[2024-01-24 14:06:14,767] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:14,769] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:14,769] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ce3515f-61c5-46d5-89e3-da098b14a65c/dqc_reference
[2024-01-24 14:06:16,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:16,281] [INFO] Task started: Prodigal
[2024-01-24 14:06:16,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d814c27-01e9-4609-b803-5c276752162f/GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/cds.fna -a GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:23,014] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:23,014] [INFO] Task started: HMMsearch
[2024-01-24 14:06:23,014] [INFO] Running command: hmmsearch --tblout GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ce3515f-61c5-46d5-89e3-da098b14a65c/dqc_reference/reference_markers.hmm GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:23,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:23,312] [INFO] Found 6/6 markers.
[2024-01-24 14:06:23,346] [INFO] Query marker FASTA was written to GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:06:23,347] [INFO] Task started: Blastn
[2024-01-24 14:06:23,347] [INFO] Running command: blastn -query GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ce3515f-61c5-46d5-89e3-da098b14a65c/dqc_reference/reference_markers.fasta -out GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:23,966] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:23,970] [INFO] Selected 22 target genomes.
[2024-01-24 14:06:23,970] [INFO] Target genome list was writen to GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:06:23,992] [INFO] Task started: fastANI
[2024-01-24 14:06:23,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d814c27-01e9-4609-b803-5c276752162f/GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna.gz --refList GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:39,962] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:39,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ce3515f-61c5-46d5-89e3-da098b14a65c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:39,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ce3515f-61c5-46d5-89e3-da098b14a65c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:39,985] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:39,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:39,985] [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
Paramaledivibacter caminithermalis	strain=DSM 15212	GCA_900142245.1	191027	191027	type	True	100.0	1264	1274	95	conclusive
Maledivibacter halophilus	strain=M1	GCA_900167445.1	36842	36842	type	True	78.7548	581	1274	95	below_threshold
Caminicella sporogenes	strain=DSM 14501	GCA_900142285.1	166485	166485	type	True	77.4024	224	1274	95	below_threshold
Caminicella sporogenes	strain=AM 1114	GCA_003609595.1	166485	166485	type	True	77.3066	231	1274	95	below_threshold
Clostridiisalibacter paucivorans	strain=DSM 22131	GCA_000620125.1	408753	408753	type	True	75.8159	77	1274	95	below_threshold
Geosporobacter ferrireducens	strain=IRF9	GCA_001750685.1	1424294	1424294	type	True	75.5376	54	1274	95	below_threshold
Tepidibacter mesophilus	strain=JCM 16806	GCA_002724055.1	655607	655607	type	True	75.39	84	1274	95	below_threshold
Anaerovirgula multivorans	strain=SCA	GCA_900188145.1	312168	312168	type	True	75.3633	74	1274	95	below_threshold
Alkaliphilus flagellatus	strain=MSJ-5	GCA_018919215.1	2841507	2841507	type	True	75.3171	74	1274	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	75.2133	76	1274	95	below_threshold
Tissierella simiarum	strain=MSJ-40	GCA_018917865.1	2841534	2841534	type	True	75.1033	88	1274	95	below_threshold
Terrisporobacter othiniensis	strain=08-306576	GCA_000808015.1	1577792	1577792	type	True	74.9856	76	1274	95	below_threshold
Clostridium ljungdahlii	strain=DSM 13528	GCA_000143685.1	1538	1538	suspected-type	True	74.9445	60	1274	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	74.8781	73	1274	95	below_threshold
Clostridium drakei	strain=SL1	GCA_000633595.2	332101	332101	type	True	74.8372	76	1274	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	74.8358	77	1274	95	below_threshold
Hathewaya massiliensis	strain=Marseille-P3545	GCA_902143515.1	1964382	1964382	type	True	74.814	51	1274	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000427255.1	84023	84023	suspected-type	True	74.804	54	1274	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:39,987] [INFO] DFAST Taxonomy check result was written to GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:06:39,987] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:39,987] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:39,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ce3515f-61c5-46d5-89e3-da098b14a65c/dqc_reference/checkm_data
[2024-01-24 14:06:39,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:40,032] [INFO] Task started: CheckM
[2024-01-24 14:06:40,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/checkm_input GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:07:06,411] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:06,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:06,435] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:06,436] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:06,436] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:07:06,437] [INFO] Task started: Blastn
[2024-01-24 14:07:06,437] [INFO] Running command: blastn -query GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ce3515f-61c5-46d5-89e3-da098b14a65c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:07,218] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:07,222] [INFO] Selected 22 target genomes.
[2024-01-24 14:07:07,222] [INFO] Target genome list was writen to GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:07,249] [INFO] Task started: fastANI
[2024-01-24 14:07:07,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d814c27-01e9-4609-b803-5c276752162f/GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna.gz --refList GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:21,990] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:22,008] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:22,008] [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_900142245.1	s__Paramaledivibacter caminithermalis	100.0	1264	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Paramaledivibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900167445.1	s__Maledivibacter halophilus	78.8112	572	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Maledivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142285.1	s__Caminicella sporogenes	77.3946	226	1274	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_019203185.1	s__143-21 sp019203185	76.3152	131	1274	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_001282725.1	s__Inediibacterium massiliense	75.6015	99	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Inediibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750685.1	s__Geosporobacter ferrireducens	75.5101	53	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Geosporobacter	95.0	99.59	99.59	0.96	0.96	2	-
GCF_009696605.1	s__Anaerosalibacter bizertensis	75.4019	70	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter	95.0	98.53	98.48	0.86	0.84	3	-
GCF_002724055.1	s__Tepidibacter_A mesophilus	75.39	84	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Tepidibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018919215.1	s__Alkaliphilus_B sp018919215	75.3045	72	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953675.1	s__Paraclostridium sordellii	75.2208	75	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.12	96.78	0.93	0.89	59	-
GCF_018917865.1	s__MSJ-40 sp018917865	75.0822	87	1274	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	-
GCF_004006395.2	s__Clostridium_B sp004006395	75.0033	53	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251085.2	s__Romboutsia_B maritimum	74.9611	63	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143685.1	s__Clostridium_B ljungdahlii	74.9354	61	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.76	97.79	0.92	0.88	9	-
GCA_904418825.1	s__Romboutsia sp904418825	74.9023	52	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	99.17	99.17	0.88	0.88	2	-
GCF_000633595.2	s__Clostridium_AM drakei	74.8372	76	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:22,010] [INFO] GTDB search result was written to GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:22,011] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:22,015] [INFO] DFAST_QC result json was written to GCF_900142245.1_IMG-taxon_2585428176_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:07:22,015] [INFO] DFAST_QC completed!
[2024-01-24 14:07:22,015] [INFO] Total running time: 0h1m7s