[2024-01-24 11:50:49,313] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,316] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg28e72a76-59b6-406a-ae42-06f70f181e1b/dqc_reference
[2024-01-24 11:50:50,547] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:50,548] [INFO] Task started: Prodigal
[2024-01-24 11:50:50,548] [INFO] Running command: gunzip -c /var/lib/cwl/stg433c5f8e-7083-4a78-a77d-e09c813bbca6/GCF_014137975.1_ASM1413797v1_genomic.fna.gz | prodigal -d GCF_014137975.1_ASM1413797v1_genomic.fna/cds.fna -a GCF_014137975.1_ASM1413797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:07,638] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:07,639] [INFO] Task started: HMMsearch
[2024-01-24 11:51:07,639] [INFO] Running command: hmmsearch --tblout GCF_014137975.1_ASM1413797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28e72a76-59b6-406a-ae42-06f70f181e1b/dqc_reference/reference_markers.hmm GCF_014137975.1_ASM1413797v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:07,948] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:07,950] [INFO] Found 6/6 markers.
[2024-01-24 11:51:07,998] [INFO] Query marker FASTA was written to GCF_014137975.1_ASM1413797v1_genomic.fna/markers.fasta
[2024-01-24 11:51:07,999] [INFO] Task started: Blastn
[2024-01-24 11:51:07,999] [INFO] Running command: blastn -query GCF_014137975.1_ASM1413797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28e72a76-59b6-406a-ae42-06f70f181e1b/dqc_reference/reference_markers.fasta -out GCF_014137975.1_ASM1413797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:09,244] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:09,248] [INFO] Selected 22 target genomes.
[2024-01-24 11:51:09,249] [INFO] Target genome list was writen to GCF_014137975.1_ASM1413797v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:09,265] [INFO] Task started: fastANI
[2024-01-24 11:51:09,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg433c5f8e-7083-4a78-a77d-e09c813bbca6/GCF_014137975.1_ASM1413797v1_genomic.fna.gz --refList GCF_014137975.1_ASM1413797v1_genomic.fna/target_genomes.txt --output GCF_014137975.1_ASM1413797v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:34,260] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:34,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28e72a76-59b6-406a-ae42-06f70f181e1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:34,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28e72a76-59b6-406a-ae42-06f70f181e1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:34,281] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:34,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:34,281] [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	80.9798	835	1784	95	below_threshold
Halopolyspora algeriensis	strain=DSM 46680	GCA_006716575.1	1500506	1500506	type	True	80.9487	827	1784	95	below_threshold
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	79.9905	889	1784	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	79.9782	794	1784	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000062885.1	1836	1836	type	True	79.9758	889	1784	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	79.9156	802	1784	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	79.8891	723	1784	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000171635.1	1836	1836	type	True	79.8789	865	1784	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	79.7276	840	1784	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	79.6896	768	1784	95	below_threshold
Saccharopolyspora rhizosphaerae	strain=H219	GCA_003931915.1	2492662	2492662	type	True	79.6589	735	1784	95	below_threshold
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	79.6228	799	1784	95	below_threshold
Saccharopolyspora dendranthemae	strain=DSM 46699	GCA_007829955.1	1181886	1181886	type	True	79.5295	710	1784	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	79.5059	818	1784	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_002263515.1	414996	414996	type	True	79.505	729	1784	95	below_threshold
Actinopolyspora mortivallis	strain=HS-1	GCA_000384035.1	33906	33906	type	True	79.5005	637	1784	95	below_threshold
Saccharopolyspora karakumensis	strain=5K548	GCA_004349225.1	2530386	2530386	type	True	79.4869	758	1784	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_000763095.1	414996	414996	type	True	79.4709	718	1784	95	below_threshold
Actinopolyspora xinjiangensis	strain=DSM 46732	GCA_900104475.1	405564	405564	type	True	79.3643	696	1784	95	below_threshold
Saccharopolyspora rectivirgula	strain=DSM 43747	GCA_000497205.1	28042	28042	type	True	79.0102	554	1784	95	below_threshold
Actinoalloteichus spitiensis	strain=RMV-1378	GCA_000239155.2	252394	252394	type	True	77.4274	359	1784	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	77.3084	459	1784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:34,283] [INFO] DFAST Taxonomy check result was written to GCF_014137975.1_ASM1413797v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:34,283] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:34,284] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:34,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28e72a76-59b6-406a-ae42-06f70f181e1b/dqc_reference/checkm_data
[2024-01-24 11:51:34,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:34,338] [INFO] Task started: CheckM
[2024-01-24 11:51:34,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014137975.1_ASM1413797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014137975.1_ASM1413797v1_genomic.fna/checkm_input GCF_014137975.1_ASM1413797v1_genomic.fna/checkm_result
[2024-01-24 11:52:29,664] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:29,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:29,691] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:29,691] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:29,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014137975.1_ASM1413797v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:29,692] [INFO] Task started: Blastn
[2024-01-24 11:52:29,692] [INFO] Running command: blastn -query GCF_014137975.1_ASM1413797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28e72a76-59b6-406a-ae42-06f70f181e1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014137975.1_ASM1413797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:31,465] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:31,470] [INFO] Selected 19 target genomes.
[2024-01-24 11:52:31,470] [INFO] Target genome list was writen to GCF_014137975.1_ASM1413797v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:31,483] [INFO] Task started: fastANI
[2024-01-24 11:52:31,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg433c5f8e-7083-4a78-a77d-e09c813bbca6/GCF_014137975.1_ASM1413797v1_genomic.fna.gz --refList GCF_014137975.1_ASM1413797v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014137975.1_ASM1413797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:54,369] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:54,388] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:54,389] [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_014137975.1	s__Halosaccharopolyspora lacisalsi	100.0	1775	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Halosaccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003337235.1	s__Halopolyspora algeriensis	80.9726	836	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Halopolyspora	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003635025.1	s__Saccharopolyspora antimicrobica	80.0222	789	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	100.00	1.00	1.00	2	-
GCF_000062885.1	s__Saccharopolyspora_D erythraea	79.9832	894	1784	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_018141105.1	s__Saccharopolyspora_D erythraea_A	79.9698	892	1784	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_013410345.1	s__Saccharopolyspora hordei	79.9501	797	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646075.1	s__Saccharopolyspora subtropica	79.8741	725	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	79.7113	843	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116135.1	s__Saccharopolyspora flava	79.6982	766	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931915.1	s__Saccharopolyspora rhizosphaerae	79.6203	740	1784	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	79.5905	804	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209505.1	s__Saccharopolyspora sp015209505	79.5856	577	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002263515.1	s__Actinopolyspora erythraea	79.5512	724	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	99.98	99.98	0.99	0.99	2	-
GCF_004348985.1	s__Saccharopolyspora sp004348985	79.5182	816	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829955.1	s__Saccharopolyspora dendranthemae	79.4804	711	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104475.1	s__Actinopolyspora xinjiangensis	79.3923	692	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000239155.1	s__Actinoalloteichus spitiensis	77.4368	356	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921205.1	s__Actinophytocola xanthii	77.2967	461	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289575.1	s__Dietzia natronolimnaea_A	75.9852	165	1784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	96.66	96.66	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:54,391] [INFO] GTDB search result was written to GCF_014137975.1_ASM1413797v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:54,392] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:54,396] [INFO] DFAST_QC result json was written to GCF_014137975.1_ASM1413797v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:54,396] [INFO] DFAST_QC completed!
[2024-01-24 11:52:54,396] [INFO] Total running time: 0h2m5s