[2024-01-25 20:03:06,081] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:06,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:06,083] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f1dcbcc-0d96-4851-8f8f-b322a0580d88/dqc_reference
[2024-01-25 20:03:07,207] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:07,208] [INFO] Task started: Prodigal
[2024-01-25 20:03:07,208] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f6f9223-e986-4c06-acfe-8c9c8b985d9c/GCF_002794255.1_ASM279425v1_genomic.fna.gz | prodigal -d GCF_002794255.1_ASM279425v1_genomic.fna/cds.fna -a GCF_002794255.1_ASM279425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:26,276] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:26,277] [INFO] Task started: HMMsearch
[2024-01-25 20:03:26,277] [INFO] Running command: hmmsearch --tblout GCF_002794255.1_ASM279425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f1dcbcc-0d96-4851-8f8f-b322a0580d88/dqc_reference/reference_markers.hmm GCF_002794255.1_ASM279425v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:26,570] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:26,571] [INFO] Found 6/6 markers.
[2024-01-25 20:03:26,628] [INFO] Query marker FASTA was written to GCF_002794255.1_ASM279425v1_genomic.fna/markers.fasta
[2024-01-25 20:03:26,629] [INFO] Task started: Blastn
[2024-01-25 20:03:26,629] [INFO] Running command: blastn -query GCF_002794255.1_ASM279425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f1dcbcc-0d96-4851-8f8f-b322a0580d88/dqc_reference/reference_markers.fasta -out GCF_002794255.1_ASM279425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:27,925] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:27,928] [INFO] Selected 22 target genomes.
[2024-01-25 20:03:27,928] [INFO] Target genome list was writen to GCF_002794255.1_ASM279425v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:27,938] [INFO] Task started: fastANI
[2024-01-25 20:03:27,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f6f9223-e986-4c06-acfe-8c9c8b985d9c/GCF_002794255.1_ASM279425v1_genomic.fna.gz --refList GCF_002794255.1_ASM279425v1_genomic.fna/target_genomes.txt --output GCF_002794255.1_ASM279425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:08,776] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:08,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f1dcbcc-0d96-4851-8f8f-b322a0580d88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:08,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f1dcbcc-0d96-4851-8f8f-b322a0580d88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:08,791] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:04:08,792] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:08,792] [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 carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	100.0	2295	2365	95	conclusive
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	87.0447	1446	2365	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	86.8533	1358	2365	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	86.8324	1440	2365	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	86.8038	1461	2365	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002843305.1	1257026	1257026	type	True	86.7992	1472	2365	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	86.6651	1418	2365	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	86.2996	1414	2365	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	81.3663	845	2365	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	81.0506	937	2365	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	80.716	1072	2365	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.6631	1224	2365	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	80.6588	1075	2365	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	80.6233	1055	2365	95	below_threshold
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	80.5682	1068	2365	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.4962	1161	2365	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	80.4911	1047	2365	95	below_threshold
Streptomyces fragilis	strain=NBRC 12862	GCA_003112515.1	67301	67301	type	True	80.2884	1061	2365	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	79.8484	1009	2365	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	79.7289	1015	2365	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	79.6546	1119	2365	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_014650815.1	68200	68200	type	True	79.5846	1107	2365	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:08,793] [INFO] DFAST Taxonomy check result was written to GCF_002794255.1_ASM279425v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:08,794] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:08,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:08,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f1dcbcc-0d96-4851-8f8f-b322a0580d88/dqc_reference/checkm_data
[2024-01-25 20:04:08,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:08,864] [INFO] Task started: CheckM
[2024-01-25 20:04:08,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002794255.1_ASM279425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002794255.1_ASM279425v1_genomic.fna/checkm_input GCF_002794255.1_ASM279425v1_genomic.fna/checkm_result
[2024-01-25 20:05:54,115] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:54,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:54,137] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:54,137] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:54,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002794255.1_ASM279425v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:54,137] [INFO] Task started: Blastn
[2024-01-25 20:05:54,138] [INFO] Running command: blastn -query GCF_002794255.1_ASM279425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f1dcbcc-0d96-4851-8f8f-b322a0580d88/dqc_reference/reference_markers_gtdb.fasta -out GCF_002794255.1_ASM279425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:56,300] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:56,303] [INFO] Selected 15 target genomes.
[2024-01-25 20:05:56,303] [INFO] Target genome list was writen to GCF_002794255.1_ASM279425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:56,316] [INFO] Task started: fastANI
[2024-01-25 20:05:56,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f6f9223-e986-4c06-acfe-8c9c8b985d9c/GCF_002794255.1_ASM279425v1_genomic.fna.gz --refList GCF_002794255.1_ASM279425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002794255.1_ASM279425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:23,638] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:23,649] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:23,649] [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_002794255.1	s__Streptomyces carminius	100.0	2291	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900110735.1	s__Streptomyces radiopugnans	87.0332	1447	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843305.1	s__Streptomyces barkulensis	86.8236	1470	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	-
GCF_000718985.1	s__Streptomyces megasporus	86.8203	1361	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114215.1	s__Streptomyces pini	86.8196	1459	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	N/A	N/A	N/A	N/A	1	-
GCF_017114865.1	s__Streptomyces verrucosisporus	86.6559	1418	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_009709575.1	s__Streptomyces taklimakanensis	86.3222	1411	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302895.1	s__Streptomyces chlorinus	80.7437	1085	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364155.1	s__Streptomyces sp013364155	80.6739	1148	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424785.1	s__Streptomyces sp000424785	80.3654	1053	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813405.1	s__Streptomyces sp002813405	80.3158	1086	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323715.1	s__Streptomyces diacarni	80.3105	1039	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	80.2542	1147	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646055.1	s__Streptomyces_A tyrosinilyticus	79.7393	985	2365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045025.1	s__Streptomyces ureilyticus	79.5414	1003	2365	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 20:06:23,650] [INFO] GTDB search result was written to GCF_002794255.1_ASM279425v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:23,651] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:23,655] [INFO] DFAST_QC result json was written to GCF_002794255.1_ASM279425v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:23,655] [INFO] DFAST_QC completed!
[2024-01-25 20:06:23,655] [INFO] Total running time: 0h3m18s