[2023-06-29 23:41:09,768] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:41:09,770] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:41:09,770] [INFO] DQC Reference Directory: /var/lib/cwl/stg53a2e18e-d823-4dba-afae-03f41c44e98e/dqc_reference
[2023-06-29 23:41:10,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:41:10,956] [INFO] Task started: Prodigal
[2023-06-29 23:41:10,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg504fbb52-0d10-425d-9872-2b84cc1829c1/GCA_025456005.1_ASM2545600v1_genomic.fna.gz | prodigal -d GCA_025456005.1_ASM2545600v1_genomic.fna/cds.fna -a GCA_025456005.1_ASM2545600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:41:18,643] [INFO] Task succeeded: Prodigal
[2023-06-29 23:41:18,644] [INFO] Task started: HMMsearch
[2023-06-29 23:41:18,644] [INFO] Running command: hmmsearch --tblout GCA_025456005.1_ASM2545600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53a2e18e-d823-4dba-afae-03f41c44e98e/dqc_reference/reference_markers.hmm GCA_025456005.1_ASM2545600v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:41:18,823] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:41:18,825] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg504fbb52-0d10-425d-9872-2b84cc1829c1/GCA_025456005.1_ASM2545600v1_genomic.fna.gz]
[2023-06-29 23:41:18,847] [INFO] Query marker FASTA was written to GCA_025456005.1_ASM2545600v1_genomic.fna/markers.fasta
[2023-06-29 23:41:18,848] [INFO] Task started: Blastn
[2023-06-29 23:41:18,848] [INFO] Running command: blastn -query GCA_025456005.1_ASM2545600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53a2e18e-d823-4dba-afae-03f41c44e98e/dqc_reference/reference_markers.fasta -out GCA_025456005.1_ASM2545600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:41:19,457] [INFO] Task succeeded: Blastn
[2023-06-29 23:41:19,461] [INFO] Selected 8 target genomes.
[2023-06-29 23:41:19,462] [INFO] Target genome list was writen to GCA_025456005.1_ASM2545600v1_genomic.fna/target_genomes.txt
[2023-06-29 23:41:19,462] [INFO] Task started: fastANI
[2023-06-29 23:41:19,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg504fbb52-0d10-425d-9872-2b84cc1829c1/GCA_025456005.1_ASM2545600v1_genomic.fna.gz --refList GCA_025456005.1_ASM2545600v1_genomic.fna/target_genomes.txt --output GCA_025456005.1_ASM2545600v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:41:26,376] [INFO] Task succeeded: fastANI
[2023-06-29 23:41:26,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53a2e18e-d823-4dba-afae-03f41c44e98e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:41:26,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53a2e18e-d823-4dba-afae-03f41c44e98e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:41:26,389] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:41:26,390] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:41:26,390] [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
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	78.4295	225	355	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	78.1842	232	355	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	78.1507	227	355	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	77.9619	234	355	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	77.7283	243	355	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	77.2726	200	355	95	below_threshold
Modestobacter altitudinis	strain=1G4	GCA_005930475.1	2213158	2213158	type	True	75.0321	105	355	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	74.9959	151	355	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:41:26,392] [INFO] DFAST Taxonomy check result was written to GCA_025456005.1_ASM2545600v1_genomic.fna/tc_result.tsv
[2023-06-29 23:41:26,393] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:41:26,393] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:41:26,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53a2e18e-d823-4dba-afae-03f41c44e98e/dqc_reference/checkm_data
[2023-06-29 23:41:26,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:41:26,421] [INFO] Task started: CheckM
[2023-06-29 23:41:26,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025456005.1_ASM2545600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025456005.1_ASM2545600v1_genomic.fna/checkm_input GCA_025456005.1_ASM2545600v1_genomic.fna/checkm_result
[2023-06-29 23:41:47,763] [INFO] Task succeeded: CheckM
[2023-06-29 23:41:47,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.04%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 23:41:47,786] [INFO] ===== Completeness check finished =====
[2023-06-29 23:41:47,786] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:41:47,786] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025456005.1_ASM2545600v1_genomic.fna/markers.fasta)
[2023-06-29 23:41:47,787] [INFO] Task started: Blastn
[2023-06-29 23:41:47,787] [INFO] Running command: blastn -query GCA_025456005.1_ASM2545600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53a2e18e-d823-4dba-afae-03f41c44e98e/dqc_reference/reference_markers_gtdb.fasta -out GCA_025456005.1_ASM2545600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:41:48,627] [INFO] Task succeeded: Blastn
[2023-06-29 23:41:48,632] [INFO] Selected 13 target genomes.
[2023-06-29 23:41:48,632] [INFO] Target genome list was writen to GCA_025456005.1_ASM2545600v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:41:48,637] [INFO] Task started: fastANI
[2023-06-29 23:41:48,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg504fbb52-0d10-425d-9872-2b84cc1829c1/GCA_025456005.1_ASM2545600v1_genomic.fna.gz --refList GCA_025456005.1_ASM2545600v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025456005.1_ASM2545600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:41:54,455] [INFO] Task succeeded: fastANI
[2023-06-29 23:41:54,471] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 23:41:54,471] [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
GCA_009699245.1	s__F1-60-MAGs163 sp009699245	80.1376	167	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699915.1	s__F1-60-MAGs163 sp009699915	79.2139	112	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017084525.1	s__Baekduia sp017084525	78.7733	227	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695395.1	s__SEOHO-28 sp013695395	78.1516	140	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463765.1	s__SYBY01 sp016463765	77.9898	173	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SYBY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882375.1	s__Palsa-744 sp017882375	77.9618	156	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806205.1	s__SEOHO-28 sp902806205	77.8914	165	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699615.1	s__F1-60-MAGs163 sp009699615	77.646	56	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699565.1	s__F1-60-MAGs163 sp009699565	77.5552	76	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884115.1	s__Palsa-744 sp005884115	77.4943	132	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959665.1	s__F1-60-MAGs163 sp903959665	77.3408	77	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	99.27	99.00	0.86	0.79	34	-
GCA_012718975.1	s__JAAYBF01 sp012718975	77.3014	190	355	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Thermoleophilaceae;g__JAAYBF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:41:54,473] [INFO] GTDB search result was written to GCA_025456005.1_ASM2545600v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:41:54,474] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:41:54,478] [INFO] DFAST_QC result json was written to GCA_025456005.1_ASM2545600v1_genomic.fna/dqc_result.json
[2023-06-29 23:41:54,478] [INFO] DFAST_QC completed!
[2023-06-29 23:41:54,478] [INFO] Total running time: 0h0m45s