[2024-01-24 11:34:42,863] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:42,872] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:42,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b7dc0c1-0706-4be2-a0c2-35e483108715/dqc_reference
[2024-01-24 11:34:44,396] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,396] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,396] [INFO] Running command: gunzip -c /var/lib/cwl/stg34fbf375-942e-4f85-9da6-4a8fdf8db815/GCF_900460335.1_52121_G01_genomic.fna.gz | prodigal -d GCF_900460335.1_52121_G01_genomic.fna/cds.fna -a GCF_900460335.1_52121_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:49,905] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:49,905] [INFO] Task started: HMMsearch
[2024-01-24 11:34:49,905] [INFO] Running command: hmmsearch --tblout GCF_900460335.1_52121_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b7dc0c1-0706-4be2-a0c2-35e483108715/dqc_reference/reference_markers.hmm GCF_900460335.1_52121_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:50,189] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:50,190] [INFO] Found 6/6 markers.
[2024-01-24 11:34:50,219] [INFO] Query marker FASTA was written to GCF_900460335.1_52121_G01_genomic.fna/markers.fasta
[2024-01-24 11:34:50,219] [INFO] Task started: Blastn
[2024-01-24 11:34:50,219] [INFO] Running command: blastn -query GCF_900460335.1_52121_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b7dc0c1-0706-4be2-a0c2-35e483108715/dqc_reference/reference_markers.fasta -out GCF_900460335.1_52121_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:50,867] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:50,870] [INFO] Selected 14 target genomes.
[2024-01-24 11:34:50,870] [INFO] Target genome list was writen to GCF_900460335.1_52121_G01_genomic.fna/target_genomes.txt
[2024-01-24 11:34:50,901] [INFO] Task started: fastANI
[2024-01-24 11:34:50,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg34fbf375-942e-4f85-9da6-4a8fdf8db815/GCF_900460335.1_52121_G01_genomic.fna.gz --refList GCF_900460335.1_52121_G01_genomic.fna/target_genomes.txt --output GCF_900460335.1_52121_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:34:58,741] [INFO] Task succeeded: fastANI
[2024-01-24 11:34:58,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b7dc0c1-0706-4be2-a0c2-35e483108715/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:34:58,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b7dc0c1-0706-4be2-a0c2-35e483108715/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:34:58,753] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:34:58,753] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:34:58,753] [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
Tissierella praeacuta	strain=NCTC11158	GCA_900460335.1	43131	43131	type	True	100.0	1068	1068	95	conclusive
Tissierella praeacuta	strain=DSM 18095	GCA_900128955.1	43131	43131	type	True	99.9719	1008	1068	95	conclusive
Tissierella pigra	strain=WCA3-693-APC-4	GCA_009695605.1	2607614	2607614	type	True	80.3463	520	1068	95	below_threshold
Tissierella simiarum	strain=MSJ-40	GCA_018917865.1	2841534	2841534	type	True	78.7562	307	1068	95	below_threshold
Keratinibaculum paraultunense	strain=KD-1	GCA_016767175.1	1278232	1278232	type	True	77.0414	151	1068	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	76.6193	142	1068	95	below_threshold
Miniphocaeibacter halophilus	strain=AMB_01	GCA_016458825.1	2931922	2931922	type	True	76.5118	65	1068	95	below_threshold
Soehngenia longivitae	strain=1933P	GCA_004684055.1	2562294	2562294	type	True	76.3475	63	1068	95	below_threshold
Proteiniborus ethanoligenes	strain=DSM 21650	GCA_900107485.1	415015	415015	type	True	75.9983	81	1068	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	75.7789	80	1068	95	below_threshold
Thermohalobacter berrensis	strain=CTT3	GCA_003609645.1	99594	99594	type	True	75.2352	82	1068	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_000409755.1	1492	1492	type	True	74.8782	54	1068	95	below_threshold
Clostridium butyricum	strain=NBRC 13949	GCA_007992895.1	1492	1492	type	True	74.8775	55	1068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:34:58,755] [INFO] DFAST Taxonomy check result was written to GCF_900460335.1_52121_G01_genomic.fna/tc_result.tsv
[2024-01-24 11:34:58,756] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:34:58,756] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:34:58,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b7dc0c1-0706-4be2-a0c2-35e483108715/dqc_reference/checkm_data
[2024-01-24 11:34:58,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:34:58,788] [INFO] Task started: CheckM
[2024-01-24 11:34:58,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460335.1_52121_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460335.1_52121_G01_genomic.fna/checkm_input GCF_900460335.1_52121_G01_genomic.fna/checkm_result
[2024-01-24 11:35:21,495] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:21,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:21,517] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:21,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:21,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460335.1_52121_G01_genomic.fna/markers.fasta)
[2024-01-24 11:35:21,519] [INFO] Task started: Blastn
[2024-01-24 11:35:21,519] [INFO] Running command: blastn -query GCF_900460335.1_52121_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b7dc0c1-0706-4be2-a0c2-35e483108715/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460335.1_52121_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:22,438] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:22,442] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:22,443] [INFO] Target genome list was writen to GCF_900460335.1_52121_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:22,466] [INFO] Task started: fastANI
[2024-01-24 11:35:22,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg34fbf375-942e-4f85-9da6-4a8fdf8db815/GCF_900460335.1_52121_G01_genomic.fna.gz --refList GCF_900460335.1_52121_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900460335.1_52121_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:31,075] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:31,085] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:31,085] [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_900128955.1	s__Tissierella praeacuta	99.9719	1008	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__Tissierella	95.0	99.01	98.20	0.93	0.86	5	conclusive
GCF_002266425.1	s__Tissierella carlieri	82.9657	678	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__Tissierella	95.0	97.51	96.78	0.86	0.84	3	-
GCF_009695605.1	s__DSM105185 sp009695605	80.3633	519	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__DSM105185	95.0	99.10	99.10	0.90	0.90	2	-
GCF_018917865.1	s__MSJ-40 sp018917865	78.7562	307	1068	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	77.3733	175	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__JAAYFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519355.1	s__JAAYFT01 sp012519355	77.3212	171	1068	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_004103715.1	s__PP17-6a sp900095615	76.9528	60	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__PP17-6a;g__PP17-6a	95.0	98.35	97.94	0.90	0.87	4	-
GCA_012735245.1	s__JAAYFT01 sp012735245	76.8894	160	1068	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_005046945.1	s__Tissierella_B creatinini	76.5867	77	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__Tissierella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728075.1	s__Keratinibaculum sp012728075	76.2744	98	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012799055.1	s__JAAZMA01 sp012799055	76.2467	130	1068	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_012798935.1	s__JAAZMG01 sp012798935	76.1074	101	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__JAAZMG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:31,087] [INFO] GTDB search result was written to GCF_900460335.1_52121_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:31,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:31,091] [INFO] DFAST_QC result json was written to GCF_900460335.1_52121_G01_genomic.fna/dqc_result.json
[2024-01-24 11:35:31,091] [INFO] DFAST_QC completed!
[2024-01-24 11:35:31,092] [INFO] Total running time: 0h0m48s