[2024-01-25 19:04:35,597] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:35,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:35,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd9823ac-3d63-4ad8-9062-211872d10f71/dqc_reference
[2024-01-25 19:04:36,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:36,790] [INFO] Task started: Prodigal
[2024-01-25 19:04:36,790] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd47c8e9-f208-4887-ae32-3661def77d8a/GCF_009811575.1_ASM981157v1_genomic.fna.gz | prodigal -d GCF_009811575.1_ASM981157v1_genomic.fna/cds.fna -a GCF_009811575.1_ASM981157v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:01,185] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:01,186] [INFO] Task started: HMMsearch
[2024-01-25 19:05:01,186] [INFO] Running command: hmmsearch --tblout GCF_009811575.1_ASM981157v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd9823ac-3d63-4ad8-9062-211872d10f71/dqc_reference/reference_markers.hmm GCF_009811575.1_ASM981157v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:01,482] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:01,483] [INFO] Found 6/6 markers.
[2024-01-25 19:05:01,542] [INFO] Query marker FASTA was written to GCF_009811575.1_ASM981157v1_genomic.fna/markers.fasta
[2024-01-25 19:05:01,543] [INFO] Task started: Blastn
[2024-01-25 19:05:01,543] [INFO] Running command: blastn -query GCF_009811575.1_ASM981157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd9823ac-3d63-4ad8-9062-211872d10f71/dqc_reference/reference_markers.fasta -out GCF_009811575.1_ASM981157v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:02,796] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:02,798] [INFO] Selected 12 target genomes.
[2024-01-25 19:05:02,799] [INFO] Target genome list was writen to GCF_009811575.1_ASM981157v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:02,803] [INFO] Task started: fastANI
[2024-01-25 19:05:02,803] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd47c8e9-f208-4887-ae32-3661def77d8a/GCF_009811575.1_ASM981157v1_genomic.fna.gz --refList GCF_009811575.1_ASM981157v1_genomic.fna/target_genomes.txt --output GCF_009811575.1_ASM981157v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:31,161] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:31,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd9823ac-3d63-4ad8-9062-211872d10f71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:31,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd9823ac-3d63-4ad8-9062-211872d10f71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:31,170] [INFO] Found 12 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:05:31,170] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:05:31,171] [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 glebosus	strain=NBRC 13786	GCA_009811575.1	249580	249580	type	True	100.0	2814	2814	95	inconclusive
Streptomyces glebosus	strain=JCM 4954	GCA_014656235.1	249580	249580	type	True	99.973	2756	2814	95	inconclusive
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	97.6279	2496	2814	95	inconclusive
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	97.6212	2411	2814	95	inconclusive
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	95.2359	2377	2814	95	inconclusive
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	89.7888	2184	2814	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	88.7821	1913	2814	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.5408	1587	2814	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.4319	1295	2814	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.6844	1680	2814	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.6692	1599	2814	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.6644	1647	2814	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:31,172] [INFO] DFAST Taxonomy check result was written to GCF_009811575.1_ASM981157v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:31,173] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:31,173] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:31,173] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd9823ac-3d63-4ad8-9062-211872d10f71/dqc_reference/checkm_data
[2024-01-25 19:05:31,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:31,251] [INFO] Task started: CheckM
[2024-01-25 19:05:31,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009811575.1_ASM981157v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009811575.1_ASM981157v1_genomic.fna/checkm_input GCF_009811575.1_ASM981157v1_genomic.fna/checkm_result
[2024-01-25 19:07:36,696] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:36,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.29%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:36,723] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:36,723] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:36,724] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009811575.1_ASM981157v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:36,724] [INFO] Task started: Blastn
[2024-01-25 19:07:36,724] [INFO] Running command: blastn -query GCF_009811575.1_ASM981157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd9823ac-3d63-4ad8-9062-211872d10f71/dqc_reference/reference_markers_gtdb.fasta -out GCF_009811575.1_ASM981157v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:38,904] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:38,907] [INFO] Selected 9 target genomes.
[2024-01-25 19:07:38,907] [INFO] Target genome list was writen to GCF_009811575.1_ASM981157v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:38,920] [INFO] Task started: fastANI
[2024-01-25 19:07:38,921] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd47c8e9-f208-4887-ae32-3661def77d8a/GCF_009811575.1_ASM981157v1_genomic.fna.gz --refList GCF_009811575.1_ASM981157v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009811575.1_ASM981157v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:00,526] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:00,533] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:00,533] [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_008704855.1	s__Streptomyces platensis	97.6641	2492	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	conclusive
GCF_009811595.1	s__Streptomyces libani	92.6897	2361	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	96.45	0.91	0.86	12	-
GCF_009811635.1	s__Streptomyces tubercidicus	92.4032	2110	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270575.1	s__Streptomyces decoyicus	90.0767	2128	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_009811555.1	s__Streptomyces caniferus	89.792	2181	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187385.1	s__Streptomyces sp900187385	89.5599	2079	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_004122735.1	s__Streptomyces sioyaensis	89.4814	1881	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_004125265.1	s__Streptomyces lydicus_C	89.3153	2037	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646275.1	s__Streptomyces kronopolitis	88.8043	1910	2814	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 19:08:00,534] [INFO] GTDB search result was written to GCF_009811575.1_ASM981157v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:00,535] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:00,537] [INFO] DFAST_QC result json was written to GCF_009811575.1_ASM981157v1_genomic.fna/dqc_result.json
[2024-01-25 19:08:00,538] [INFO] DFAST_QC completed!
[2024-01-25 19:08:00,538] [INFO] Total running time: 0h3m25s