[2024-01-24 12:44:52,524] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:52,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:52,528] [INFO] DQC Reference Directory: /var/lib/cwl/stgadbc0cd5-6751-4575-823e-e6211e9efdbf/dqc_reference
[2024-01-24 12:44:53,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:53,790] [INFO] Task started: Prodigal
[2024-01-24 12:44:53,790] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb5089ef-c160-40e3-80be-53b3efe0e33b/GCF_016767175.1_ASM1676717v1_genomic.fna.gz | prodigal -d GCF_016767175.1_ASM1676717v1_genomic.fna/cds.fna -a GCF_016767175.1_ASM1676717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:57,551] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:57,551] [INFO] Task started: HMMsearch
[2024-01-24 12:44:57,552] [INFO] Running command: hmmsearch --tblout GCF_016767175.1_ASM1676717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadbc0cd5-6751-4575-823e-e6211e9efdbf/dqc_reference/reference_markers.hmm GCF_016767175.1_ASM1676717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:57,791] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:57,793] [INFO] Found 6/6 markers.
[2024-01-24 12:44:57,820] [INFO] Query marker FASTA was written to GCF_016767175.1_ASM1676717v1_genomic.fna/markers.fasta
[2024-01-24 12:44:57,821] [INFO] Task started: Blastn
[2024-01-24 12:44:57,821] [INFO] Running command: blastn -query GCF_016767175.1_ASM1676717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadbc0cd5-6751-4575-823e-e6211e9efdbf/dqc_reference/reference_markers.fasta -out GCF_016767175.1_ASM1676717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:58,413] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:58,418] [INFO] Selected 15 target genomes.
[2024-01-24 12:44:58,418] [INFO] Target genome list was writen to GCF_016767175.1_ASM1676717v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:58,531] [INFO] Task started: fastANI
[2024-01-24 12:44:58,531] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb5089ef-c160-40e3-80be-53b3efe0e33b/GCF_016767175.1_ASM1676717v1_genomic.fna.gz --refList GCF_016767175.1_ASM1676717v1_genomic.fna/target_genomes.txt --output GCF_016767175.1_ASM1676717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:06,076] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:06,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadbc0cd5-6751-4575-823e-e6211e9efdbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:06,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadbc0cd5-6751-4575-823e-e6211e9efdbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:06,088] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:45:06,088] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:06,088] [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
Keratinibaculum paraultunense	strain=KD-1	GCA_016767175.1	1278232	1278232	type	True	100.0	769	769	95	conclusive
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	99.9505	730	769	95	conclusive
Sporanaerobacter acetigenes	strain=DSM 13106	GCA_900130025.1	165813	165813	type	True	76.9749	166	769	95	below_threshold
Tissierella praeacuta	strain=NCTC11158	GCA_900460335.1	43131	43131	type	True	76.9695	143	769	95	below_threshold
Tissierella simiarum	strain=MSJ-40	GCA_018917865.1	2841534	2841534	type	True	76.9251	182	769	95	below_threshold
Tissierella praeacuta	strain=DSM 18095	GCA_900128955.1	43131	43131	type	True	76.4782	137	769	95	below_threshold
Tissierella pigra	strain=WCA3-693-APC-4	GCA_009695605.1	2607614	2607614	type	True	76.4125	148	769	95	below_threshold
Tissierella creatinophila	strain=DSM 6911	GCA_001940565.1	79681	79681	type	True	76.062	72	769	95	below_threshold
Anaeromonas gelatinilytica	strain=D2Q-14	GCA_016820635.1	2683194	2683194	type	True	75.689	90	769	95	below_threshold
Caldisalinibacter kiritimatiensis	strain=L21-TH-D2	GCA_000387765.1	1304284	1304284	type	True	75.5935	65	769	95	below_threshold
Proteiniborus ethanoligenes	strain=DSM 21650	GCA_900107485.1	415015	415015	type	True	75.5384	82	769	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:06,090] [INFO] DFAST Taxonomy check result was written to GCF_016767175.1_ASM1676717v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:06,091] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:06,091] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:06,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadbc0cd5-6751-4575-823e-e6211e9efdbf/dqc_reference/checkm_data
[2024-01-24 12:45:06,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:06,116] [INFO] Task started: CheckM
[2024-01-24 12:45:06,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016767175.1_ASM1676717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016767175.1_ASM1676717v1_genomic.fna/checkm_input GCF_016767175.1_ASM1676717v1_genomic.fna/checkm_result
[2024-01-24 12:45:25,041] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:25,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:25,059] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:25,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:25,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016767175.1_ASM1676717v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:25,061] [INFO] Task started: Blastn
[2024-01-24 12:45:25,061] [INFO] Running command: blastn -query GCF_016767175.1_ASM1676717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadbc0cd5-6751-4575-823e-e6211e9efdbf/dqc_reference/reference_markers_gtdb.fasta -out GCF_016767175.1_ASM1676717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:25,847] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:25,852] [INFO] Selected 17 target genomes.
[2024-01-24 12:45:25,852] [INFO] Target genome list was writen to GCF_016767175.1_ASM1676717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:25,879] [INFO] Task started: fastANI
[2024-01-24 12:45:25,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb5089ef-c160-40e3-80be-53b3efe0e33b/GCF_016767175.1_ASM1676717v1_genomic.fna.gz --refList GCF_016767175.1_ASM1676717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016767175.1_ASM1676717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:33,931] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:33,948] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:33,948] [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_016767175.1	s__Keratinibaculum paraultunense	100.0	769	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_012728075.1	s__Keratinibaculum sp012728075	85.0614	470	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511955.1	s__Schnuerera ultunensis	78.3091	269	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Schnuerera	95.0	99.51	99.51	0.99	0.99	2	-
GCA_012799055.1	s__JAAZMA01 sp012799055	78.0315	211	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__JAAZMA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001282665.1	s__Mt11 sp001282665	77.9793	277	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Mt11	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002398845.1	s__Mt11 sp002398845	77.4861	157	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Mt11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798935.1	s__JAAZMG01 sp012798935	77.3016	189	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__JAAZMG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728595.1	s__Tepidimicrobium sp012728595	77.1066	115	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Tepidimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018917865.1	s__MSJ-40 sp018917865	76.8948	184	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__MSJ-40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728125.1	s__JAAYFT01 sp012728125	76.532	62	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__JAAYFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695605.1	s__DSM105185 sp009695605	76.4125	148	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__DSM105185	95.0	99.10	99.10	0.90	0.90	2	-
GCA_012839395.1	s__DUNJ01 sp012839395	76.0204	60	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__DUNJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000387765.1	s__Caldisalinibacter kiritimatiensis	75.5792	66	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Caldisalinibacteraceae;g__Caldisalinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:33,950] [INFO] GTDB search result was written to GCF_016767175.1_ASM1676717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:33,950] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:33,954] [INFO] DFAST_QC result json was written to GCF_016767175.1_ASM1676717v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:33,955] [INFO] DFAST_QC completed!
[2024-01-24 12:45:33,955] [INFO] Total running time: 0h0m41s