[2024-01-25 19:03:06,385] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:06,386] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:06,386] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfa39e90-6a12-44e9-9e93-1cdb37d7d560/dqc_reference
[2024-01-25 19:03:07,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:07,518] [INFO] Task started: Prodigal
[2024-01-25 19:03:07,519] [INFO] Running command: gunzip -c /var/lib/cwl/stgee1daf0a-89f9-4cb2-8cce-36b8a1fbb15a/GCF_024171735.1_ASM2417173v1_genomic.fna.gz | prodigal -d GCF_024171735.1_ASM2417173v1_genomic.fna/cds.fna -a GCF_024171735.1_ASM2417173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:22,982] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:22,982] [INFO] Task started: HMMsearch
[2024-01-25 19:03:22,982] [INFO] Running command: hmmsearch --tblout GCF_024171735.1_ASM2417173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfa39e90-6a12-44e9-9e93-1cdb37d7d560/dqc_reference/reference_markers.hmm GCF_024171735.1_ASM2417173v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:23,250] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:23,251] [INFO] Found 6/6 markers.
[2024-01-25 19:03:23,297] [INFO] Query marker FASTA was written to GCF_024171735.1_ASM2417173v1_genomic.fna/markers.fasta
[2024-01-25 19:03:23,297] [INFO] Task started: Blastn
[2024-01-25 19:03:23,297] [INFO] Running command: blastn -query GCF_024171735.1_ASM2417173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfa39e90-6a12-44e9-9e93-1cdb37d7d560/dqc_reference/reference_markers.fasta -out GCF_024171735.1_ASM2417173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:24,495] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:24,497] [INFO] Selected 14 target genomes.
[2024-01-25 19:03:24,498] [INFO] Target genome list was writen to GCF_024171735.1_ASM2417173v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:24,508] [INFO] Task started: fastANI
[2024-01-25 19:03:24,508] [INFO] Running command: fastANI --query /var/lib/cwl/stgee1daf0a-89f9-4cb2-8cce-36b8a1fbb15a/GCF_024171735.1_ASM2417173v1_genomic.fna.gz --refList GCF_024171735.1_ASM2417173v1_genomic.fna/target_genomes.txt --output GCF_024171735.1_ASM2417173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:44,280] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:44,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfa39e90-6a12-44e9-9e93-1cdb37d7d560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:44,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfa39e90-6a12-44e9-9e93-1cdb37d7d560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:44,291] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:03:44,291] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:03:44,291] [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 isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	88.6011	1414	1866	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	88.5875	1443	1866	95	below_threshold
Prauserella rugosa	strain=NRRL B-2295	GCA_000719975.1	43354	43354	type	True	83.8374	1292	1866	95	below_threshold
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	83.7993	1297	1866	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.1415	967	1866	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.5744	816	1866	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	79.2859	766	1866	95	below_threshold
Saccharomonospora piscinae	strain=KCTC 19743	GCA_005862235.1	687388	687388	type	True	79.2761	702	1866	95	below_threshold
Saccharomonospora iraqiensis subsp. paurometabolica	strain=YIM 90007	GCA_000231035.3	208085	52698	type	True	79.2609	676	1866	95	below_threshold
Saccharomonospora cyanea	strain=NA-134	GCA_000244975.1	40989	40989	type	True	79.1752	735	1866	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	79.0587	793	1866	95	below_threshold
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	78.8171	818	1866	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	78.6411	832	1866	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.5703	840	1866	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:44,292] [INFO] DFAST Taxonomy check result was written to GCF_024171735.1_ASM2417173v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:44,293] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:44,293] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:44,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfa39e90-6a12-44e9-9e93-1cdb37d7d560/dqc_reference/checkm_data
[2024-01-25 19:03:44,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:44,346] [INFO] Task started: CheckM
[2024-01-25 19:03:44,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171735.1_ASM2417173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171735.1_ASM2417173v1_genomic.fna/checkm_input GCF_024171735.1_ASM2417173v1_genomic.fna/checkm_result
[2024-01-25 19:04:59,970] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:59,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:59,991] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:59,991] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:59,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171735.1_ASM2417173v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:59,992] [INFO] Task started: Blastn
[2024-01-25 19:04:59,992] [INFO] Running command: blastn -query GCF_024171735.1_ASM2417173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfa39e90-6a12-44e9-9e93-1cdb37d7d560/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171735.1_ASM2417173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:01,849] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:01,851] [INFO] Selected 15 target genomes.
[2024-01-25 19:05:01,851] [INFO] Target genome list was writen to GCF_024171735.1_ASM2417173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:01,872] [INFO] Task started: fastANI
[2024-01-25 19:05:01,872] [INFO] Running command: fastANI --query /var/lib/cwl/stgee1daf0a-89f9-4cb2-8cce-36b8a1fbb15a/GCF_024171735.1_ASM2417173v1_genomic.fna.gz --refList GCF_024171735.1_ASM2417173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171735.1_ASM2417173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:23,028] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:23,037] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:05:23,037] [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	90.8222	1573	1866	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	88.6011	1414	1866	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	83.8236	1294	1866	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	83.4997	1136	1866	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	80.272	1027	1866	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	80.1189	969	1866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001955.1	s__Saccharomonospora shujinwangii	79.9084	881	1866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005862235.1	s__Saccharomonospora piscinae	79.3171	696	1866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	98.79	98.27	0.95	0.94	3	-
GCF_011758765.1	s__Amycolatopsis viridis	79.2937	763	1866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_000231035.2	s__Saccharomonospora paurometabolica	79.2546	677	1866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	96.0038	N/A	N/A	N/A	N/A	1	-
GCF_000244975.1	s__Saccharomonospora cyanea	79.1687	736	1866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473265.1	s__Amycolatopsis thermoflava	79.0761	926	1866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	98.72	98.72	0.92	0.92	2	-
GCF_003312875.1	s__Amycolatopsis albispora	78.824	817	1866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016889705.1	s__Amycolatopsis sp016889705	78.7183	781	1866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765355.1	s__Amycolatopsis anabasis	78.6483	831	1866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:23,039] [INFO] GTDB search result was written to GCF_024171735.1_ASM2417173v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:23,039] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:23,047] [INFO] DFAST_QC result json was written to GCF_024171735.1_ASM2417173v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:23,047] [INFO] DFAST_QC completed!
[2024-01-25 19:05:23,047] [INFO] Total running time: 0h2m17s