[2024-01-24 13:58:10,918] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,920] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,920] [INFO] DQC Reference Directory: /var/lib/cwl/stgfda63396-396c-4cc2-bcbd-0e9c735d005f/dqc_reference
[2024-01-24 13:58:12,295] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,295] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,296] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b98a6d4-fd51-4c5c-8251-267a451d2dd2/GCF_000420025.1_ASM42002v1_genomic.fna.gz | prodigal -d GCF_000420025.1_ASM42002v1_genomic.fna/cds.fna -a GCF_000420025.1_ASM42002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:24,215] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:24,215] [INFO] Task started: HMMsearch
[2024-01-24 13:58:24,215] [INFO] Running command: hmmsearch --tblout GCF_000420025.1_ASM42002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfda63396-396c-4cc2-bcbd-0e9c735d005f/dqc_reference/reference_markers.hmm GCF_000420025.1_ASM42002v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:24,503] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:24,504] [INFO] Found 6/6 markers.
[2024-01-24 13:58:24,544] [INFO] Query marker FASTA was written to GCF_000420025.1_ASM42002v1_genomic.fna/markers.fasta
[2024-01-24 13:58:24,544] [INFO] Task started: Blastn
[2024-01-24 13:58:24,545] [INFO] Running command: blastn -query GCF_000420025.1_ASM42002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda63396-396c-4cc2-bcbd-0e9c735d005f/dqc_reference/reference_markers.fasta -out GCF_000420025.1_ASM42002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:25,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:25,338] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:25,338] [INFO] Target genome list was writen to GCF_000420025.1_ASM42002v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:25,348] [INFO] Task started: fastANI
[2024-01-24 13:58:25,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b98a6d4-fd51-4c5c-8251-267a451d2dd2/GCF_000420025.1_ASM42002v1_genomic.fna.gz --refList GCF_000420025.1_ASM42002v1_genomic.fna/target_genomes.txt --output GCF_000420025.1_ASM42002v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:36,780] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:36,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfda63396-396c-4cc2-bcbd-0e9c735d005f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:36,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfda63396-396c-4cc2-bcbd-0e9c735d005f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:36,797] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:36,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:36,798] [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
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	100.0	1473	1474	95	conclusive
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	82.2567	929	1474	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	80.1458	712	1474	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	77.2462	556	1474	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	76.9607	618	1474	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	76.8312	554	1474	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	76.8093	625	1474	95	below_threshold
Microbacterium rhizomatis	strain=JCM 30598	GCA_008710745.1	1631477	1631477	type	True	75.1912	147	1474	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	75.1216	232	1474	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	75.0292	177	1474	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,799] [INFO] DFAST Taxonomy check result was written to GCF_000420025.1_ASM42002v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:36,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:36,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:36,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfda63396-396c-4cc2-bcbd-0e9c735d005f/dqc_reference/checkm_data
[2024-01-24 13:58:36,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:36,846] [INFO] Task started: CheckM
[2024-01-24 13:58:36,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000420025.1_ASM42002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000420025.1_ASM42002v1_genomic.fna/checkm_input GCF_000420025.1_ASM42002v1_genomic.fna/checkm_result
[2024-01-24 13:59:26,827] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:26,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:26,846] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:26,847] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:26,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000420025.1_ASM42002v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:26,847] [INFO] Task started: Blastn
[2024-01-24 13:59:26,848] [INFO] Running command: blastn -query GCF_000420025.1_ASM42002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda63396-396c-4cc2-bcbd-0e9c735d005f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000420025.1_ASM42002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:27,955] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:27,959] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:27,959] [INFO] Target genome list was writen to GCF_000420025.1_ASM42002v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:27,971] [INFO] Task started: fastANI
[2024-01-24 13:59:27,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b98a6d4-fd51-4c5c-8251-267a451d2dd2/GCF_000420025.1_ASM42002v1_genomic.fna.gz --refList GCF_000420025.1_ASM42002v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000420025.1_ASM42002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:38,609] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:38,627] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:38,628] [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_000420025.1	s__Patulibacter americanus	100.0	1473	1474	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017916475.1	s__Patulibacter sp017916475	82.9218	947	1474	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519325.1	s__Patulibacter minatonensis	82.2761	927	1474	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699505.1	s__Patulibacter sp009699505	82.0504	697	1474	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478825.1	s__Patulibacter sp015478825	80.4327	538	1474	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000240225.1	s__Patulibacter medicamentivorans	80.0906	720	1474	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017084525.1	s__Baekduia sp017084525	77.4087	591	1474	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463765.1	s__SYBY01 sp016463765	76.839	448	1474	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SYBY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000688095.1	s__Baekduia sp000688095	76.7932	607	1474	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:38,630] [INFO] GTDB search result was written to GCF_000420025.1_ASM42002v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:38,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:38,635] [INFO] DFAST_QC result json was written to GCF_000420025.1_ASM42002v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:38,635] [INFO] DFAST_QC completed!
[2024-01-24 13:59:38,635] [INFO] Total running time: 0h1m28s