[2023-06-28 05:38:03,103] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:38:03,107] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:38:03,107] [INFO] DQC Reference Directory: /var/lib/cwl/stg643aa6c9-0cdc-48dc-94f7-16b47f71393e/dqc_reference
[2023-06-28 05:38:04,580] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:38:04,581] [INFO] Task started: Prodigal
[2023-06-28 05:38:04,581] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bf7d86a-c680-4c20-9143-63daaf452631/GCA_017962045.1_ASM1796204v1_genomic.fna.gz | prodigal -d GCA_017962045.1_ASM1796204v1_genomic.fna/cds.fna -a GCA_017962045.1_ASM1796204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:38:10,392] [INFO] Task succeeded: Prodigal
[2023-06-28 05:38:10,393] [INFO] Task started: HMMsearch
[2023-06-28 05:38:10,393] [INFO] Running command: hmmsearch --tblout GCA_017962045.1_ASM1796204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg643aa6c9-0cdc-48dc-94f7-16b47f71393e/dqc_reference/reference_markers.hmm GCA_017962045.1_ASM1796204v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:38:10,607] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:38:10,608] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg5bf7d86a-c680-4c20-9143-63daaf452631/GCA_017962045.1_ASM1796204v1_genomic.fna.gz]
[2023-06-28 05:38:10,621] [INFO] Query marker FASTA was written to GCA_017962045.1_ASM1796204v1_genomic.fna/markers.fasta
[2023-06-28 05:38:10,621] [INFO] Task started: Blastn
[2023-06-28 05:38:10,621] [INFO] Running command: blastn -query GCA_017962045.1_ASM1796204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg643aa6c9-0cdc-48dc-94f7-16b47f71393e/dqc_reference/reference_markers.fasta -out GCA_017962045.1_ASM1796204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:38:11,122] [INFO] Task succeeded: Blastn
[2023-06-28 05:38:11,126] [INFO] Selected 15 target genomes.
[2023-06-28 05:38:11,126] [INFO] Target genome list was writen to GCA_017962045.1_ASM1796204v1_genomic.fna/target_genomes.txt
[2023-06-28 05:38:11,135] [INFO] Task started: fastANI
[2023-06-28 05:38:11,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bf7d86a-c680-4c20-9143-63daaf452631/GCA_017962045.1_ASM1796204v1_genomic.fna.gz --refList GCA_017962045.1_ASM1796204v1_genomic.fna/target_genomes.txt --output GCA_017962045.1_ASM1796204v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:38:19,140] [INFO] Task succeeded: fastANI
[2023-06-28 05:38:19,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg643aa6c9-0cdc-48dc-94f7-16b47f71393e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:38:19,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg643aa6c9-0cdc-48dc-94f7-16b47f71393e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:38:19,144] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:38:19,144] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 05:38:19,144] [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
--------------------------------------------------------------------------------
[2023-06-28 05:38:19,146] [INFO] DFAST Taxonomy check result was written to GCA_017962045.1_ASM1796204v1_genomic.fna/tc_result.tsv
[2023-06-28 05:38:19,147] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:38:19,147] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:38:19,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg643aa6c9-0cdc-48dc-94f7-16b47f71393e/dqc_reference/checkm_data
[2023-06-28 05:38:19,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:38:19,170] [INFO] Task started: CheckM
[2023-06-28 05:38:19,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017962045.1_ASM1796204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017962045.1_ASM1796204v1_genomic.fna/checkm_input GCA_017962045.1_ASM1796204v1_genomic.fna/checkm_result
[2023-06-28 05:38:42,621] [INFO] Task succeeded: CheckM
[2023-06-28 05:38:42,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 30.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:38:42,652] [INFO] ===== Completeness check finished =====
[2023-06-28 05:38:42,652] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:38:42,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017962045.1_ASM1796204v1_genomic.fna/markers.fasta)
[2023-06-28 05:38:42,653] [INFO] Task started: Blastn
[2023-06-28 05:38:42,653] [INFO] Running command: blastn -query GCA_017962045.1_ASM1796204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg643aa6c9-0cdc-48dc-94f7-16b47f71393e/dqc_reference/reference_markers_gtdb.fasta -out GCA_017962045.1_ASM1796204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:38:43,275] [INFO] Task succeeded: Blastn
[2023-06-28 05:38:43,280] [INFO] Selected 8 target genomes.
[2023-06-28 05:38:43,281] [INFO] Target genome list was writen to GCA_017962045.1_ASM1796204v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:38:43,289] [INFO] Task started: fastANI
[2023-06-28 05:38:43,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bf7d86a-c680-4c20-9143-63daaf452631/GCA_017962045.1_ASM1796204v1_genomic.fna.gz --refList GCA_017962045.1_ASM1796204v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017962045.1_ASM1796204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:38:46,630] [INFO] Task succeeded: fastANI
[2023-06-28 05:38:46,644] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 05:38:46,644] [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_900320435.1	s__UBA4372 sp900320435	94.688	215	279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.93	95.36	0.84	0.75	10	-
GCA_902784475.1	s__UBA4372 sp902784475	93.1386	227	279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791295.1	s__UBA4372 sp902791295	87.8565	220	279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017958545.1	s__UBA4372 sp017958545	80.004	124	279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292045.1	s__UBA4372 sp016292045	79.8036	165	279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802815.1	s__UBA4372 sp902802815	79.6353	171	279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543815.1	s__UBA4372 sp900543815	76.5206	52	279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.82	97.58	0.92	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-28 05:38:46,646] [INFO] GTDB search result was written to GCA_017962045.1_ASM1796204v1_genomic.fna/result_gtdb.tsv
[2023-06-28 05:38:46,647] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:38:46,650] [INFO] DFAST_QC result json was written to GCA_017962045.1_ASM1796204v1_genomic.fna/dqc_result.json
[2023-06-28 05:38:46,650] [INFO] DFAST_QC completed!
[2023-06-28 05:38:46,650] [INFO] Total running time: 0h0m44s