[2024-01-24 11:44:23,166] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg8211fdae-361d-4604-ac55-08ff305a5b04/dqc_reference
[2024-01-24 11:44:26,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,339] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,340] [INFO] Running command: gunzip -c /var/lib/cwl/stg176fa94a-a6f9-4c78-a9c0-683cd0f513b2/GCF_003416765.1_ASM341676v1_genomic.fna.gz | prodigal -d GCF_003416765.1_ASM341676v1_genomic.fna/cds.fna -a GCF_003416765.1_ASM341676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:32,988] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:32,989] [INFO] Task started: HMMsearch
[2024-01-24 11:44:32,989] [INFO] Running command: hmmsearch --tblout GCF_003416765.1_ASM341676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8211fdae-361d-4604-ac55-08ff305a5b04/dqc_reference/reference_markers.hmm GCF_003416765.1_ASM341676v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:33,211] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:33,213] [INFO] Found 6/6 markers.
[2024-01-24 11:44:33,240] [INFO] Query marker FASTA was written to GCF_003416765.1_ASM341676v1_genomic.fna/markers.fasta
[2024-01-24 11:44:33,240] [INFO] Task started: Blastn
[2024-01-24 11:44:33,240] [INFO] Running command: blastn -query GCF_003416765.1_ASM341676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8211fdae-361d-4604-ac55-08ff305a5b04/dqc_reference/reference_markers.fasta -out GCF_003416765.1_ASM341676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:33,981] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:33,985] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:33,986] [INFO] Target genome list was writen to GCF_003416765.1_ASM341676v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:34,001] [INFO] Task started: fastANI
[2024-01-24 11:44:34,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg176fa94a-a6f9-4c78-a9c0-683cd0f513b2/GCF_003416765.1_ASM341676v1_genomic.fna.gz --refList GCF_003416765.1_ASM341676v1_genomic.fna/target_genomes.txt --output GCF_003416765.1_ASM341676v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:39,381] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:39,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8211fdae-361d-4604-ac55-08ff305a5b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:39,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8211fdae-361d-4604-ac55-08ff305a5b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:39,394] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:39,394] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:39,394] [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	82.1667	388	700	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	81.9878	361	700	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	81.3094	293	700	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	81.2772	358	700	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	80.881	309	700	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.4554	290	700	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	80.4227	242	700	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	80.2112	267	700	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	80.0034	259	700	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	79.5872	234	700	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.5846	223	700	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	78.9471	162	700	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	76.0552	57	700	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:39,396] [INFO] DFAST Taxonomy check result was written to GCF_003416765.1_ASM341676v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:39,396] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:39,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:39,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8211fdae-361d-4604-ac55-08ff305a5b04/dqc_reference/checkm_data
[2024-01-24 11:44:39,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:39,424] [INFO] Task started: CheckM
[2024-01-24 11:44:39,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003416765.1_ASM341676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003416765.1_ASM341676v1_genomic.fna/checkm_input GCF_003416765.1_ASM341676v1_genomic.fna/checkm_result
[2024-01-24 11:45:03,539] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:03,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:03,573] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:03,573] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:03,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003416765.1_ASM341676v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:03,574] [INFO] Task started: Blastn
[2024-01-24 11:45:03,574] [INFO] Running command: blastn -query GCF_003416765.1_ASM341676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8211fdae-361d-4604-ac55-08ff305a5b04/dqc_reference/reference_markers_gtdb.fasta -out GCF_003416765.1_ASM341676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:04,824] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:04,827] [INFO] Selected 14 target genomes.
[2024-01-24 11:45:04,827] [INFO] Target genome list was writen to GCF_003416765.1_ASM341676v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:04,838] [INFO] Task started: fastANI
[2024-01-24 11:45:04,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg176fa94a-a6f9-4c78-a9c0-683cd0f513b2/GCF_003416765.1_ASM341676v1_genomic.fna.gz --refList GCF_003416765.1_ASM341676v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003416765.1_ASM341676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:11,364] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:11,379] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:11,380] [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_003416765.1	s__Paratractidigestivibacter faecalis	100.0	700	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.79	95.48	0.89	0.83	10	conclusive
GCA_905215465.1	s__Paratractidigestivibacter sp905215465	93.6007	526	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540955.1	s__Paratractidigestivibacter sp900540955	83.407	390	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.08	96.08	0.89	0.89	2	-
GCA_002440065.1	s__Paratractidigestivibacter sp002440065	82.9279	342	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	98.71	98.71	0.71	0.71	2	-
GCA_003150175.1	s__Paratractidigestivibacter sp003150175	82.7105	376	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	98.50	98.31	0.84	0.80	5	-
GCF_016900315.1	s__Thermophilibacter profusa_A	82.5246	385	700	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	82.4112	365	700	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	82.4012	367	700	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	82.3936	361	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.98	97.98	0.90	0.90	2	-
GCF_002159535.1	s__Thermophilibacter sp002159535	82.3522	373	700	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	82.1803	352	700	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	81.9464	363	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116265.1	s__Thermophilibacter stercoravium	81.8736	285	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155635.1	s__Olsenella_G urininfantis	80.4232	242	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:11,382] [INFO] GTDB search result was written to GCF_003416765.1_ASM341676v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:11,382] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:11,387] [INFO] DFAST_QC result json was written to GCF_003416765.1_ASM341676v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:11,388] [INFO] DFAST_QC completed!
[2024-01-24 11:45:11,388] [INFO] Total running time: 0h0m48s