[2023-06-29 07:57:51,305] [INFO] DFAST_QC pipeline started.
[2023-06-29 07:57:51,307] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 07:57:51,307] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf4703cf-28f4-41e0-a530-b24e77b4147a/dqc_reference
[2023-06-29 07:57:52,810] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 07:57:52,811] [INFO] Task started: Prodigal
[2023-06-29 07:57:52,811] [INFO] Running command: gunzip -c /var/lib/cwl/stg003ae336-c6bc-4cd1-b0c9-7a1a2aa5b272/GCA_027593055.1_ASM2759305v1_genomic.fna.gz | prodigal -d GCA_027593055.1_ASM2759305v1_genomic.fna/cds.fna -a GCA_027593055.1_ASM2759305v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 07:58:01,548] [INFO] Task succeeded: Prodigal
[2023-06-29 07:58:01,548] [INFO] Task started: HMMsearch
[2023-06-29 07:58:01,548] [INFO] Running command: hmmsearch --tblout GCA_027593055.1_ASM2759305v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf4703cf-28f4-41e0-a530-b24e77b4147a/dqc_reference/reference_markers.hmm GCA_027593055.1_ASM2759305v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 07:58:01,864] [INFO] Task succeeded: HMMsearch
[2023-06-29 07:58:01,865] [INFO] Found 6/6 markers.
[2023-06-29 07:58:01,900] [INFO] Query marker FASTA was written to GCA_027593055.1_ASM2759305v1_genomic.fna/markers.fasta
[2023-06-29 07:58:01,901] [INFO] Task started: Blastn
[2023-06-29 07:58:01,901] [INFO] Running command: blastn -query GCA_027593055.1_ASM2759305v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf4703cf-28f4-41e0-a530-b24e77b4147a/dqc_reference/reference_markers.fasta -out GCA_027593055.1_ASM2759305v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:58:02,584] [INFO] Task succeeded: Blastn
[2023-06-29 07:58:02,596] [INFO] Selected 30 target genomes.
[2023-06-29 07:58:02,597] [INFO] Target genome list was writen to GCA_027593055.1_ASM2759305v1_genomic.fna/target_genomes.txt
[2023-06-29 07:58:02,611] [INFO] Task started: fastANI
[2023-06-29 07:58:02,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg003ae336-c6bc-4cd1-b0c9-7a1a2aa5b272/GCA_027593055.1_ASM2759305v1_genomic.fna.gz --refList GCA_027593055.1_ASM2759305v1_genomic.fna/target_genomes.txt --output GCA_027593055.1_ASM2759305v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 07:58:24,125] [INFO] Task succeeded: fastANI
[2023-06-29 07:58:24,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf4703cf-28f4-41e0-a530-b24e77b4147a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 07:58:24,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf4703cf-28f4-41e0-a530-b24e77b4147a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 07:58:24,127] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 07:58:24,127] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 07:58:24,127] [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
--------------------------------------------------------------------------------
[2023-06-29 07:58:24,129] [INFO] DFAST Taxonomy check result was written to GCA_027593055.1_ASM2759305v1_genomic.fna/tc_result.tsv
[2023-06-29 07:58:24,129] [INFO] ===== Taxonomy check completed =====
[2023-06-29 07:58:24,129] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 07:58:24,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf4703cf-28f4-41e0-a530-b24e77b4147a/dqc_reference/checkm_data
[2023-06-29 07:58:24,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 07:58:24,176] [INFO] Task started: CheckM
[2023-06-29 07:58:24,176] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027593055.1_ASM2759305v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027593055.1_ASM2759305v1_genomic.fna/checkm_input GCA_027593055.1_ASM2759305v1_genomic.fna/checkm_result
[2023-06-29 07:58:54,247] [INFO] Task succeeded: CheckM
[2023-06-29 07:58:54,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 07:58:54,274] [INFO] ===== Completeness check finished =====
[2023-06-29 07:58:54,274] [INFO] ===== Start GTDB Search =====
[2023-06-29 07:58:54,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027593055.1_ASM2759305v1_genomic.fna/markers.fasta)
[2023-06-29 07:58:54,275] [INFO] Task started: Blastn
[2023-06-29 07:58:54,275] [INFO] Running command: blastn -query GCA_027593055.1_ASM2759305v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf4703cf-28f4-41e0-a530-b24e77b4147a/dqc_reference/reference_markers_gtdb.fasta -out GCA_027593055.1_ASM2759305v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:58:55,109] [INFO] Task succeeded: Blastn
[2023-06-29 07:58:55,114] [INFO] Selected 28 target genomes.
[2023-06-29 07:58:55,115] [INFO] Target genome list was writen to GCA_027593055.1_ASM2759305v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 07:58:55,174] [INFO] Task started: fastANI
[2023-06-29 07:58:55,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg003ae336-c6bc-4cd1-b0c9-7a1a2aa5b272/GCA_027593055.1_ASM2759305v1_genomic.fna.gz --refList GCA_027593055.1_ASM2759305v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027593055.1_ASM2759305v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 07:59:09,508] [INFO] Task succeeded: fastANI
[2023-06-29 07:59:09,522] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 07:59:09,522] [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
GCA_009937285.1	s__UBA1138 sp009937285	78.2355	110	905	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.12	98.44	0.93	0.79	16	-
GCA_009692205.1	s__UBA2982 sp009692205	76.5582	76	905	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015664885.1	s__UBA1138 sp003447875	76.3948	117	905	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
GCA_016873995.1	s__UBA2982 sp016873995	76.2785	79	905	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015492755.1	s__S146-37 sp015492755	76.2473	63	905	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__S146-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002885.1	s__UBA2589 sp013002885	76.1037	73	905	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.00	99.00	0.85	0.85	2	-
GCA_003248075.1	s__SZUA-318 sp003248075	76.0262	84	905	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SZUA-318	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 07:59:09,525] [INFO] GTDB search result was written to GCA_027593055.1_ASM2759305v1_genomic.fna/result_gtdb.tsv
[2023-06-29 07:59:09,526] [INFO] ===== GTDB Search completed =====
[2023-06-29 07:59:09,529] [INFO] DFAST_QC result json was written to GCA_027593055.1_ASM2759305v1_genomic.fna/dqc_result.json
[2023-06-29 07:59:09,530] [INFO] DFAST_QC completed!
[2023-06-29 07:59:09,530] [INFO] Total running time: 0h1m18s