[2024-01-24 14:22:01,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg08909d58-fb46-460c-b5ec-068ee256186a/dqc_reference
[2024-01-24 14:22:03,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:03,045] [INFO] Task started: Prodigal
[2024-01-24 14:22:03,045] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbe3668c-8203-4250-ace4-e1a8d3c42998/GCF_000695095.2_ASM69509v2_genomic.fna.gz | prodigal -d GCF_000695095.2_ASM69509v2_genomic.fna/cds.fna -a GCF_000695095.2_ASM69509v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:20,940] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:20,940] [INFO] Task started: HMMsearch
[2024-01-24 14:22:20,940] [INFO] Running command: hmmsearch --tblout GCF_000695095.2_ASM69509v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08909d58-fb46-460c-b5ec-068ee256186a/dqc_reference/reference_markers.hmm GCF_000695095.2_ASM69509v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:21,216] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:21,218] [INFO] Found 6/6 markers.
[2024-01-24 14:22:21,255] [INFO] Query marker FASTA was written to GCF_000695095.2_ASM69509v2_genomic.fna/markers.fasta
[2024-01-24 14:22:21,256] [INFO] Task started: Blastn
[2024-01-24 14:22:21,256] [INFO] Running command: blastn -query GCF_000695095.2_ASM69509v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg08909d58-fb46-460c-b5ec-068ee256186a/dqc_reference/reference_markers.fasta -out GCF_000695095.2_ASM69509v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:21,936] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:21,939] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:21,940] [INFO] Target genome list was writen to GCF_000695095.2_ASM69509v2_genomic.fna/target_genomes.txt
[2024-01-24 14:22:21,948] [INFO] Task started: fastANI
[2024-01-24 14:22:21,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbe3668c-8203-4250-ace4-e1a8d3c42998/GCF_000695095.2_ASM69509v2_genomic.fna.gz --refList GCF_000695095.2_ASM69509v2_genomic.fna/target_genomes.txt --output GCF_000695095.2_ASM69509v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:34,992] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:34,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08909d58-fb46-460c-b5ec-068ee256186a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:34,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08909d58-fb46-460c-b5ec-068ee256186a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:35,002] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:35,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:35,002] [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
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	100.0	1571	1572	95	conclusive
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	78.8391	453	1572	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	78.4465	510	1572	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	76.4914	196	1572	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.9567	85	1572	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.4529	82	1572	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.4169	82	1572	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	74.8332	69	1572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:35,004] [INFO] DFAST Taxonomy check result was written to GCF_000695095.2_ASM69509v2_genomic.fna/tc_result.tsv
[2024-01-24 14:22:35,005] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:35,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:35,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08909d58-fb46-460c-b5ec-068ee256186a/dqc_reference/checkm_data
[2024-01-24 14:22:35,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:35,051] [INFO] Task started: CheckM
[2024-01-24 14:22:35,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000695095.2_ASM69509v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000695095.2_ASM69509v2_genomic.fna/checkm_input GCF_000695095.2_ASM69509v2_genomic.fna/checkm_result
[2024-01-24 14:23:34,569] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:34,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:34,588] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:34,588] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:34,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000695095.2_ASM69509v2_genomic.fna/markers.fasta)
[2024-01-24 14:23:34,588] [INFO] Task started: Blastn
[2024-01-24 14:23:34,588] [INFO] Running command: blastn -query GCF_000695095.2_ASM69509v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg08909d58-fb46-460c-b5ec-068ee256186a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000695095.2_ASM69509v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:35,455] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:35,458] [INFO] Selected 13 target genomes.
[2024-01-24 14:23:35,459] [INFO] Target genome list was writen to GCF_000695095.2_ASM69509v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:35,468] [INFO] Task started: fastANI
[2024-01-24 14:23:35,468] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbe3668c-8203-4250-ace4-e1a8d3c42998/GCF_000695095.2_ASM69509v2_genomic.fna.gz --refList GCF_000695095.2_ASM69509v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000695095.2_ASM69509v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:45,464] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:45,474] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:45,474] [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_000695095.2	s__Gemmatimonas phototrophica	100.0	1572	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016741895.1	s__Gemmatimonas sp016741895	79.2893	506	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483225.1	s__Gemmatimonas sp002483225	79.2764	566	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	97.70	97.70	0.96	0.96	2	-
GCA_016742275.1	s__Gemmatimonas sp016742275	78.9367	467	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010305.1	s__Gemmatimonas aurantiaca	78.8526	451	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013004105.1	s__Gemmatimonas sp013004105	78.4507	509	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737115.1	s__Gemmatimonas sp002737115	78.3937	256	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	97.83	97.76	0.72	0.69	3	-
GCA_903900795.1	s__Gemmatimonas sp903900795	78.379	369	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969225.1	s__Gemmatimonas sp018969225	77.4032	304	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724275.1	s__SCN-70-22 sp001724275	76.4375	129	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713435.1	s__JADJOM01 sp016713435	76.0943	101	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JADJOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876745.1	s__Fen-1231 sp903876745	75.8289	92	1572	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:45,476] [INFO] GTDB search result was written to GCF_000695095.2_ASM69509v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:45,476] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:45,480] [INFO] DFAST_QC result json was written to GCF_000695095.2_ASM69509v2_genomic.fna/dqc_result.json
[2024-01-24 14:23:45,481] [INFO] DFAST_QC completed!
[2024-01-24 14:23:45,481] [INFO] Total running time: 0h1m44s