[2024-01-24 11:43:52,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:52,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:52,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg56a7983c-3edd-432f-80bc-27113a633548/dqc_reference
[2024-01-24 11:43:54,193] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,194] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,194] [INFO] Running command: gunzip -c /var/lib/cwl/stg28cf69de-a1ff-4130-8752-928becc466c7/GCF_017676365.1_ASM1767636v1_genomic.fna.gz | prodigal -d GCF_017676365.1_ASM1767636v1_genomic.fna/cds.fna -a GCF_017676365.1_ASM1767636v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:15,463] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:15,463] [INFO] Task started: HMMsearch
[2024-01-24 11:44:15,464] [INFO] Running command: hmmsearch --tblout GCF_017676365.1_ASM1767636v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56a7983c-3edd-432f-80bc-27113a633548/dqc_reference/reference_markers.hmm GCF_017676365.1_ASM1767636v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:15,777] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:15,779] [INFO] Found 6/6 markers.
[2024-01-24 11:44:15,840] [INFO] Query marker FASTA was written to GCF_017676365.1_ASM1767636v1_genomic.fna/markers.fasta
[2024-01-24 11:44:15,840] [INFO] Task started: Blastn
[2024-01-24 11:44:15,840] [INFO] Running command: blastn -query GCF_017676365.1_ASM1767636v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56a7983c-3edd-432f-80bc-27113a633548/dqc_reference/reference_markers.fasta -out GCF_017676365.1_ASM1767636v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:17,108] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:17,111] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:17,111] [INFO] Target genome list was writen to GCF_017676365.1_ASM1767636v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:17,117] [INFO] Task started: fastANI
[2024-01-24 11:44:17,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg28cf69de-a1ff-4130-8752-928becc466c7/GCF_017676365.1_ASM1767636v1_genomic.fna.gz --refList GCF_017676365.1_ASM1767636v1_genomic.fna/target_genomes.txt --output GCF_017676365.1_ASM1767636v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:42,905] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:42,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56a7983c-3edd-432f-80bc-27113a633548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:42,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56a7983c-3edd-432f-80bc-27113a633548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:42,919] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:42,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:42,919] [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 oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	100.0	2340	2362	95	conclusive
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	88.7084	1751	2362	95	below_threshold
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	88.6485	1790	2362	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	86.9794	1645	2362	95	below_threshold
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	86.9554	1657	2362	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	85.1255	1487	2362	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	85.1176	1483	2362	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	85.0657	1523	2362	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	82.8735	1196	2362	95	below_threshold
Streptomyces cacaoi	strain=NBRC 12748	GCA_006539165.1	1898	1898	type	True	82.8346	1383	2362	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	80.4146	864	2362	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.3773	1137	2362	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.1788	1213	2362	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	79.9359	1023	2362	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	79.746	1070	2362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:42,921] [INFO] DFAST Taxonomy check result was written to GCF_017676365.1_ASM1767636v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:42,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:42,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:42,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56a7983c-3edd-432f-80bc-27113a633548/dqc_reference/checkm_data
[2024-01-24 11:44:42,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:42,991] [INFO] Task started: CheckM
[2024-01-24 11:44:42,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017676365.1_ASM1767636v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017676365.1_ASM1767636v1_genomic.fna/checkm_input GCF_017676365.1_ASM1767636v1_genomic.fna/checkm_result
[2024-01-24 11:45:50,990] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:50,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:51,012] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:51,012] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:51,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017676365.1_ASM1767636v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:51,013] [INFO] Task started: Blastn
[2024-01-24 11:45:51,013] [INFO] Running command: blastn -query GCF_017676365.1_ASM1767636v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56a7983c-3edd-432f-80bc-27113a633548/dqc_reference/reference_markers_gtdb.fasta -out GCF_017676365.1_ASM1767636v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:52,965] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:52,968] [INFO] Selected 10 target genomes.
[2024-01-24 11:45:52,968] [INFO] Target genome list was writen to GCF_017676365.1_ASM1767636v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:52,974] [INFO] Task started: fastANI
[2024-01-24 11:45:52,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg28cf69de-a1ff-4130-8752-928becc466c7/GCF_017676365.1_ASM1767636v1_genomic.fna.gz --refList GCF_017676365.1_ASM1767636v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017676365.1_ASM1767636v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:10,238] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:10,247] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:10,247] [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_017676365.1	s__Streptomyces oryzae	100.0	2340	2362	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_017676385.1	s__Streptomyces sp017676385	88.6951	1752	2362	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	88.655	1789	2362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.11	97.08	0.90	0.88	5	-
GCF_000424765.1	s__Streptomyces sp000424765	86.9876	1609	2362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.13	98.98	0.93	0.92	5	-
GCF_900111245.1	s__Streptomyces qinglanensis	86.9431	1659	2362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_013302895.1	s__Streptomyces chlorinus	85.8466	1588	2362	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	85.155	1538	2362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725885.1	s__Streptomyces albus	85.1451	1479	2362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	97.77	0.97	0.92	14	-
GCF_003323715.1	s__Streptomyces diacarni	85.0601	1524	2362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797655.1	s__Streptomyces sp002797655	79.4885	1054	2362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.99	97.30	0.92	0.88	9	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:10,249] [INFO] GTDB search result was written to GCF_017676365.1_ASM1767636v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:10,249] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:10,252] [INFO] DFAST_QC result json was written to GCF_017676365.1_ASM1767636v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:10,253] [INFO] DFAST_QC completed!
[2024-01-24 11:46:10,253] [INFO] Total running time: 0h2m17s