[2024-01-24 15:02:46,043] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:46,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:46,048] [INFO] DQC Reference Directory: /var/lib/cwl/stg42e5e949-97eb-4a50-a87c-55dd32795c10/dqc_reference
[2024-01-24 15:02:47,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:47,425] [INFO] Task started: Prodigal
[2024-01-24 15:02:47,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cae3f7d-b18c-46a4-ac39-83c795198daa/GCF_000813365.1_ASM81336v1_genomic.fna.gz | prodigal -d GCF_000813365.1_ASM81336v1_genomic.fna/cds.fna -a GCF_000813365.1_ASM81336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:11,663] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:11,664] [INFO] Task started: HMMsearch
[2024-01-24 15:03:11,664] [INFO] Running command: hmmsearch --tblout GCF_000813365.1_ASM81336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42e5e949-97eb-4a50-a87c-55dd32795c10/dqc_reference/reference_markers.hmm GCF_000813365.1_ASM81336v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:12,060] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:12,061] [INFO] Found 6/6 markers.
[2024-01-24 15:03:12,118] [INFO] Query marker FASTA was written to GCF_000813365.1_ASM81336v1_genomic.fna/markers.fasta
[2024-01-24 15:03:12,118] [INFO] Task started: Blastn
[2024-01-24 15:03:12,118] [INFO] Running command: blastn -query GCF_000813365.1_ASM81336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42e5e949-97eb-4a50-a87c-55dd32795c10/dqc_reference/reference_markers.fasta -out GCF_000813365.1_ASM81336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:13,484] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:13,487] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:13,487] [INFO] Target genome list was writen to GCF_000813365.1_ASM81336v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:13,503] [INFO] Task started: fastANI
[2024-01-24 15:03:13,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cae3f7d-b18c-46a4-ac39-83c795198daa/GCF_000813365.1_ASM81336v1_genomic.fna.gz --refList GCF_000813365.1_ASM81336v1_genomic.fna/target_genomes.txt --output GCF_000813365.1_ASM81336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:41,637] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:41,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42e5e949-97eb-4a50-a87c-55dd32795c10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:41,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42e5e949-97eb-4a50-a87c-55dd32795c10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:41,649] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:41,649] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:41,650] [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 albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	100.0	2474	2479	95	conclusive
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	99.9868	2450	2479	95	conclusive
Streptomyces reniochalinae	strain=LHW50302	GCA_003323735.1	2250578	2250578	type	True	85.543	1677	2479	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	85.4492	1685	2479	95	below_threshold
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	85.0654	1675	2479	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	85.031	1569	2479	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	85.0289	1462	2479	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	82.8281	1359	2479	95	below_threshold
Streptomyces cacaoi	strain=NBRC 12748	GCA_006539165.1	1898	1898	type	True	82.7174	1591	2479	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	80.1667	1093	2479	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	80.0623	1139	2479	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	79.9137	1134	2479	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.8374	1296	2479	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	79.5112	1120	2479	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:41,651] [INFO] DFAST Taxonomy check result was written to GCF_000813365.1_ASM81336v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:41,651] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:41,652] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:41,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42e5e949-97eb-4a50-a87c-55dd32795c10/dqc_reference/checkm_data
[2024-01-24 15:03:41,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:41,721] [INFO] Task started: CheckM
[2024-01-24 15:03:41,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000813365.1_ASM81336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000813365.1_ASM81336v1_genomic.fna/checkm_input GCF_000813365.1_ASM81336v1_genomic.fna/checkm_result
[2024-01-24 15:05:20,543] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:20,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:20,570] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:20,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:20,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000813365.1_ASM81336v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:20,571] [INFO] Task started: Blastn
[2024-01-24 15:05:20,572] [INFO] Running command: blastn -query GCF_000813365.1_ASM81336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42e5e949-97eb-4a50-a87c-55dd32795c10/dqc_reference/reference_markers_gtdb.fasta -out GCF_000813365.1_ASM81336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:22,754] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:22,759] [INFO] Selected 9 target genomes.
[2024-01-24 15:05:22,759] [INFO] Target genome list was writen to GCF_000813365.1_ASM81336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:22,769] [INFO] Task started: fastANI
[2024-01-24 15:05:22,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cae3f7d-b18c-46a4-ac39-83c795198daa/GCF_000813365.1_ASM81336v1_genomic.fna.gz --refList GCF_000813365.1_ASM81336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000813365.1_ASM81336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:41,520] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:41,536] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:41,537] [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_000725885.1	s__Streptomyces albus	99.9868	2450	2479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	97.77	0.97	0.92	14	conclusive
GCF_013302895.1	s__Streptomyces chlorinus	86.6008	1789	2479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323735.1	s__Streptomyces reniochalinae	85.567	1672	2479	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	85.4173	1691	2479	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	85.3186	1662	2479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676345.1	s__Streptomyces smyrnaeus	85.0715	1674	2479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.11	97.08	0.90	0.88	5	-
GCF_017676365.1	s__Streptomyces oryzae	85.0399	1461	2479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676385.1	s__Streptomyces sp017676385	85.0108	1573	2479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539165.1	s__Streptomyces cacaoi	82.7225	1592	2479	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.44	99.09	0.96	0.94	7	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:41,539] [INFO] GTDB search result was written to GCF_000813365.1_ASM81336v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:41,539] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:41,544] [INFO] DFAST_QC result json was written to GCF_000813365.1_ASM81336v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:41,545] [INFO] DFAST_QC completed!
[2024-01-24 15:05:41,545] [INFO] Total running time: 0h2m56s