[2024-01-24 11:26:38,389] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e199c1d-a522-42e2-a21d-125d1283120f/dqc_reference
[2024-01-24 11:26:39,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:39,752] [INFO] Task started: Prodigal
[2024-01-24 11:26:39,752] [INFO] Running command: gunzip -c /var/lib/cwl/stgd748a064-1f47-4bbc-9d5e-948bf43842ba/GCF_024171895.1_ASM2417189v1_genomic.fna.gz | prodigal -d GCF_024171895.1_ASM2417189v1_genomic.fna/cds.fna -a GCF_024171895.1_ASM2417189v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:54,996] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:54,997] [INFO] Task started: HMMsearch
[2024-01-24 11:26:54,997] [INFO] Running command: hmmsearch --tblout GCF_024171895.1_ASM2417189v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e199c1d-a522-42e2-a21d-125d1283120f/dqc_reference/reference_markers.hmm GCF_024171895.1_ASM2417189v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:55,284] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:55,285] [INFO] Found 6/6 markers.
[2024-01-24 11:26:55,328] [INFO] Query marker FASTA was written to GCF_024171895.1_ASM2417189v1_genomic.fna/markers.fasta
[2024-01-24 11:26:55,328] [INFO] Task started: Blastn
[2024-01-24 11:26:55,329] [INFO] Running command: blastn -query GCF_024171895.1_ASM2417189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e199c1d-a522-42e2-a21d-125d1283120f/dqc_reference/reference_markers.fasta -out GCF_024171895.1_ASM2417189v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:56,612] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:56,615] [INFO] Selected 14 target genomes.
[2024-01-24 11:26:56,615] [INFO] Target genome list was writen to GCF_024171895.1_ASM2417189v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:56,625] [INFO] Task started: fastANI
[2024-01-24 11:26:56,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgd748a064-1f47-4bbc-9d5e-948bf43842ba/GCF_024171895.1_ASM2417189v1_genomic.fna.gz --refList GCF_024171895.1_ASM2417189v1_genomic.fna/target_genomes.txt --output GCF_024171895.1_ASM2417189v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:15,704] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:15,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e199c1d-a522-42e2-a21d-125d1283120f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:15,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e199c1d-a522-42e2-a21d-125d1283120f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:15,721] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:15,721] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:15,722] [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
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	87.9709	1326	1675	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	87.8901	1257	1675	95	below_threshold
Prauserella rugosa	strain=NRRL B-2295	GCA_000719975.1	43354	43354	type	True	83.7089	1127	1675	95	below_threshold
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	83.6652	1147	1675	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	80.2594	873	1675	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	80.2182	879	1675	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.2159	885	1675	95	below_threshold
Saccharomonospora piscinae	strain=KCTC 19743	GCA_005862235.1	687388	687388	type	True	79.4034	655	1675	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	79.0852	766	1675	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.9913	729	1675	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	78.6243	746	1675	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	78.6052	740	1675	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	77.5015	571	1675	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	77.4379	558	1675	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:15,723] [INFO] DFAST Taxonomy check result was written to GCF_024171895.1_ASM2417189v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:15,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:15,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:15,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e199c1d-a522-42e2-a21d-125d1283120f/dqc_reference/checkm_data
[2024-01-24 11:27:15,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:15,774] [INFO] Task started: CheckM
[2024-01-24 11:27:15,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171895.1_ASM2417189v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171895.1_ASM2417189v1_genomic.fna/checkm_input GCF_024171895.1_ASM2417189v1_genomic.fna/checkm_result
[2024-01-24 11:28:28,028] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:28,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:28,058] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:28,058] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:28,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171895.1_ASM2417189v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:28,059] [INFO] Task started: Blastn
[2024-01-24 11:28:28,060] [INFO] Running command: blastn -query GCF_024171895.1_ASM2417189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e199c1d-a522-42e2-a21d-125d1283120f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171895.1_ASM2417189v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:30,023] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:30,027] [INFO] Selected 13 target genomes.
[2024-01-24 11:28:30,027] [INFO] Target genome list was writen to GCF_024171895.1_ASM2417189v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:30,040] [INFO] Task started: fastANI
[2024-01-24 11:28:30,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgd748a064-1f47-4bbc-9d5e-948bf43842ba/GCF_024171895.1_ASM2417189v1_genomic.fna.gz --refList GCF_024171895.1_ASM2417189v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171895.1_ASM2417189v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:48,224] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:48,238] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:28:48,238] [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_014195435.1	s__Saccharomonospora sediminis	88.7856	1337	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191605.1	s__Saccharomonospora isguenensis	87.8705	1259	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719975.1	s__Saccharomonospora rugosa	83.7166	1126	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.54	99.08	0.98	0.95	3	-
GCF_001942305.1	s__Saccharomonospora sp001942305	83.2932	1082	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202235.1	s__Saccharomonospora sp003202235	80.4004	927	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595675.1	s__Saccharomonospora sp016595675	80.2264	883	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202285.1	s__Saccharomonospora muralis	80.2117	880	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115565.1	s__Yuhushiella arida	79.2213	748	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900114035.1	s__Amycolatopsis sacchari	79.1348	746	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410405.1	s__Amycolatopsis endophytica	79.1098	760	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713745.1	s__Amycolatopsis acidiphila	78.9103	714	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001995215.1	s__Amycolatopsis azurea	78.6125	747	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	78.5814	758	1675	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:48,240] [INFO] GTDB search result was written to GCF_024171895.1_ASM2417189v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:48,241] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:48,244] [INFO] DFAST_QC result json was written to GCF_024171895.1_ASM2417189v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:48,244] [INFO] DFAST_QC completed!
[2024-01-24 11:28:48,244] [INFO] Total running time: 0h2m10s