[2024-01-24 13:49:40,750] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg216c07ed-dcb7-452c-92f2-10fd021eec40/dqc_reference
[2024-01-24 13:49:42,147] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,148] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,149] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ba8836d-a98f-4578-9278-353b419127e1/GCF_000718005.1_ASM71800v1_genomic.fna.gz | prodigal -d GCF_000718005.1_ASM71800v1_genomic.fna/cds.fna -a GCF_000718005.1_ASM71800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:05,350] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:05,350] [INFO] Task started: HMMsearch
[2024-01-24 13:50:05,351] [INFO] Running command: hmmsearch --tblout GCF_000718005.1_ASM71800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg216c07ed-dcb7-452c-92f2-10fd021eec40/dqc_reference/reference_markers.hmm GCF_000718005.1_ASM71800v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:05,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:05,753] [INFO] Found 6/6 markers.
[2024-01-24 13:50:05,811] [INFO] Query marker FASTA was written to GCF_000718005.1_ASM71800v1_genomic.fna/markers.fasta
[2024-01-24 13:50:05,811] [INFO] Task started: Blastn
[2024-01-24 13:50:05,811] [INFO] Running command: blastn -query GCF_000718005.1_ASM71800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg216c07ed-dcb7-452c-92f2-10fd021eec40/dqc_reference/reference_markers.fasta -out GCF_000718005.1_ASM71800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:07,180] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:07,184] [INFO] Selected 19 target genomes.
[2024-01-24 13:50:07,185] [INFO] Target genome list was writen to GCF_000718005.1_ASM71800v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:07,192] [INFO] Task started: fastANI
[2024-01-24 13:50:07,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ba8836d-a98f-4578-9278-353b419127e1/GCF_000718005.1_ASM71800v1_genomic.fna.gz --refList GCF_000718005.1_ASM71800v1_genomic.fna/target_genomes.txt --output GCF_000718005.1_ASM71800v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:33,402] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:33,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg216c07ed-dcb7-452c-92f2-10fd021eec40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:33,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg216c07ed-dcb7-452c-92f2-10fd021eec40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:33,418] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:33,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:33,418] [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
Actinoalloteichus cyanogriseus	strain=DSM 43889	GCA_000429185.2	65497	65497	type	True	99.4483	1920	1958	95	conclusive
Actinoalloteichus spitiensis	strain=RMV-1378	GCA_000239155.2	252394	252394	type	True	92.5376	1287	1958	95	below_threshold
Actinoalloteichus hoggarensis	strain=CECT 8639	GCA_014203625.1	1470176	1470176	type	True	78.2528	692	1958	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	78.2376	652	1958	95	below_threshold
Actinoalloteichus hoggarensis	strain=DSM 45943	GCA_002234535.1	1470176	1470176	type	True	78.1961	708	1958	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	78.0667	519	1958	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	78.0447	666	1958	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	78.0412	600	1958	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	77.9875	664	1958	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	77.9082	705	1958	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	77.8115	634	1958	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	77.6029	635	1958	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	77.5371	682	1958	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	77.4861	575	1958	95	below_threshold
Crossiella equi	strain=NRRL B-24104	GCA_002155995.1	130796	130796	type	True	77.4623	637	1958	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	77.4477	521	1958	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	77.2958	525	1958	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	76.8997	625	1958	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	76.1816	543	1958	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:33,431] [INFO] DFAST Taxonomy check result was written to GCF_000718005.1_ASM71800v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:33,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:33,433] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:33,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg216c07ed-dcb7-452c-92f2-10fd021eec40/dqc_reference/checkm_data
[2024-01-24 13:50:33,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:33,494] [INFO] Task started: CheckM
[2024-01-24 13:50:33,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000718005.1_ASM71800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000718005.1_ASM71800v1_genomic.fna/checkm_input GCF_000718005.1_ASM71800v1_genomic.fna/checkm_result
[2024-01-24 13:51:58,498] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:58,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:58,523] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:58,523] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:58,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000718005.1_ASM71800v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:58,524] [INFO] Task started: Blastn
[2024-01-24 13:51:58,524] [INFO] Running command: blastn -query GCF_000718005.1_ASM71800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg216c07ed-dcb7-452c-92f2-10fd021eec40/dqc_reference/reference_markers_gtdb.fasta -out GCF_000718005.1_ASM71800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:00,389] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:00,394] [INFO] Selected 17 target genomes.
[2024-01-24 13:52:00,394] [INFO] Target genome list was writen to GCF_000718005.1_ASM71800v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:00,791] [INFO] Task started: fastANI
[2024-01-24 13:52:00,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ba8836d-a98f-4578-9278-353b419127e1/GCF_000718005.1_ASM71800v1_genomic.fna.gz --refList GCF_000718005.1_ASM71800v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000718005.1_ASM71800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:23,354] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:23,373] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:23,374] [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_000429185.1	s__Actinoalloteichus cyanogriseus	99.4721	1901	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	99.50	99.47	0.98	0.97	3	conclusive
GCF_000239155.1	s__Actinoalloteichus spitiensis	92.5509	1286	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941625.1	s__Actinoalloteichus fjordicus	78.3386	714	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	99.71	99.71	0.98	0.98	2	-
GCF_002234535.1	s__Actinoalloteichus hoggarensis	78.2031	706	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013410345.1	s__Saccharopolyspora hordei	78.0345	602	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	78.0083	673	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645795.1	s__Longimycelium tulufanense	77.9991	519	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Longimycelium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648515.1	s__Actinosynnema coeruleofuscum	77.9841	664	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCF_003635025.1	s__Saccharopolyspora antimicrobica	77.8029	635	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	100.00	1.00	1.00	2	-
GCA_000715825.1	s__Goodfellowiella coeruleoviolacea	77.7844	747	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203355.1	s__Kutzneria kofuensis	77.6067	636	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	77.5365	682	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758765.1	s__Amycolatopsis viridis	77.4762	516	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_017876755.1	s__Crossiella equi	77.4691	679	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004214935.1	s__Amycolatopsis suaedae	77.3729	601	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	77.3253	621	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	76.8711	510	1958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:23,378] [INFO] GTDB search result was written to GCF_000718005.1_ASM71800v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:23,379] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:23,384] [INFO] DFAST_QC result json was written to GCF_000718005.1_ASM71800v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:23,384] [INFO] DFAST_QC completed!
[2024-01-24 13:52:23,384] [INFO] Total running time: 0h2m43s