[2024-01-24 12:25:20,684] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:25:20,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:25:20,685] [INFO] DQC Reference Directory: /var/lib/cwl/stge9c54989-2f62-44a9-9b37-75a437788d3e/dqc_reference
[2024-01-24 12:25:21,934] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:25:21,935] [INFO] Task started: Prodigal
[2024-01-24 12:25:21,935] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf7b8425-f249-4581-965d-ea21655e0659/GCF_013410355.1_ASM1341035v1_genomic.fna.gz | prodigal -d GCF_013410355.1_ASM1341035v1_genomic.fna/cds.fna -a GCF_013410355.1_ASM1341035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:25:33,111] [INFO] Task succeeded: Prodigal
[2024-01-24 12:25:33,111] [INFO] Task started: HMMsearch
[2024-01-24 12:25:33,112] [INFO] Running command: hmmsearch --tblout GCF_013410355.1_ASM1341035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9c54989-2f62-44a9-9b37-75a437788d3e/dqc_reference/reference_markers.hmm GCF_013410355.1_ASM1341035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:25:33,378] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:25:33,380] [INFO] Found 6/6 markers.
[2024-01-24 12:25:33,420] [INFO] Query marker FASTA was written to GCF_013410355.1_ASM1341035v1_genomic.fna/markers.fasta
[2024-01-24 12:25:33,420] [INFO] Task started: Blastn
[2024-01-24 12:25:33,420] [INFO] Running command: blastn -query GCF_013410355.1_ASM1341035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c54989-2f62-44a9-9b37-75a437788d3e/dqc_reference/reference_markers.fasta -out GCF_013410355.1_ASM1341035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:34,661] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:34,665] [INFO] Selected 13 target genomes.
[2024-01-24 12:25:34,666] [INFO] Target genome list was writen to GCF_013410355.1_ASM1341035v1_genomic.fna/target_genomes.txt
[2024-01-24 12:25:34,672] [INFO] Task started: fastANI
[2024-01-24 12:25:34,672] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf7b8425-f249-4581-965d-ea21655e0659/GCF_013410355.1_ASM1341035v1_genomic.fna.gz --refList GCF_013410355.1_ASM1341035v1_genomic.fna/target_genomes.txt --output GCF_013410355.1_ASM1341035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:25:47,405] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:47,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9c54989-2f62-44a9-9b37-75a437788d3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:25:47,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9c54989-2f62-44a9-9b37-75a437788d3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:25:47,424] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:25:47,424] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:25:47,424] [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
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	100.0	1301	1301	95	conclusive
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	93.1105	1167	1301	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	90.4608	1074	1301	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	87.1675	824	1301	95	below_threshold
Agromyces laixinhei	strain=HY052	GCA_006337065.1	2585717	2585717	type	True	86.8442	839	1301	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	86.0637	944	1301	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	84.6923	928	1301	95	below_threshold
Agromyces italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	84.2466	845	1301	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.7391	863	1301	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	83.6775	829	1301	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	83.572	859	1301	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	82.1256	755	1301	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	81.1593	648	1301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:25:47,426] [INFO] DFAST Taxonomy check result was written to GCF_013410355.1_ASM1341035v1_genomic.fna/tc_result.tsv
[2024-01-24 12:25:47,427] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:25:47,427] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:25:47,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9c54989-2f62-44a9-9b37-75a437788d3e/dqc_reference/checkm_data
[2024-01-24 12:25:47,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:25:47,467] [INFO] Task started: CheckM
[2024-01-24 12:25:47,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410355.1_ASM1341035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410355.1_ASM1341035v1_genomic.fna/checkm_input GCF_013410355.1_ASM1341035v1_genomic.fna/checkm_result
[2024-01-24 12:26:39,902] [INFO] Task succeeded: CheckM
[2024-01-24 12:26:39,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:26:39,927] [INFO] ===== Completeness check finished =====
[2024-01-24 12:26:39,928] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:26:39,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410355.1_ASM1341035v1_genomic.fna/markers.fasta)
[2024-01-24 12:26:39,929] [INFO] Task started: Blastn
[2024-01-24 12:26:39,929] [INFO] Running command: blastn -query GCF_013410355.1_ASM1341035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c54989-2f62-44a9-9b37-75a437788d3e/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410355.1_ASM1341035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:26:41,944] [INFO] Task succeeded: Blastn
[2024-01-24 12:26:41,949] [INFO] Selected 7 target genomes.
[2024-01-24 12:26:41,949] [INFO] Target genome list was writen to GCF_013410355.1_ASM1341035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:26:41,955] [INFO] Task started: fastANI
[2024-01-24 12:26:41,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf7b8425-f249-4581-965d-ea21655e0659/GCF_013410355.1_ASM1341035v1_genomic.fna.gz --refList GCF_013410355.1_ASM1341035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410355.1_ASM1341035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:49,956] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:49,970] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:49,970] [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_013410355.1	s__Agromyces hippuratus	100.0	1301	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016907835.1	s__Agromyces cerinus_A	94.6221	1167	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142065.1	s__Agromyces cerinus	93.1261	1166	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004134865.1	s__Agromyces fucosus	90.4608	1074	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.23	98.22	0.96	0.96	3	-
GCF_001429165.1	s__Agromyces sp001429165	90.2507	1024	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003070885.1	s__Agromyces badenianii	87.1675	824	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.76	98.76	0.96	0.96	2	-
GCF_009749405.1	s__Agromyces lapidis	84.7151	927	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:26:49,972] [INFO] GTDB search result was written to GCF_013410355.1_ASM1341035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:49,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:49,975] [INFO] DFAST_QC result json was written to GCF_013410355.1_ASM1341035v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:49,976] [INFO] DFAST_QC completed!
[2024-01-24 12:26:49,976] [INFO] Total running time: 0h1m29s