[2024-01-24 12:40:05,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:05,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:05,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e2cd91b-ad6c-4ac4-b235-a66ae792a42d/dqc_reference
[2024-01-24 12:40:06,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:06,949] [INFO] Task started: Prodigal
[2024-01-24 12:40:06,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg762394e6-a19c-4eae-88cb-f557ffe87ef7/GCF_000024845.1_ASM2484v1_genomic.fna.gz | prodigal -d GCF_000024845.1_ASM2484v1_genomic.fna/cds.fna -a GCF_000024845.1_ASM2484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:25,750] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:25,750] [INFO] Task started: HMMsearch
[2024-01-24 12:40:25,750] [INFO] Running command: hmmsearch --tblout GCF_000024845.1_ASM2484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e2cd91b-ad6c-4ac4-b235-a66ae792a42d/dqc_reference/reference_markers.hmm GCF_000024845.1_ASM2484v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:25,970] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:25,971] [INFO] Found 6/6 markers.
[2024-01-24 12:40:26,000] [INFO] Query marker FASTA was written to GCF_000024845.1_ASM2484v1_genomic.fna/markers.fasta
[2024-01-24 12:40:26,000] [INFO] Task started: Blastn
[2024-01-24 12:40:26,000] [INFO] Running command: blastn -query GCF_000024845.1_ASM2484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e2cd91b-ad6c-4ac4-b235-a66ae792a42d/dqc_reference/reference_markers.fasta -out GCF_000024845.1_ASM2484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:26,632] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:26,636] [INFO] Selected 23 target genomes.
[2024-01-24 12:40:26,636] [INFO] Target genome list was writen to GCF_000024845.1_ASM2484v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:26,644] [INFO] Task started: fastANI
[2024-01-24 12:40:26,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg762394e6-a19c-4eae-88cb-f557ffe87ef7/GCF_000024845.1_ASM2484v1_genomic.fna.gz --refList GCF_000024845.1_ASM2484v1_genomic.fna/target_genomes.txt --output GCF_000024845.1_ASM2484v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:41,327] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:41,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e2cd91b-ad6c-4ac4-b235-a66ae792a42d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:41,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e2cd91b-ad6c-4ac4-b235-a66ae792a42d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:41,339] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:41,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:41,340] [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
Rhodothermus profundi	strain=DSM 22212	GCA_900142415.1	633813	633813	type	True	79.6653	649	1128	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	77.866	300	1128	95	below_threshold
Rhodothermus bifroesti	strain=ISCAR-7401	GCA_017908595.1	2823335	2823335	type	True	77.3847	255	1128	95	below_threshold
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	76.2761	96	1128	95	below_threshold
Salisaeta longa	strain=DSM 21114	GCA_000419585.1	503170	503170	type	True	76.2746	106	1128	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	76.0	126	1128	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	75.9327	101	1128	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	75.3937	59	1128	95	below_threshold
Hymenobacter jeollabukensis	strain=1-3-3-8	GCA_005771675.1	2025313	2025313	type	True	75.2922	81	1128	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	75.0372	70	1128	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	75.0356	70	1128	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	74.9802	73	1128	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	74.9678	69	1128	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	74.8474	69	1128	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	74.7677	68	1128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:41,342] [INFO] DFAST Taxonomy check result was written to GCF_000024845.1_ASM2484v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:41,343] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:41,343] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:41,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e2cd91b-ad6c-4ac4-b235-a66ae792a42d/dqc_reference/checkm_data
[2024-01-24 12:40:41,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:41,378] [INFO] Task started: CheckM
[2024-01-24 12:40:41,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024845.1_ASM2484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024845.1_ASM2484v1_genomic.fna/checkm_input GCF_000024845.1_ASM2484v1_genomic.fna/checkm_result
[2024-01-24 12:41:32,068] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:32,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:32,084] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:32,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:32,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024845.1_ASM2484v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:32,085] [INFO] Task started: Blastn
[2024-01-24 12:41:32,085] [INFO] Running command: blastn -query GCF_000024845.1_ASM2484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e2cd91b-ad6c-4ac4-b235-a66ae792a42d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024845.1_ASM2484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:33,047] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:33,050] [INFO] Selected 13 target genomes.
[2024-01-24 12:41:33,050] [INFO] Target genome list was writen to GCF_000024845.1_ASM2484v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:33,059] [INFO] Task started: fastANI
[2024-01-24 12:41:33,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg762394e6-a19c-4eae-88cb-f557ffe87ef7/GCF_000024845.1_ASM2484v1_genomic.fna.gz --refList GCF_000024845.1_ASM2484v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024845.1_ASM2484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:42,167] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:42,176] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:42,176] [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_000024845.1	s__Rhodothermus marinus	100.0	1128	1128	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	95.50	95.42	0.92	0.91	8	conclusive
GCA_015487635.1	s__Rhodothermus sp015487635	90.3694	787	1128	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142415.1	s__Rhodothermus profundi	79.6616	649	1128	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011682235.1	s__ISCAR-4553 sp011682235	77.8323	292	1128	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__ISCAR-4553;g__ISCAR-4553	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017908595.1	s__Rhodothermus sp002898335	77.3847	255	1128	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	99.70	99.65	0.98	0.96	5	-
GCA_003285105.1	s__MEBICO9517 sp003285105	77.2568	300	1128	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__MEBIC09517;g__MEBICO9517	95.0	96.96	96.85	0.95	0.94	3	-
GCA_009908885.1	s__JAAAOL01 sp009908885	77.1082	162	1128	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAOL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960515.1	s__Rubricoccus sp012960515	75.9317	86	1128	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257665.1	s__Rubricoccus marinus	75.9188	102	1128	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170275.1	s__PALSA-1104 sp003170275	74.9237	59	1128	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__Palsa-1104;g__PALSA-1104	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:42,178] [INFO] GTDB search result was written to GCF_000024845.1_ASM2484v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:42,178] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:42,181] [INFO] DFAST_QC result json was written to GCF_000024845.1_ASM2484v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:42,181] [INFO] DFAST_QC completed!
[2024-01-24 12:41:42,181] [INFO] Total running time: 0h1m36s