[2024-01-24 14:47:55,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:55,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:55,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgaee858c4-0833-45cb-bca0-70961e9c4ad2/dqc_reference
[2024-01-24 14:47:58,525] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:58,526] [INFO] Task started: Prodigal
[2024-01-24 14:47:58,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d796766-754b-4018-961e-944ceb9a6a93/GCF_014205015.1_ASM1420501v1_genomic.fna.gz | prodigal -d GCF_014205015.1_ASM1420501v1_genomic.fna/cds.fna -a GCF_014205015.1_ASM1420501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:37,900] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:37,901] [INFO] Task started: HMMsearch
[2024-01-24 14:48:37,901] [INFO] Running command: hmmsearch --tblout GCF_014205015.1_ASM1420501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaee858c4-0833-45cb-bca0-70961e9c4ad2/dqc_reference/reference_markers.hmm GCF_014205015.1_ASM1420501v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:38,365] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:38,366] [INFO] Found 6/6 markers.
[2024-01-24 14:48:38,448] [INFO] Query marker FASTA was written to GCF_014205015.1_ASM1420501v1_genomic.fna/markers.fasta
[2024-01-24 14:48:38,449] [INFO] Task started: Blastn
[2024-01-24 14:48:38,449] [INFO] Running command: blastn -query GCF_014205015.1_ASM1420501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaee858c4-0833-45cb-bca0-70961e9c4ad2/dqc_reference/reference_markers.fasta -out GCF_014205015.1_ASM1420501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:39,847] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:39,851] [INFO] Selected 15 target genomes.
[2024-01-24 14:48:39,851] [INFO] Target genome list was writen to GCF_014205015.1_ASM1420501v1_genomic.fna/target_genomes.txt
[2024-01-24 14:48:39,860] [INFO] Task started: fastANI
[2024-01-24 14:48:39,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d796766-754b-4018-961e-944ceb9a6a93/GCF_014205015.1_ASM1420501v1_genomic.fna.gz --refList GCF_014205015.1_ASM1420501v1_genomic.fna/target_genomes.txt --output GCF_014205015.1_ASM1420501v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:49:15,947] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:15,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaee858c4-0833-45cb-bca0-70961e9c4ad2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:49:15,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaee858c4-0833-45cb-bca0-70961e9c4ad2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:49:15,963] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:49:15,964] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:49:15,964] [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
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	100.0	3229	3229	95	conclusive
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	88.6009	2105	3229	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	87.7808	2089	3229	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	87.4971	2075	3229	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	87.2278	2048	3229	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	84.1685	1940	3229	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	83.2183	1532	3229	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	83.1377	1462	3229	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	83.0691	1657	3229	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	82.7525	1462	3229	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	80.3247	1293	3229	95	below_threshold
Lentzea albidocapillata subsp. violacea	strain=DSM 44796	GCA_900100275.1	128104	40571	type	True	80.0029	1307	3229	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	79.9628	1354	3229	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	79.9106	1385	3229	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.9922	1066	3229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:49:15,965] [INFO] DFAST Taxonomy check result was written to GCF_014205015.1_ASM1420501v1_genomic.fna/tc_result.tsv
[2024-01-24 14:49:15,966] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:49:15,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:49:15,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaee858c4-0833-45cb-bca0-70961e9c4ad2/dqc_reference/checkm_data
[2024-01-24 14:49:15,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:49:16,065] [INFO] Task started: CheckM
[2024-01-24 14:49:16,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205015.1_ASM1420501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205015.1_ASM1420501v1_genomic.fna/checkm_input GCF_014205015.1_ASM1420501v1_genomic.fna/checkm_result
[2024-01-24 14:52:31,183] [INFO] Task succeeded: CheckM
[2024-01-24 14:52:31,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:52:31,210] [INFO] ===== Completeness check finished =====
[2024-01-24 14:52:31,210] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:52:31,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205015.1_ASM1420501v1_genomic.fna/markers.fasta)
[2024-01-24 14:52:31,211] [INFO] Task started: Blastn
[2024-01-24 14:52:31,211] [INFO] Running command: blastn -query GCF_014205015.1_ASM1420501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaee858c4-0833-45cb-bca0-70961e9c4ad2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205015.1_ASM1420501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:52:33,293] [INFO] Task succeeded: Blastn
[2024-01-24 14:52:33,297] [INFO] Selected 11 target genomes.
[2024-01-24 14:52:33,297] [INFO] Target genome list was writen to GCF_014205015.1_ASM1420501v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:52:33,305] [INFO] Task started: fastANI
[2024-01-24 14:52:33,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d796766-754b-4018-961e-944ceb9a6a93/GCF_014205015.1_ASM1420501v1_genomic.fna.gz --refList GCF_014205015.1_ASM1420501v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205015.1_ASM1420501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:53:03,080] [INFO] Task succeeded: fastANI
[2024-01-24 14:53:03,096] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:53:03,096] [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_014205015.1	s__Actinosynnema ecbatanense	100.0	3229	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000716595.1	s__Actinosynnema sp000716595	92.3703	2363	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769385.1	s__Actinosynnema deserti	88.6101	2100	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984175.1	s__Actinosynnema sp001984175	88.3215	2042	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280085.1	s__Actinosynnema sp001280085	87.9844	2196	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014735.1	s__Actinosynnema carneum	87.7785	2088	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_003752005.1	s__Actinosynnema texasense	87.5128	2073	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_006716745.1	s__Actinosynnema saharense	87.2248	2047	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	83.1651	1538	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	83.1279	1464	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328705.1	s__Actinosynnema espanaense	83.041	1665	3229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:53:03,098] [INFO] GTDB search result was written to GCF_014205015.1_ASM1420501v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:53:03,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:53:03,104] [INFO] DFAST_QC result json was written to GCF_014205015.1_ASM1420501v1_genomic.fna/dqc_result.json
[2024-01-24 14:53:03,105] [INFO] DFAST_QC completed!
[2024-01-24 14:53:03,105] [INFO] Total running time: 0h5m7s