[2024-01-24 11:05:34,663] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg97126f03-f45b-4e75-b2d5-ef217231103a/dqc_reference
[2024-01-24 11:05:35,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:35,898] [INFO] Task started: Prodigal
[2024-01-24 11:05:35,899] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1f925bc-59b7-46bc-a02b-7288483e748e/GCF_900128445.1_PRJEB18031_genomic.fna.gz | prodigal -d GCF_900128445.1_PRJEB18031_genomic.fna/cds.fna -a GCF_900128445.1_PRJEB18031_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:43,600] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:43,601] [INFO] Task started: HMMsearch
[2024-01-24 11:05:43,601] [INFO] Running command: hmmsearch --tblout GCF_900128445.1_PRJEB18031_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97126f03-f45b-4e75-b2d5-ef217231103a/dqc_reference/reference_markers.hmm GCF_900128445.1_PRJEB18031_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:43,841] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:43,842] [INFO] Found 6/6 markers.
[2024-01-24 11:05:43,869] [INFO] Query marker FASTA was written to GCF_900128445.1_PRJEB18031_genomic.fna/markers.fasta
[2024-01-24 11:05:43,869] [INFO] Task started: Blastn
[2024-01-24 11:05:43,869] [INFO] Running command: blastn -query GCF_900128445.1_PRJEB18031_genomic.fna/markers.fasta -db /var/lib/cwl/stg97126f03-f45b-4e75-b2d5-ef217231103a/dqc_reference/reference_markers.fasta -out GCF_900128445.1_PRJEB18031_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:44,661] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:44,666] [INFO] Selected 12 target genomes.
[2024-01-24 11:05:44,666] [INFO] Target genome list was writen to GCF_900128445.1_PRJEB18031_genomic.fna/target_genomes.txt
[2024-01-24 11:05:44,671] [INFO] Task started: fastANI
[2024-01-24 11:05:44,671] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1f925bc-59b7-46bc-a02b-7288483e748e/GCF_900128445.1_PRJEB18031_genomic.fna.gz --refList GCF_900128445.1_PRJEB18031_genomic.fna/target_genomes.txt --output GCF_900128445.1_PRJEB18031_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:50,664] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:50,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97126f03-f45b-4e75-b2d5-ef217231103a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:50,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97126f03-f45b-4e75-b2d5-ef217231103a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:50,682] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:50,682] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:50,682] [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
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	100.0	877	877	95	conclusive
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	85.7714	549	877	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	81.9953	394	877	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	80.8555	282	877	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.383	313	877	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	80.3481	302	877	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	80.3428	272	877	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.9201	295	877	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.8001	238	877	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	79.598	256	877	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.5918	264	877	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.5663	251	877	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:50,684] [INFO] DFAST Taxonomy check result was written to GCF_900128445.1_PRJEB18031_genomic.fna/tc_result.tsv
[2024-01-24 11:05:50,685] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:50,685] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:50,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97126f03-f45b-4e75-b2d5-ef217231103a/dqc_reference/checkm_data
[2024-01-24 11:05:50,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:50,735] [INFO] Task started: CheckM
[2024-01-24 11:05:50,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900128445.1_PRJEB18031_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900128445.1_PRJEB18031_genomic.fna/checkm_input GCF_900128445.1_PRJEB18031_genomic.fna/checkm_result
[2024-01-24 11:06:18,284] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:18,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:18,308] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:18,308] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:18,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900128445.1_PRJEB18031_genomic.fna/markers.fasta)
[2024-01-24 11:06:18,309] [INFO] Task started: Blastn
[2024-01-24 11:06:18,309] [INFO] Running command: blastn -query GCF_900128445.1_PRJEB18031_genomic.fna/markers.fasta -db /var/lib/cwl/stg97126f03-f45b-4e75-b2d5-ef217231103a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900128445.1_PRJEB18031_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:19,654] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:19,658] [INFO] Selected 11 target genomes.
[2024-01-24 11:06:19,658] [INFO] Target genome list was writen to GCF_900128445.1_PRJEB18031_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:19,661] [INFO] Task started: fastANI
[2024-01-24 11:06:19,661] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1f925bc-59b7-46bc-a02b-7288483e748e/GCF_900128445.1_PRJEB18031_genomic.fna.gz --refList GCF_900128445.1_PRJEB18031_genomic.fna/target_genomes_gtdb.txt --output GCF_900128445.1_PRJEB18031_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:25,890] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:25,905] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:25,905] [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_900128445.1	s__Thermophilibacter provencensis	100.0	876	877	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	96.98	96.17	0.87	0.80	3	conclusive
GCF_012027725.1	s__Thermophilibacter sp012027725	93.0637	662	877	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900775.1	s__Thermophilibacter uli_A	91.4999	662	877	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159535.1	s__Thermophilibacter sp002159535	86.8888	508	877	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014982725.1	s__Thermophilibacter sp014982725	86.3156	480	877	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159735.1	s__Thermophilibacter sp002159735	86.2505	477	877	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159625.1	s__Thermophilibacter avicola	86.207	555	877	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.98	97.98	0.90	0.90	2	-
GCA_019116265.1	s__Thermophilibacter stercoravium	86.193	399	877	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159495.1	s__Thermophilibacter sp002159495	86.0614	544	877	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899935.1	s__Thermophilibacter uli_B	85.9625	497	877	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119385.1	s__Thermophilibacter mediterraneus	85.7383	551	877	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:25,907] [INFO] GTDB search result was written to GCF_900128445.1_PRJEB18031_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:25,908] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:25,913] [INFO] DFAST_QC result json was written to GCF_900128445.1_PRJEB18031_genomic.fna/dqc_result.json
[2024-01-24 11:06:25,914] [INFO] DFAST_QC completed!
[2024-01-24 11:06:25,914] [INFO] Total running time: 0h0m51s