[2024-01-24 13:31:11,021] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:11,022] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:11,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg29b27cee-f578-4de8-b9e4-7d7162e329ad/dqc_reference
[2024-01-24 13:31:12,238] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:12,239] [INFO] Task started: Prodigal
[2024-01-24 13:31:12,239] [INFO] Running command: gunzip -c /var/lib/cwl/stg314904e2-c33a-4d9b-9320-bfcab2716f3d/GCF_002564045.1_ASM256404v1_genomic.fna.gz | prodigal -d GCF_002564045.1_ASM256404v1_genomic.fna/cds.fna -a GCF_002564045.1_ASM256404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:32,275] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:32,276] [INFO] Task started: HMMsearch
[2024-01-24 13:31:32,276] [INFO] Running command: hmmsearch --tblout GCF_002564045.1_ASM256404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29b27cee-f578-4de8-b9e4-7d7162e329ad/dqc_reference/reference_markers.hmm GCF_002564045.1_ASM256404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:32,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:32,535] [INFO] Found 6/6 markers.
[2024-01-24 13:31:32,590] [INFO] Query marker FASTA was written to GCF_002564045.1_ASM256404v1_genomic.fna/markers.fasta
[2024-01-24 13:31:32,590] [INFO] Task started: Blastn
[2024-01-24 13:31:32,590] [INFO] Running command: blastn -query GCF_002564045.1_ASM256404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29b27cee-f578-4de8-b9e4-7d7162e329ad/dqc_reference/reference_markers.fasta -out GCF_002564045.1_ASM256404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:33,862] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:33,866] [INFO] Selected 14 target genomes.
[2024-01-24 13:31:33,866] [INFO] Target genome list was writen to GCF_002564045.1_ASM256404v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:33,871] [INFO] Task started: fastANI
[2024-01-24 13:31:33,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg314904e2-c33a-4d9b-9320-bfcab2716f3d/GCF_002564045.1_ASM256404v1_genomic.fna.gz --refList GCF_002564045.1_ASM256404v1_genomic.fna/target_genomes.txt --output GCF_002564045.1_ASM256404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:00,705] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:00,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29b27cee-f578-4de8-b9e4-7d7162e329ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:00,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29b27cee-f578-4de8-b9e4-7d7162e329ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:00,718] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:00,718] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:32:00,718] [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
Amycolatopsis sulphurea	strain=DSM 46092	GCA_002564045.1	76022	76022	type	True	100.0	2284	2284	95	inconclusive
Amycolatopsis panacis	strain=YIM PH21725	GCA_003600245.1	2340917	2340917	type	True	95.0921	1879	2284	95	inconclusive
Amycolatopsis jiangsuensis	strain=DSM 45859	GCA_014204865.1	1181879	1181879	type	True	85.9652	1512	2284	95	below_threshold
Amycolatopsis benzoatilytica	strain=AK 16/65	GCA_000383915.1	346045	346045	type	True	83.3655	1337	2284	95	below_threshold
Amycolatopsis nivea	strain=CFH S0261	GCA_004522235.1	1644109	1644109	type	True	83.2736	1376	2284	95	below_threshold
Amycolatopsis rubida	strain=DSM 44637	GCA_900115345.1	112413	112413	type	True	83.2459	1390	2284	95	below_threshold
Amycolatopsis circi	strain=DSM 45561	GCA_003385235.1	871959	871959	type	True	83.2033	1316	2284	95	below_threshold
Amycolatopsis dendrobii	strain=DR6-1	GCA_014145675.1	2760662	2760662	type	True	83.1343	1372	2284	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	82.9739	1355	2284	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.1622	1233	2284	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	80.0255	937	2284	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.919	927	2284	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	79.3031	846	2284	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.0179	821	2284	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:00,720] [INFO] DFAST Taxonomy check result was written to GCF_002564045.1_ASM256404v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:00,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:00,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:00,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29b27cee-f578-4de8-b9e4-7d7162e329ad/dqc_reference/checkm_data
[2024-01-24 13:32:00,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:00,785] [INFO] Task started: CheckM
[2024-01-24 13:32:00,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002564045.1_ASM256404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002564045.1_ASM256404v1_genomic.fna/checkm_input GCF_002564045.1_ASM256404v1_genomic.fna/checkm_result
[2024-01-24 13:33:13,424] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:13,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:13,441] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:13,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:13,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002564045.1_ASM256404v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:13,442] [INFO] Task started: Blastn
[2024-01-24 13:33:13,442] [INFO] Running command: blastn -query GCF_002564045.1_ASM256404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29b27cee-f578-4de8-b9e4-7d7162e329ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_002564045.1_ASM256404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:15,494] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:15,497] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:15,497] [INFO] Target genome list was writen to GCF_002564045.1_ASM256404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:15,524] [INFO] Task started: fastANI
[2024-01-24 13:33:15,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg314904e2-c33a-4d9b-9320-bfcab2716f3d/GCF_002564045.1_ASM256404v1_genomic.fna.gz --refList GCF_002564045.1_ASM256404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002564045.1_ASM256404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:43,334] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:43,345] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:43,346] [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_002564045.1	s__Amycolatopsis sulphurea	100.0	2284	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	95.19	95.19	0.83	0.83	2	conclusive
GCF_014204865.1	s__Amycolatopsis jiangsuensis	86.0007	1508	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411975.1	s__Amycolatopsis orientalis_D	83.4951	1335	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796545.1	s__Amycolatopsis sp002796545	83.3879	1379	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_004522235.1	s__Amycolatopsis nivea	83.3164	1367	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.97	97.28	0.91	0.88	6	-
GCF_000383915.1	s__Amycolatopsis benzoatilytica	83.3066	1349	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174495.1	s__Amycolatopsis echigonensis	83.2648	1336	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	98.67	98.67	0.88	0.88	2	-
GCF_900115345.1	s__Amycolatopsis rubida	83.2504	1390	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.28	99.27	0.88	0.87	4	-
GCF_014145675.1	s__Amycolatopsis sp014145675	83.1441	1370	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385235.1	s__Amycolatopsis circi	83.1317	1330	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717335.1	s__Amycolatopsis jejuensis	83.0898	1323	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110575.1	s__Amycolatopsis saalfeldensis	82.9298	1362	2284	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	82.0347	1324	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:43,347] [INFO] GTDB search result was written to GCF_002564045.1_ASM256404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:43,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:43,351] [INFO] DFAST_QC result json was written to GCF_002564045.1_ASM256404v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:43,352] [INFO] DFAST_QC completed!
[2024-01-24 13:33:43,352] [INFO] Total running time: 0h2m32s