[2024-01-25 18:05:50,529] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:05:50,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:05:50,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg76a5748a-4963-4f4a-8565-25395402d8e1/dqc_reference
[2024-01-25 18:05:51,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:05:51,645] [INFO] Task started: Prodigal
[2024-01-25 18:05:51,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b6537e9-40a3-44cf-8214-25e452df696c/GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/cds.fna -a GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:00,261] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:00,262] [INFO] Task started: HMMsearch
[2024-01-25 18:06:00,262] [INFO] Running command: hmmsearch --tblout GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76a5748a-4963-4f4a-8565-25395402d8e1/dqc_reference/reference_markers.hmm GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:00,515] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:00,516] [INFO] Found 6/6 markers.
[2024-01-25 18:06:00,562] [INFO] Query marker FASTA was written to GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:06:00,563] [INFO] Task started: Blastn
[2024-01-25 18:06:00,563] [INFO] Running command: blastn -query GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg76a5748a-4963-4f4a-8565-25395402d8e1/dqc_reference/reference_markers.fasta -out GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:01,085] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:01,089] [INFO] Selected 17 target genomes.
[2024-01-25 18:06:01,089] [INFO] Target genome list was writen to GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:06:01,097] [INFO] Task started: fastANI
[2024-01-25 18:06:01,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6537e9-40a3-44cf-8214-25e452df696c/GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna.gz --refList GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:12,275] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:12,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76a5748a-4963-4f4a-8565-25395402d8e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:12,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76a5748a-4963-4f4a-8565-25395402d8e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:12,285] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:12,285] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:12,285] [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
Maledivibacter halophilus	strain=M1	GCA_900167445.1	36842	36842	type	True	100.0	1902	1915	95	conclusive
Paramaledivibacter caminithermalis	strain=DSM 15212	GCA_900142245.1	191027	191027	type	True	78.9063	557	1915	95	below_threshold
Caminicella sporogenes	strain=AM 1114	GCA_003609595.1	166485	166485	type	True	76.6519	190	1915	95	below_threshold
Caminicella sporogenes	strain=DSM 14501	GCA_900142285.1	166485	166485	type	True	76.5749	197	1915	95	below_threshold
Tepidibacter formicigenes	strain=DSM 15518	GCA_900142235.1	227138	227138	type	True	75.4669	119	1915	95	below_threshold
Acetoanaerobium pronyense	strain=DSM 27512	GCA_017874355.1	1482736	1482736	type	True	75.3527	63	1915	95	below_threshold
Clostridium pascui	strain=DSM 10365	GCA_016908015.1	46609	46609	type	True	75.1078	80	1915	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	75.088	59	1915	95	below_threshold
Haloimpatiens massiliensis	strain=Mt13	GCA_900184255.1	1658110	1658110	type	True	75.0011	92	1915	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_000175595.1	217159	217159	type	True	74.8971	94	1915	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	74.8741	99	1915	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	74.7905	78	1915	95	below_threshold
Clostridium frigoris	strain=DSM 14204	GCA_018861865.1	205327	205327	type	True	74.6985	78	1915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:12,286] [INFO] DFAST Taxonomy check result was written to GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:06:12,288] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:12,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:12,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76a5748a-4963-4f4a-8565-25395402d8e1/dqc_reference/checkm_data
[2024-01-25 18:06:12,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:12,343] [INFO] Task started: CheckM
[2024-01-25 18:06:12,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/checkm_input GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:06:41,733] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:41,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:06:41,771] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:41,771] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:41,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:06:41,772] [INFO] Task started: Blastn
[2024-01-25 18:06:41,772] [INFO] Running command: blastn -query GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg76a5748a-4963-4f4a-8565-25395402d8e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:42,544] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:42,548] [INFO] Selected 20 target genomes.
[2024-01-25 18:06:42,548] [INFO] Target genome list was writen to GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:42,562] [INFO] Task started: fastANI
[2024-01-25 18:06:42,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6537e9-40a3-44cf-8214-25e452df696c/GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna.gz --refList GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:55,870] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:55,879] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:55,879] [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_900167445.1	s__Maledivibacter halophilus	100.0	1899	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Maledivibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142245.1	s__Paramaledivibacter caminithermalis	78.9099	559	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Paramaledivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142285.1	s__Caminicella sporogenes	76.5759	197	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Caminicella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004345705.1	s__Marinisporobacter balticus	76.0624	112	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Marinisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203185.1	s__143-21 sp019203185	75.6843	120	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__143-21	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142235.1	s__Tepidibacter formicigenes	75.4463	119	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Tepidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874355.1	s__Acetoanaerobium pronyense	75.3527	63	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Acetoanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479485.1	s__UBA1535 sp002479485	75.3415	65	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__UBA1535	95.0	98.88	98.88	0.91	0.91	2	-
GCA_000751555.1	s__Anaerosalibacter massiliensis	75.1696	84	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016908015.1	s__Clostridium_AK pascui	75.0985	81	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184255.1	s__Haloimpatiens massiliensis	74.9927	94	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Haloimpatiens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889265.1	s__JAGHEK01 sp017889265	74.8259	52	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__JAGHEK01	95.0	98.99	98.99	0.83	0.83	2	-
GCF_001243045.1	s__Clostridium_F niameyense	74.7743	88	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.56	99.11	0.96	0.92	3	-
GCA_016650035.1	s__Clostridium_AD sp016650035	74.7091	62	1915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:55,881] [INFO] GTDB search result was written to GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:55,881] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:55,884] [INFO] DFAST_QC result json was written to GCF_900167445.1_IMG-taxon_2524614863_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:06:55,885] [INFO] DFAST_QC completed!
[2024-01-25 18:06:55,885] [INFO] Total running time: 0h1m5s