[2023-06-28 16:01:12,450] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:01:12,451] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:01:12,451] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bf754dc-4d3e-411b-9205-9b1159bebc77/dqc_reference
[2023-06-28 16:01:13,652] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:01:13,652] [INFO] Task started: Prodigal
[2023-06-28 16:01:13,653] [INFO] Running command: gunzip -c /var/lib/cwl/stg9514ed5e-1f93-44bb-be17-99dc97e70431/GCA_017404555.1_ASM1740455v1_genomic.fna.gz | prodigal -d GCA_017404555.1_ASM1740455v1_genomic.fna/cds.fna -a GCA_017404555.1_ASM1740455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:01:14,893] [INFO] Task succeeded: Prodigal
[2023-06-28 16:01:14,893] [INFO] Task started: HMMsearch
[2023-06-28 16:01:14,893] [INFO] Running command: hmmsearch --tblout GCA_017404555.1_ASM1740455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bf754dc-4d3e-411b-9205-9b1159bebc77/dqc_reference/reference_markers.hmm GCA_017404555.1_ASM1740455v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:01:15,063] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:01:15,065] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9514ed5e-1f93-44bb-be17-99dc97e70431/GCA_017404555.1_ASM1740455v1_genomic.fna.gz]
[2023-06-28 16:01:15,076] [INFO] Query marker FASTA was written to GCA_017404555.1_ASM1740455v1_genomic.fna/markers.fasta
[2023-06-28 16:01:15,077] [INFO] Task started: Blastn
[2023-06-28 16:01:15,077] [INFO] Running command: blastn -query GCA_017404555.1_ASM1740455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bf754dc-4d3e-411b-9205-9b1159bebc77/dqc_reference/reference_markers.fasta -out GCA_017404555.1_ASM1740455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:01:16,251] [INFO] Task succeeded: Blastn
[2023-06-28 16:01:16,255] [INFO] Selected 26 target genomes.
[2023-06-28 16:01:16,256] [INFO] Target genome list was writen to GCA_017404555.1_ASM1740455v1_genomic.fna/target_genomes.txt
[2023-06-28 16:01:16,274] [INFO] Task started: fastANI
[2023-06-28 16:01:16,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg9514ed5e-1f93-44bb-be17-99dc97e70431/GCA_017404555.1_ASM1740455v1_genomic.fna.gz --refList GCA_017404555.1_ASM1740455v1_genomic.fna/target_genomes.txt --output GCA_017404555.1_ASM1740455v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:01:27,097] [INFO] Task succeeded: fastANI
[2023-06-28 16:01:27,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bf754dc-4d3e-411b-9205-9b1159bebc77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:01:27,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bf754dc-4d3e-411b-9205-9b1159bebc77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:01:27,099] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:01:27,100] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:01:27,100] [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 16:01:27,101] [INFO] DFAST Taxonomy check result was written to GCA_017404555.1_ASM1740455v1_genomic.fna/tc_result.tsv
[2023-06-28 16:01:27,102] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:01:27,102] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:01:27,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bf754dc-4d3e-411b-9205-9b1159bebc77/dqc_reference/checkm_data
[2023-06-28 16:01:27,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:01:27,129] [INFO] Task started: CheckM
[2023-06-28 16:01:27,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017404555.1_ASM1740455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017404555.1_ASM1740455v1_genomic.fna/checkm_input GCA_017404555.1_ASM1740455v1_genomic.fna/checkm_result
[2023-06-28 16:01:38,495] [INFO] Task succeeded: CheckM
[2023-06-28 16:01:38,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:01:38,516] [INFO] ===== Completeness check finished =====
[2023-06-28 16:01:38,516] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:01:38,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017404555.1_ASM1740455v1_genomic.fna/markers.fasta)
[2023-06-28 16:01:38,517] [INFO] Task started: Blastn
[2023-06-28 16:01:38,517] [INFO] Running command: blastn -query GCA_017404555.1_ASM1740455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bf754dc-4d3e-411b-9205-9b1159bebc77/dqc_reference/reference_markers_gtdb.fasta -out GCA_017404555.1_ASM1740455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:01:39,320] [INFO] Task succeeded: Blastn
[2023-06-28 16:01:39,323] [INFO] Selected 21 target genomes.
[2023-06-28 16:01:39,323] [INFO] Target genome list was writen to GCA_017404555.1_ASM1740455v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:01:39,378] [INFO] Task started: fastANI
[2023-06-28 16:01:39,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg9514ed5e-1f93-44bb-be17-99dc97e70431/GCA_017404555.1_ASM1740455v1_genomic.fna.gz --refList GCA_017404555.1_ASM1740455v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017404555.1_ASM1740455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:01:44,232] [INFO] Task succeeded: fastANI
[2023-06-28 16:01:44,238] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:01:44,238] [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_017404555.1	s__RGIG2361 sp017404555	100.0	310	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG2361	95.0	96.78	96.78	0.89	0.89	2	conclusive
GCA_017512495.1	s__UBA3789 sp017512495	77.8243	73	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541885.1	s__UBA3789 sp017541885	77.1866	50	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801525.1	s__RUG14670 sp902801525	76.9781	71	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14670	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432665.1	s__UBA3789 sp017432665	76.9062	69	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433455.1	s__CAG-877 sp000433455	76.8382	55	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	97.81	97.70	0.90	0.89	3	-
GCA_910589335.1	s__UBA3789 sp910589335	76.2112	52	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:01:44,240] [INFO] GTDB search result was written to GCA_017404555.1_ASM1740455v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:01:44,241] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:01:44,243] [INFO] DFAST_QC result json was written to GCA_017404555.1_ASM1740455v1_genomic.fna/dqc_result.json
[2023-06-28 16:01:44,243] [INFO] DFAST_QC completed!
[2023-06-28 16:01:44,243] [INFO] Total running time: 0h0m32s