101v1_genomic.fna.gz | prodigal -d GCF_014651015.1_ASM1465101v1_genomic.fna/cds.fna -a GCF_014651015.1_ASM1465101v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:33,745] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:33,746] [INFO] Task started: HMMsearch
[2024-01-24 11:59:33,746] [INFO] Running command: hmmsearch --tblout GCF_014651015.1_ASM1465101v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffe0c15a-2763-466d-bc7a-d806fe2cae1f/dqc_reference/reference_markers.hmm GCF_014651015.1_ASM1465101v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:34,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:34,189] [INFO] Found 6/6 markers.
[2024-01-24 11:59:34,279] [INFO] Query marker FASTA was written to GCF_014651015.1_ASM1465101v1_genomic.fna/markers.fasta
[2024-01-24 11:59:34,280] [INFO] Task started: Blastn
[2024-01-24 11:59:34,280] [INFO] Running command: blastn -query GCF_014651015.1_ASM1465101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffe0c15a-2763-466d-bc7a-d806fe2cae1f/dqc_reference/reference_markers.fasta -out GCF_014651015.1_ASM1465101v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:35,645] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:35,649] [INFO] Selected 15 target genomes.
[2024-01-24 11:59:35,649] [INFO] Target genome list was writen to GCF_014651015.1_ASM1465101v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:35,656] [INFO] Task started: fastANI
[2024-01-24 11:59:35,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4c611e9-fa21-47c5-af46-be4c8988bcf2/GCF_014651015.1_ASM1465101v1_genomic.fna.gz --refList GCF_014651015.1_ASM1465101v1_genomic.fna/target_genomes.txt --output GCF_014651015.1_ASM1465101v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:05,970] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:05,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffe0c15a-2763-466d-bc7a-d806fe2cae1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:05,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffe0c15a-2763-466d-bc7a-d806fe2cae1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:05,987] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:05,987] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:05,987] [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 xantholiticus	strain=JCM 4863	GCA_014651015.1	68285	68285	type	True	100.0	2561	2565	95	conclusive
Streptomyces kurssanovii	strain=JCM 4388	GCA_014649695.1	67312	67312	type	True	88.0397	1782	2565	95	below_threshold
Streptomyces lunaelactis	strain=MM109	GCA_003054555.1	1535768	1535768	type	True	84.2679	1524	2565	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	84.1458	1551	2565	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	83.8317	1511	2565	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.2502	1409	2565	95	below_threshold
Streptomyces wuyuanensis	strain=CGMCC 4.7042	GCA_900103455.1	1196353	1196353	type	True	82.6725	1451	2565	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	82.5831	1333	2565	95	below_threshold
Streptomyces inusitatus	strain=JCM 4988	GCA_014651115.1	68221	68221	type	True	82.2376	1253	2565	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.1548	1053	2565	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	81.6526	1293	2565	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	81.5447	1290	2565	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.3488	1260	2565	95	below_threshold
Streptomyces lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	81.2325	1345	2565	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.1574	1298	2565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:05,989] [INFO] DFAST Taxonomy check result was written to GCF_014651015.1_ASM1465101v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:05,989] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:05,989] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:05,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffe0c15a-2763-466d-bc7a-d806fe2cae1f/dqc_reference/checkm_data
[2024-01-24 12:00:05,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:06,123] [INFO] Task started: CheckM
[2024-01-24 12:00:06,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651015.1_ASM1465101v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651015.1_ASM1465101v1_genomic.fna/checkm_input GCF_014651015.1_ASM1465101v1_genomic.fna/checkm_result
[2024-01-24 12:01:29,625] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:29,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.82%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:29,656] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:29,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:29,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651015.1_ASM1465101v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:29,657] [INFO] Task started: Blastn
[2024-01-24 12:01:29,657] [INFO] Running command: blastn -query GCF_014651015.1_ASM1465101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffe0c15a-2763-466d-bc7a-d806fe2cae1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651015.1_ASM1465101v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:31,749] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:31,754] [INFO] Selected 8 target genomes.
[2024-01-24 12:01:31,754] [INFO] Target genome list was writen to GCF_014651015.1_ASM1465101v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:31,762] [INFO] Task started: fastANI
[2024-01-24 12:01:31,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4c611e9-fa21-47c5-af46-be4c8988bcf2/GCF_014651015.1_ASM1465101v1_genomic.fna.gz --refList GCF_014651015.1_ASM1465101v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651015.1_ASM1465101v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:47,584] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:47,593] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:47,594] [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_014651015.1	s__Streptomyces xantholiticus	100.0	2561	2565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.93	95.93	0.86	0.86	2	conclusive
GCF_014649695.1	s__Streptomyces kurssanovii	88.0509	1780	2565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278075.1	s__Streptomyces pristinaespiralis	87.9266	1736	2565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
GCF_009832925.1	s__Streptomyces sp009832925	87.8733	1751	2565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387495.1	s__Streptomyces sp013387495	85.7854	1696	2565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614575.1	s__Streptomyces sp018614575	85.4456	1654	2565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054555.1	s__Streptomyces lunaelactis	84.2679	1524	2565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.21	97.91	0.90	0.85	18	-
GCF_000377145.1	s__Streptomyces sp000377145	83.7517	1423	2565	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 12:01:47,595] [INFO] GTDB search result was written to GCF_014651015.1_ASM1465101v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:47,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:47,601] [INFO] DFAST_QC result json was written to GCF_014651015.1_ASM1465101v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:47,601] [INFO] DFAST_QC completed!
[2024-01-24 12:01:47,601] [INFO] Total running time: 0h2m38s