[2024-01-24 13:32:34,982] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:34,984] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:34,984] [INFO] DQC Reference Directory: /var/lib/cwl/stga8e86df0-3dc7-4073-bc02-e9e08fffb8c1/dqc_reference
[2024-01-24 13:32:36,380] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,384] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg350f6433-4ae4-42f2-a7be-05e0f68330b1/GCF_031458135.1_ASM3145813v1_genomic.fna.gz | prodigal -d GCF_031458135.1_ASM3145813v1_genomic.fna/cds.fna -a GCF_031458135.1_ASM3145813v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:55,476] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:55,477] [INFO] Task started: HMMsearch
[2024-01-24 13:32:55,477] [INFO] Running command: hmmsearch --tblout GCF_031458135.1_ASM3145813v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8e86df0-3dc7-4073-bc02-e9e08fffb8c1/dqc_reference/reference_markers.hmm GCF_031458135.1_ASM3145813v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:55,906] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:55,907] [INFO] Found 6/6 markers.
[2024-01-24 13:32:55,976] [INFO] Query marker FASTA was written to GCF_031458135.1_ASM3145813v1_genomic.fna/markers.fasta
[2024-01-24 13:32:55,976] [INFO] Task started: Blastn
[2024-01-24 13:32:55,976] [INFO] Running command: blastn -query GCF_031458135.1_ASM3145813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8e86df0-3dc7-4073-bc02-e9e08fffb8c1/dqc_reference/reference_markers.fasta -out GCF_031458135.1_ASM3145813v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:57,188] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:57,191] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:57,192] [INFO] Target genome list was writen to GCF_031458135.1_ASM3145813v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:57,197] [INFO] Task started: fastANI
[2024-01-24 13:32:57,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg350f6433-4ae4-42f2-a7be-05e0f68330b1/GCF_031458135.1_ASM3145813v1_genomic.fna.gz --refList GCF_031458135.1_ASM3145813v1_genomic.fna/target_genomes.txt --output GCF_031458135.1_ASM3145813v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:15,243] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:15,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8e86df0-3dc7-4073-bc02-e9e08fffb8c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:15,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8e86df0-3dc7-4073-bc02-e9e08fffb8c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:15,257] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:15,257] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:15,257] [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
Halopolyspora algeriensis	strain=CECT 8575	GCA_003337235.1	1500506	1500506	type	True	85.3251	1138	1746	95	below_threshold
Halopolyspora algeriensis	strain=DSM 46680	GCA_006716575.1	1500506	1500506	type	True	85.3246	1113	1746	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000062885.1	1836	1836	type	True	79.5746	732	1746	95	below_threshold
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	79.4889	738	1746	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	79.4108	609	1746	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000171635.1	1836	1836	type	True	79.3605	718	1746	95	below_threshold
Actinopolyspora halophila	strain=DSM 43834	GCA_000371785.1	1850	1850	type	True	79.3313	603	1746	95	below_threshold
Actinopolyspora saharensis	strain=DSM 45459	GCA_900100925.1	995062	995062	type	True	79.2088	614	1746	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	79.2052	717	1746	95	below_threshold
Saccharopolyspora gloriosae	strain=DSM 45582	GCA_014203325.1	455344	455344	type	True	79.1674	667	1746	95	below_threshold
Actinopolyspora righensis	strain=DSM 45501	GCA_900116555.1	995060	995060	type	True	79.1643	565	1746	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	79.1135	655	1746	95	below_threshold
Actinopolyspora biskrensis	strain=CECT 8576	GCA_013408175.1	1470178	1470178	type	True	78.9619	583	1746	95	below_threshold
Actinopolyspora xinjiangensis	strain=DSM 46732	GCA_900104475.1	405564	405564	type	True	78.7776	618	1746	95	below_threshold
Amycolatopsis alkalitolerans	strain=SYSUP0005	GCA_006152065.1	2547244	2547244	type	True	77.2818	342	1746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:15,259] [INFO] DFAST Taxonomy check result was written to GCF_031458135.1_ASM3145813v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:15,259] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:15,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:15,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8e86df0-3dc7-4073-bc02-e9e08fffb8c1/dqc_reference/checkm_data
[2024-01-24 13:33:15,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:15,313] [INFO] Task started: CheckM
[2024-01-24 13:33:15,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031458135.1_ASM3145813v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031458135.1_ASM3145813v1_genomic.fna/checkm_input GCF_031458135.1_ASM3145813v1_genomic.fna/checkm_result
[2024-01-24 13:34:32,204] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:32,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:32,229] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:32,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:32,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031458135.1_ASM3145813v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:32,230] [INFO] Task started: Blastn
[2024-01-24 13:34:32,230] [INFO] Running command: blastn -query GCF_031458135.1_ASM3145813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8e86df0-3dc7-4073-bc02-e9e08fffb8c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_031458135.1_ASM3145813v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:33,871] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:33,875] [INFO] Selected 20 target genomes.
[2024-01-24 13:34:33,875] [INFO] Target genome list was writen to GCF_031458135.1_ASM3145813v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:33,894] [INFO] Task started: fastANI
[2024-01-24 13:34:33,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg350f6433-4ae4-42f2-a7be-05e0f68330b1/GCF_031458135.1_ASM3145813v1_genomic.fna.gz --refList GCF_031458135.1_ASM3145813v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031458135.1_ASM3145813v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:56,611] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:56,631] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:34:56,632] [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_003337235.1	s__Halopolyspora algeriensis	85.316	1140	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Halopolyspora	95.0	99.99	99.99	0.98	0.98	2	-
GCF_014137975.1	s__Halosaccharopolyspora lacisalsi	80.6408	823	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Halosaccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000062885.1	s__Saccharopolyspora_D erythraea	79.576	731	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	99.99	99.99	1.00	1.00	5	-
GCF_006716775.1	s__Actinopolyspora sp006716775	79.5572	611	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016526145.1	s__Saccharopolyspora_C sp016526145	79.4318	683	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646075.1	s__Saccharopolyspora subtropica	79.4253	608	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141105.1	s__Saccharopolyspora_D erythraea_A	79.401	737	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000371785.1	s__Actinopolyspora halophila	79.3801	605	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100925.1	s__Actinopolyspora saharensis	79.2185	615	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	98.98	98.97	0.92	0.92	3	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	79.2098	717	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203395.1	s__Saccharopolyspora phatthalungensis	79.1616	601	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	99.57	99.57	0.93	0.93	2	-
GCF_900101095.1	s__Actinopolyspora mzabensis	79.1295	602	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009664835.1	s__Allosaccharopolyspora coralli	79.1195	567	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Allosaccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116135.1	s__Saccharopolyspora flava	79.0969	657	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384035.1	s__Actinopolyspora mortivallis	79.0207	552	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	95.34	95.34	0.86	0.86	2	-
GCF_003931915.1	s__Saccharopolyspora rhizosphaerae	78.9866	623	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106995.1	s__Saccharopolyspora shandongensis	78.9787	719	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408175.1	s__Actinopolyspora biskrensis	78.9543	585	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104475.1	s__Actinopolyspora xinjiangensis	78.7744	618	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	77.3058	441	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:56,634] [INFO] GTDB search result was written to GCF_031458135.1_ASM3145813v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:56,634] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:56,638] [INFO] DFAST_QC result json was written to GCF_031458135.1_ASM3145813v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:56,638] [INFO] DFAST_QC completed!
[2024-01-24 13:34:56,638] [INFO] Total running time: 0h2m22s