[2024-01-24 14:14:47,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:47,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:47,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg8acd15aa-9044-422a-8579-21453860bc65/dqc_reference
[2024-01-24 14:14:49,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,426] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg778a0755-36dd-4d2f-8793-3023fbe17adb/GCF_016745505.1_ASM1674550v1_genomic.fna.gz | prodigal -d GCF_016745505.1_ASM1674550v1_genomic.fna/cds.fna -a GCF_016745505.1_ASM1674550v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:11,590] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:11,591] [INFO] Task started: HMMsearch
[2024-01-24 14:15:11,591] [INFO] Running command: hmmsearch --tblout GCF_016745505.1_ASM1674550v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8acd15aa-9044-422a-8579-21453860bc65/dqc_reference/reference_markers.hmm GCF_016745505.1_ASM1674550v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:11,948] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:11,950] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg778a0755-36dd-4d2f-8793-3023fbe17adb/GCF_016745505.1_ASM1674550v1_genomic.fna.gz]
[2024-01-24 14:15:12,014] [INFO] Query marker FASTA was written to GCF_016745505.1_ASM1674550v1_genomic.fna/markers.fasta
[2024-01-24 14:15:12,015] [INFO] Task started: Blastn
[2024-01-24 14:15:12,015] [INFO] Running command: blastn -query GCF_016745505.1_ASM1674550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8acd15aa-9044-422a-8579-21453860bc65/dqc_reference/reference_markers.fasta -out GCF_016745505.1_ASM1674550v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:13,184] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:13,188] [INFO] Selected 18 target genomes.
[2024-01-24 14:15:13,189] [INFO] Target genome list was writen to GCF_016745505.1_ASM1674550v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:13,219] [INFO] Task started: fastANI
[2024-01-24 14:15:13,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg778a0755-36dd-4d2f-8793-3023fbe17adb/GCF_016745505.1_ASM1674550v1_genomic.fna.gz --refList GCF_016745505.1_ASM1674550v1_genomic.fna/target_genomes.txt --output GCF_016745505.1_ASM1674550v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:44,404] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:44,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8acd15aa-9044-422a-8579-21453860bc65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:44,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8acd15aa-9044-422a-8579-21453860bc65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:44,425] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:44,425] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:44,425] [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
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	89.6917	1879	2545	95	below_threshold
Streptomyces clavifer	strain=DSM 40843	GCA_017876255.1	68188	68188	type	True	87.7856	1764	2545	95	below_threshold
Streptomyces clavifer	strain=JCM 5059	GCA_014651175.1	68188	68188	type	True	87.7741	1777	2545	95	below_threshold
Streptomyces griseolus	strain=NRRL B-2925	GCA_000721185.1	1909	1909	type	True	86.9457	1623	2545	95	below_threshold
Streptomyces nitrosporeus	strain=JCM 4598	GCA_014650375.1	28894	28894	type	True	86.1483	1649	2545	95	below_threshold
Streptomyces nitrosporeus	strain=ATCC 12769	GCA_008704555.1	28894	28894	type	True	86.0728	1664	2545	95	below_threshold
Streptomyces fulvorobeus	strain=DSM 41455	GCA_013409565.1	284028	284028	type	True	85.4652	1417	2545	95	below_threshold
Streptomyces fulvorobeus	strain=NBRC 15897	GCA_013167895.1	284028	284028	type	True	85.4113	1405	2545	95	below_threshold
Streptomyces poriferorum	strain=P01-B04	GCA_019399235.1	2798799	2798799	type	True	85.0752	1503	2545	95	below_threshold
Streptomyces brevispora	strain=DSM 42059	GCA_007829885.1	887462	887462	type	True	85.0739	1549	2545	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	85.0715	1588	2545	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	85.0444	1487	2545	95	below_threshold
Streptomyces gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	84.9751	1478	2545	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	84.9031	1579	2545	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.513	1367	2545	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.319	1177	2545	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	81.1014	1157	2545	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.8587	1210	2545	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:44,427] [INFO] DFAST Taxonomy check result was written to GCF_016745505.1_ASM1674550v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:44,428] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:44,428] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:44,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8acd15aa-9044-422a-8579-21453860bc65/dqc_reference/checkm_data
[2024-01-24 14:15:44,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:44,503] [INFO] Task started: CheckM
[2024-01-24 14:15:44,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016745505.1_ASM1674550v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016745505.1_ASM1674550v1_genomic.fna/checkm_input GCF_016745505.1_ASM1674550v1_genomic.fna/checkm_result
[2024-01-24 14:17:22,094] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:22,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:22,120] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:22,121] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:22,121] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016745505.1_ASM1674550v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:22,122] [INFO] Task started: Blastn
[2024-01-24 14:17:22,122] [INFO] Running command: blastn -query GCF_016745505.1_ASM1674550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8acd15aa-9044-422a-8579-21453860bc65/dqc_reference/reference_markers_gtdb.fasta -out GCF_016745505.1_ASM1674550v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:23,844] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:23,848] [INFO] Selected 10 target genomes.
[2024-01-24 14:17:23,848] [INFO] Target genome list was writen to GCF_016745505.1_ASM1674550v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:23,856] [INFO] Task started: fastANI
[2024-01-24 14:17:23,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg778a0755-36dd-4d2f-8793-3023fbe17adb/GCF_016745505.1_ASM1674550v1_genomic.fna.gz --refList GCF_016745505.1_ASM1674550v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016745505.1_ASM1674550v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:43,419] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:43,428] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:43,428] [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_002711365.1	s__Streptomyces sp002711365	96.823	2246	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	96.67	0.92	0.87	7	conclusive
GCF_002941025.1	s__Streptomyces sp002941025	91.517	2073	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016804005.1	s__Streptomyces pratensis_A	90.1801	1901	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717025.1	s__Streptomyces atroolivaceus	90.1251	1892	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002910915.1	s__Streptomyces sp002910915	90.0212	1708	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001700505.1	s__Streptomyces mutomycini	90.0082	1636	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.53	0.96	0.96	2	-
GCF_008042155.1	s__Streptomyces sp008042155	89.7633	1946	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717245.1	s__Streptomyces papulosus	89.6755	1881	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.21	99.06	0.94	0.87	14	-
GCF_001905505.1	s__Streptomyces sp001905505	89.5379	1915	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829855.1	s__Streptomyces argenteolus	88.7602	1857	2545	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 14:17:43,430] [INFO] GTDB search result was written to GCF_016745505.1_ASM1674550v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:43,430] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:43,434] [INFO] DFAST_QC result json was written to GCF_016745505.1_ASM1674550v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:43,434] [INFO] DFAST_QC completed!
[2024-01-24 14:17:43,434] [INFO] Total running time: 0h2m56s