[2023-06-13 15:57:54,530] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:57:54,538] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:57:54,538] [INFO] DQC Reference Directory: /var/lib/cwl/stged8ad77f-f783-493a-a36d-7ef546ce05f1/dqc_reference
[2023-06-13 15:57:57,261] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:57:57,262] [INFO] Task started: Prodigal
[2023-06-13 15:57:57,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg5faebf0e-0f2c-455a-99ac-67e2e3902359/GCA_022708245.1_ASM2270824v1_genomic.fna.gz | prodigal -d GCA_022708245.1_ASM2270824v1_genomic.fna/cds.fna -a GCA_022708245.1_ASM2270824v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:58:06,045] [INFO] Task succeeded: Prodigal
[2023-06-13 15:58:06,046] [INFO] Task started: HMMsearch
[2023-06-13 15:58:06,046] [INFO] Running command: hmmsearch --tblout GCA_022708245.1_ASM2270824v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged8ad77f-f783-493a-a36d-7ef546ce05f1/dqc_reference/reference_markers.hmm GCA_022708245.1_ASM2270824v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:58:06,298] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:58:06,300] [INFO] Found 6/6 markers.
[2023-06-13 15:58:06,325] [INFO] Query marker FASTA was written to GCA_022708245.1_ASM2270824v1_genomic.fna/markers.fasta
[2023-06-13 15:58:06,326] [INFO] Task started: Blastn
[2023-06-13 15:58:06,326] [INFO] Running command: blastn -query GCA_022708245.1_ASM2270824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged8ad77f-f783-493a-a36d-7ef546ce05f1/dqc_reference/reference_markers.fasta -out GCA_022708245.1_ASM2270824v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:58:06,986] [INFO] Task succeeded: Blastn
[2023-06-13 15:58:06,997] [INFO] Selected 23 target genomes.
[2023-06-13 15:58:06,997] [INFO] Target genome list was writen to GCA_022708245.1_ASM2270824v1_genomic.fna/target_genomes.txt
[2023-06-13 15:58:07,009] [INFO] Task started: fastANI
[2023-06-13 15:58:07,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg5faebf0e-0f2c-455a-99ac-67e2e3902359/GCA_022708245.1_ASM2270824v1_genomic.fna.gz --refList GCA_022708245.1_ASM2270824v1_genomic.fna/target_genomes.txt --output GCA_022708245.1_ASM2270824v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:58:23,916] [INFO] Task succeeded: fastANI
[2023-06-13 15:58:23,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged8ad77f-f783-493a-a36d-7ef546ce05f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:58:23,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged8ad77f-f783-493a-a36d-7ef546ce05f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:58:23,918] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:58:23,919] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 15:58:23,919] [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
--------------------------------------------------------------------------------
[2023-06-13 15:58:23,921] [INFO] DFAST Taxonomy check result was written to GCA_022708245.1_ASM2270824v1_genomic.fna/tc_result.tsv
[2023-06-13 15:58:23,921] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:58:23,922] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:58:23,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged8ad77f-f783-493a-a36d-7ef546ce05f1/dqc_reference/checkm_data
[2023-06-13 15:58:23,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:58:23,947] [INFO] Task started: CheckM
[2023-06-13 15:58:23,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708245.1_ASM2270824v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708245.1_ASM2270824v1_genomic.fna/checkm_input GCA_022708245.1_ASM2270824v1_genomic.fna/checkm_result
[2023-06-13 15:58:54,951] [INFO] Task succeeded: CheckM
[2023-06-13 15:58:54,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:58:54,988] [INFO] ===== Completeness check finished =====
[2023-06-13 15:58:54,989] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:58:54,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708245.1_ASM2270824v1_genomic.fna/markers.fasta)
[2023-06-13 15:58:54,990] [INFO] Task started: Blastn
[2023-06-13 15:58:54,990] [INFO] Running command: blastn -query GCA_022708245.1_ASM2270824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged8ad77f-f783-493a-a36d-7ef546ce05f1/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708245.1_ASM2270824v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:58:55,793] [INFO] Task succeeded: Blastn
[2023-06-13 15:58:55,799] [INFO] Selected 15 target genomes.
[2023-06-13 15:58:55,799] [INFO] Target genome list was writen to GCA_022708245.1_ASM2270824v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:58:55,849] [INFO] Task started: fastANI
[2023-06-13 15:58:55,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg5faebf0e-0f2c-455a-99ac-67e2e3902359/GCA_022708245.1_ASM2270824v1_genomic.fna.gz --refList GCA_022708245.1_ASM2270824v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708245.1_ASM2270824v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:59:02,594] [INFO] Task succeeded: fastANI
[2023-06-13 15:59:02,602] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:59:02,602] [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_002071175.1	s__DMER64 sp002071175	99.9872	453	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001603455.1	s__DMER64 sp001603455	81.637	372	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.83	99.68	0.89	0.76	4	-
GCA_002071385.1	s__DMER64 sp002071385	78.663	195	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.62	99.43	0.93	0.90	7	-
GCA_002305545.1	s__DMER64 sp002305545	78.3802	218	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.79	99.75	0.96	0.96	3	-
GCA_001512865.1	s__DMER64 sp001512865	78.3371	233	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.73	99.73	0.89	0.89	2	-
GCA_002409325.1	s__DMER64 sp002409325	78.1779	207	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002070565.1	s__DMER64 sp002070565	78.147	187	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.14	99.14	0.85	0.85	2	-
GCA_002427525.1	s__DMER64 sp002427525	77.3537	99	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.85	99.85	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-13 15:59:02,604] [INFO] GTDB search result was written to GCA_022708245.1_ASM2270824v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:59:02,605] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:59:02,607] [INFO] DFAST_QC result json was written to GCA_022708245.1_ASM2270824v1_genomic.fna/dqc_result.json
[2023-06-13 15:59:02,608] [INFO] DFAST_QC completed!
[2023-06-13 15:59:02,608] [INFO] Total running time: 0h1m8s