[2024-01-24 13:21:46,066] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:46,070] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:46,070] [INFO] DQC Reference Directory: /var/lib/cwl/stg220116e6-a2ae-4816-90ae-9f96278cda01/dqc_reference
[2024-01-24 13:21:47,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:47,396] [INFO] Task started: Prodigal
[2024-01-24 13:21:47,397] [INFO] Running command: gunzip -c /var/lib/cwl/stg937f4100-043d-4b9a-9bf1-7426c74b0c05/GCF_014192995.1_ASM1419299v1_genomic.fna.gz | prodigal -d GCF_014192995.1_ASM1419299v1_genomic.fna/cds.fna -a GCF_014192995.1_ASM1419299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:55,400] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:55,400] [INFO] Task started: HMMsearch
[2024-01-24 13:21:55,400] [INFO] Running command: hmmsearch --tblout GCF_014192995.1_ASM1419299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg220116e6-a2ae-4816-90ae-9f96278cda01/dqc_reference/reference_markers.hmm GCF_014192995.1_ASM1419299v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:55,628] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:55,629] [INFO] Found 6/6 markers.
[2024-01-24 13:21:55,651] [INFO] Query marker FASTA was written to GCF_014192995.1_ASM1419299v1_genomic.fna/markers.fasta
[2024-01-24 13:21:55,651] [INFO] Task started: Blastn
[2024-01-24 13:21:55,651] [INFO] Running command: blastn -query GCF_014192995.1_ASM1419299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg220116e6-a2ae-4816-90ae-9f96278cda01/dqc_reference/reference_markers.fasta -out GCF_014192995.1_ASM1419299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:56,257] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:56,261] [INFO] Selected 13 target genomes.
[2024-01-24 13:21:56,262] [INFO] Target genome list was writen to GCF_014192995.1_ASM1419299v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:56,269] [INFO] Task started: fastANI
[2024-01-24 13:21:56,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg937f4100-043d-4b9a-9bf1-7426c74b0c05/GCF_014192995.1_ASM1419299v1_genomic.fna.gz --refList GCF_014192995.1_ASM1419299v1_genomic.fna/target_genomes.txt --output GCF_014192995.1_ASM1419299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:02,456] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:02,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg220116e6-a2ae-4816-90ae-9f96278cda01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:02,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg220116e6-a2ae-4816-90ae-9f96278cda01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:02,468] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:02,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:02,469] [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
Slackia isoflavoniconvertens	strain=DSM 22006	GCA_014192995.1	572010	572010	type	True	100.0	771	772	95	conclusive
Slackia isoflavoniconvertens	strain=DSM 22006	GCA_003725955.1	572010	572010	type	True	99.9478	728	772	95	conclusive
Senegalimassilia anaerobia	strain=type strain: JC110	GCA_000236865.1	1473216	1473216	type	True	79.432	177	772	95	below_threshold
Slackia equolifaciens	strain=DSM 24851	GCA_003725995.1	498718	498718	type	True	78.6717	179	772	95	below_threshold
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	78.6624	203	772	95	below_threshold
Slackia piriformis	strain=YIT 12062	GCA_000296445.1	626934	626934	type	True	78.5684	168	772	95	below_threshold
Adlercreutzia hattorii	strain=8CFCBH1	GCA_011405655.1	2707299	2707299	type	True	78.0111	116	772	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	78.0052	61	772	95	below_threshold
Slackia heliotrinireducens	strain=NCTC11029	GCA_900637575.1	84110	84110	type	True	77.8868	126	772	95	below_threshold
Slackia heliotrinireducens	strain=DSM 20476	GCA_000023885.1	84110	84110	type	True	77.8292	123	772	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	77.5588	129	772	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	77.5357	129	772	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_008831045.1	1796610	1796610	type	True	77.0577	89	772	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:02,470] [INFO] DFAST Taxonomy check result was written to GCF_014192995.1_ASM1419299v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:02,471] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:02,471] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:02,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg220116e6-a2ae-4816-90ae-9f96278cda01/dqc_reference/checkm_data
[2024-01-24 13:22:02,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:02,499] [INFO] Task started: CheckM
[2024-01-24 13:22:02,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192995.1_ASM1419299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192995.1_ASM1419299v1_genomic.fna/checkm_input GCF_014192995.1_ASM1419299v1_genomic.fna/checkm_result
[2024-01-24 13:22:31,594] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:31,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:31,617] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:31,617] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:31,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192995.1_ASM1419299v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:31,618] [INFO] Task started: Blastn
[2024-01-24 13:22:31,618] [INFO] Running command: blastn -query GCF_014192995.1_ASM1419299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg220116e6-a2ae-4816-90ae-9f96278cda01/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192995.1_ASM1419299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:32,533] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:32,537] [INFO] Selected 17 target genomes.
[2024-01-24 13:22:32,537] [INFO] Target genome list was writen to GCF_014192995.1_ASM1419299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:32,562] [INFO] Task started: fastANI
[2024-01-24 13:22:32,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg937f4100-043d-4b9a-9bf1-7426c74b0c05/GCF_014192995.1_ASM1419299v1_genomic.fna.gz --refList GCF_014192995.1_ASM1419299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192995.1_ASM1419299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:41,969] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:41,985] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:41,985] [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_003725955.1	s__Slackia_A isoflavoniconvertens	99.9478	728	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	96.92	96.02	0.86	0.81	13	conclusive
GCF_004135645.1	s__Senegalimassilia faecalis	79.5988	173	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	96.85	96.73	0.92	0.89	4	-
GCF_003725995.1	s__Slackia_A equolifaciens	78.6717	179	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725295.1	s__Slackia_A faecicanis	78.6712	201	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296445.1	s__Slackia_A piriformis	78.5912	167	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	98.02	96.04	0.96	0.92	3	-
GCF_008831035.1	s__Ellagibacter isourolithinifaciens	78.5221	136	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter	95.0	96.52	96.27	0.85	0.76	13	-
GCA_900553775.1	s__Slackia_A sp900553775	78.3941	169	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	98.24	98.24	0.77	0.77	2	-
GCA_905215325.1	s__Senegalimassilia sp905215325	78.2654	152	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024265.1	s__Eggerthella lenta	77.8401	139	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCA_900555495.1	s__Slackia_A sp900555495	77.7498	124	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	100.00	100.00	0.96	0.96	2	-
GCA_900553655.1	s__Slackia_A sp900553655	77.5465	86	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	97.68	97.68	0.69	0.69	2	-
GCA_017459925.1	s__UBA9715 sp017459925	77.382	86	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339845.1	s__Gordonibacter sp003339845	77.3408	139	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_901411515.1	s__Raoultibacter sp901411515	77.1364	106	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Raoultibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903789375.1	s__CAIFEB01 sp903789375	77.0482	108	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAIFEB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008831045.1	s__Adlercreutzia muris	77.0292	90	772	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.80	97.69	0.87	0.84	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:41,987] [INFO] GTDB search result was written to GCF_014192995.1_ASM1419299v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:41,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:41,991] [INFO] DFAST_QC result json was written to GCF_014192995.1_ASM1419299v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:41,991] [INFO] DFAST_QC completed!
[2024-01-24 13:22:41,991] [INFO] Total running time: 0h0m56s