[2024-01-24 13:55:26,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:26,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:26,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bc3b517-26f6-4b8c-b78e-22384d46ece9/dqc_reference
[2024-01-24 13:55:27,543] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:27,544] [INFO] Task started: Prodigal
[2024-01-24 13:55:27,545] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a746a4d-5116-42ec-8e67-04d580c520d6/GCF_000340335.1_ASM34033v2_genomic.fna.gz | prodigal -d GCF_000340335.1_ASM34033v2_genomic.fna/cds.fna -a GCF_000340335.1_ASM34033v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:52,042] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:52,043] [INFO] Task started: HMMsearch
[2024-01-24 13:55:52,043] [INFO] Running command: hmmsearch --tblout GCF_000340335.1_ASM34033v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bc3b517-26f6-4b8c-b78e-22384d46ece9/dqc_reference/reference_markers.hmm GCF_000340335.1_ASM34033v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:52,349] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:52,350] [INFO] Found 6/6 markers.
[2024-01-24 13:55:52,412] [INFO] Query marker FASTA was written to GCF_000340335.1_ASM34033v2_genomic.fna/markers.fasta
[2024-01-24 13:55:52,412] [INFO] Task started: Blastn
[2024-01-24 13:55:52,412] [INFO] Running command: blastn -query GCF_000340335.1_ASM34033v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bc3b517-26f6-4b8c-b78e-22384d46ece9/dqc_reference/reference_markers.fasta -out GCF_000340335.1_ASM34033v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:53,610] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:53,613] [INFO] Selected 10 target genomes.
[2024-01-24 13:55:53,614] [INFO] Target genome list was writen to GCF_000340335.1_ASM34033v2_genomic.fna/target_genomes.txt
[2024-01-24 13:55:53,624] [INFO] Task started: fastANI
[2024-01-24 13:55:53,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a746a4d-5116-42ec-8e67-04d580c520d6/GCF_000340335.1_ASM34033v2_genomic.fna.gz --refList GCF_000340335.1_ASM34033v2_genomic.fna/target_genomes.txt --output GCF_000340335.1_ASM34033v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:18,230] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:18,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bc3b517-26f6-4b8c-b78e-22384d46ece9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:18,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bc3b517-26f6-4b8c-b78e-22384d46ece9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:18,239] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:56:18,240] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:56:18,240] [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 bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	100.0	2952	2952	95	inconclusive
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	99.988	2950	2952	95	inconclusive
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	96.7866	2524	2952	95	inconclusive
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	90.4718	2104	2952	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	90.3758	2217	2952	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	90.2109	2288	2952	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	90.1874	2318	2952	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	87.7282	1782	2952	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	87.5266	2124	2952	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.6616	1734	2952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:18,241] [INFO] DFAST Taxonomy check result was written to GCF_000340335.1_ASM34033v2_genomic.fna/tc_result.tsv
[2024-01-24 13:56:18,242] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:18,242] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:18,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bc3b517-26f6-4b8c-b78e-22384d46ece9/dqc_reference/checkm_data
[2024-01-24 13:56:18,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:18,319] [INFO] Task started: CheckM
[2024-01-24 13:56:18,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000340335.1_ASM34033v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000340335.1_ASM34033v2_genomic.fna/checkm_input GCF_000340335.1_ASM34033v2_genomic.fna/checkm_result
[2024-01-24 13:58:15,016] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:15,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:15,037] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:15,038] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:15,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000340335.1_ASM34033v2_genomic.fna/markers.fasta)
[2024-01-24 13:58:15,038] [INFO] Task started: Blastn
[2024-01-24 13:58:15,038] [INFO] Running command: blastn -query GCF_000340335.1_ASM34033v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bc3b517-26f6-4b8c-b78e-22384d46ece9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000340335.1_ASM34033v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:17,046] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:17,049] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:17,049] [INFO] Target genome list was writen to GCF_000340335.1_ASM34033v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:17,061] [INFO] Task started: fastANI
[2024-01-24 13:58:17,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a746a4d-5116-42ec-8e67-04d580c520d6/GCF_000340335.1_ASM34033v2_genomic.fna.gz --refList GCF_000340335.1_ASM34033v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000340335.1_ASM34033v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:44,764] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:44,777] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:58:44,777] [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_000383595.1	s__Streptomyces bottropensis	99.988	2950	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	inconclusive
GCF_014873495.1	s__Streptomyces stelliscabiei	96.7895	2524	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	inconclusive
GCF_000091305.1	s__Streptomyces scabiei	92.38	2377	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	97.09	0.94	0.86	16	-
GCF_001550375.1	s__Streptomyces europaeiscabiei	91.6755	2104	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_018927715.1	s__Streptomyces brasiliscabiei	90.459	2106	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	90.3715	2218	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772895.1	s__Streptomyces galbus_A	90.3051	2248	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114955.1	s__Streptomyces sp900114955	90.2662	2298	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.68	97.04	0.90	0.85	10	-
GCF_014203845.1	s__Streptomyces scabiei_E	89.8839	2192	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_014648915.1	s__Streptomyces phaeofaciens	83.9478	1835	2952	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 13:58:44,779] [INFO] GTDB search result was written to GCF_000340335.1_ASM34033v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:44,779] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:44,783] [INFO] DFAST_QC result json was written to GCF_000340335.1_ASM34033v2_genomic.fna/dqc_result.json
[2024-01-24 13:58:44,783] [INFO] DFAST_QC completed!
[2024-01-24 13:58:44,783] [INFO] Total running time: 0h3m18s