[2023-06-28 00:19:19,312] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:19:19,316] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:19:19,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f9c4d3b-bdbf-4f80-83f7-bfb7e778c3dc/dqc_reference
[2023-06-28 00:19:20,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:19:20,606] [INFO] Task started: Prodigal
[2023-06-28 00:19:20,606] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9455d2f-4d19-4b9d-8e7b-14d638fb5251/GCA_002331325.1_ASM233132v1_genomic.fna.gz | prodigal -d GCA_002331325.1_ASM233132v1_genomic.fna/cds.fna -a GCA_002331325.1_ASM233132v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:19:26,492] [INFO] Task succeeded: Prodigal
[2023-06-28 00:19:26,492] [INFO] Task started: HMMsearch
[2023-06-28 00:19:26,493] [INFO] Running command: hmmsearch --tblout GCA_002331325.1_ASM233132v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f9c4d3b-bdbf-4f80-83f7-bfb7e778c3dc/dqc_reference/reference_markers.hmm GCA_002331325.1_ASM233132v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:19:26,708] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:19:26,712] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb9455d2f-4d19-4b9d-8e7b-14d638fb5251/GCA_002331325.1_ASM233132v1_genomic.fna.gz]
[2023-06-28 00:19:26,738] [INFO] Query marker FASTA was written to GCA_002331325.1_ASM233132v1_genomic.fna/markers.fasta
[2023-06-28 00:19:26,739] [INFO] Task started: Blastn
[2023-06-28 00:19:26,739] [INFO] Running command: blastn -query GCA_002331325.1_ASM233132v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f9c4d3b-bdbf-4f80-83f7-bfb7e778c3dc/dqc_reference/reference_markers.fasta -out GCA_002331325.1_ASM233132v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:19:27,307] [INFO] Task succeeded: Blastn
[2023-06-28 00:19:27,313] [INFO] Selected 10 target genomes.
[2023-06-28 00:19:27,314] [INFO] Target genome list was writen to GCA_002331325.1_ASM233132v1_genomic.fna/target_genomes.txt
[2023-06-28 00:19:27,317] [INFO] Task started: fastANI
[2023-06-28 00:19:27,317] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9455d2f-4d19-4b9d-8e7b-14d638fb5251/GCA_002331325.1_ASM233132v1_genomic.fna.gz --refList GCA_002331325.1_ASM233132v1_genomic.fna/target_genomes.txt --output GCA_002331325.1_ASM233132v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:19:31,062] [INFO] Task succeeded: fastANI
[2023-06-28 00:19:31,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f9c4d3b-bdbf-4f80-83f7-bfb7e778c3dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:19:31,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f9c4d3b-bdbf-4f80-83f7-bfb7e778c3dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:19:31,074] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:19:31,074] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 00:19:31,075] [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
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	78.2584	167	618	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	78.2567	163	618	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	78.1034	132	618	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	78.0188	144	618	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	78.0145	118	618	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	78.0027	137	618	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	77.8718	116	618	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	77.7608	155	618	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	77.7532	121	618	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	77.3503	144	618	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:19:31,077] [INFO] DFAST Taxonomy check result was written to GCA_002331325.1_ASM233132v1_genomic.fna/tc_result.tsv
[2023-06-28 00:19:31,077] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:19:31,078] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:19:31,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f9c4d3b-bdbf-4f80-83f7-bfb7e778c3dc/dqc_reference/checkm_data
[2023-06-28 00:19:31,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:19:31,109] [INFO] Task started: CheckM
[2023-06-28 00:19:31,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002331325.1_ASM233132v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002331325.1_ASM233132v1_genomic.fna/checkm_input GCA_002331325.1_ASM233132v1_genomic.fna/checkm_result
[2023-06-28 00:19:54,442] [INFO] Task succeeded: CheckM
[2023-06-28 00:19:54,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.31%
Contamintation: 0.76%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 00:19:54,468] [INFO] ===== Completeness check finished =====
[2023-06-28 00:19:54,469] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:19:54,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002331325.1_ASM233132v1_genomic.fna/markers.fasta)
[2023-06-28 00:19:54,469] [INFO] Task started: Blastn
[2023-06-28 00:19:54,470] [INFO] Running command: blastn -query GCA_002331325.1_ASM233132v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f9c4d3b-bdbf-4f80-83f7-bfb7e778c3dc/dqc_reference/reference_markers_gtdb.fasta -out GCA_002331325.1_ASM233132v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:19:55,093] [INFO] Task succeeded: Blastn
[2023-06-28 00:19:55,098] [INFO] Selected 17 target genomes.
[2023-06-28 00:19:55,098] [INFO] Target genome list was writen to GCA_002331325.1_ASM233132v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:19:55,103] [INFO] Task started: fastANI
[2023-06-28 00:19:55,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9455d2f-4d19-4b9d-8e7b-14d638fb5251/GCA_002331325.1_ASM233132v1_genomic.fna.gz --refList GCA_002331325.1_ASM233132v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002331325.1_ASM233132v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:20:02,938] [INFO] Task succeeded: fastANI
[2023-06-28 00:20:02,957] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:20:02,957] [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_900314535.1	s__UBA7748 sp900314535	96.1164	518	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7748	95.0	97.59	96.11	0.86	0.80	25	conclusive
GCA_900313905.1	s__UBA7748 sp900313905	82.7887	399	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7748	95.0	98.35	97.65	0.88	0.82	5	-
GCA_003862195.1	s__Parafannyhessea sp003862195	78.9913	187	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCA_902780325.1	s__Parafannyhessea sp902787335	78.3118	149	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCF_016899935.1	s__Thermophilibacter uli_B	78.2202	159	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002331575.1	s__Olsenella_D sp002331575	78.0909	160	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000752675.2	s__Tractidigestivibacter sp000752675	78.0055	157	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.74	96.78	0.93	0.90	14	-
GCA_902795065.1	s__RUG721 sp900321745	77.8516	138	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG721	95.0	99.01	98.55	0.89	0.82	11	-
GCA_004557505.1	s__Tractidigestivibacter sp004557505	77.7987	155	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119385.1	s__Thermophilibacter mediterraneus	77.7605	155	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777325.1	s__UBA1367 sp902777325	77.5729	118	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314645.1	s__UBA1367 sp900314645	77.5421	95	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.42	97.54	0.93	0.89	4	-
GCA_019116525.1	s__Thermophilibacter pullistercoris	77.4661	132	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778135.1	s__UBA1367 sp902778135	77.4156	115	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.30	98.30	0.89	0.89	2	-
GCA_900549525.1	s__Parolsenella sp900549525	77.3325	88	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	99.58	99.58	0.87	0.87	2	-
GCA_902790135.1	s__UBA1367 sp902790135	77.1997	104	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017513965.1	s__RUG440 sp017513965	76.6503	51	618	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:20:02,959] [INFO] GTDB search result was written to GCA_002331325.1_ASM233132v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:20:02,960] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:20:02,964] [INFO] DFAST_QC result json was written to GCA_002331325.1_ASM233132v1_genomic.fna/dqc_result.json
[2023-06-28 00:20:02,964] [INFO] DFAST_QC completed!
[2023-06-28 00:20:02,964] [INFO] Total running time: 0h0m44s