[2023-06-28 11:34:14,646] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:34:14,648] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:34:14,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg398fc520-c696-41b1-a605-35d366f4e44d/dqc_reference
[2023-06-28 11:34:15,743] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:34:15,743] [INFO] Task started: Prodigal
[2023-06-28 11:34:15,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg21ea9a7c-83e1-434a-92db-017c58161605/GCA_017403015.1_ASM1740301v1_genomic.fna.gz | prodigal -d GCA_017403015.1_ASM1740301v1_genomic.fna/cds.fna -a GCA_017403015.1_ASM1740301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:34:27,564] [INFO] Task succeeded: Prodigal
[2023-06-28 11:34:27,565] [INFO] Task started: HMMsearch
[2023-06-28 11:34:27,565] [INFO] Running command: hmmsearch --tblout GCA_017403015.1_ASM1740301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg398fc520-c696-41b1-a605-35d366f4e44d/dqc_reference/reference_markers.hmm GCA_017403015.1_ASM1740301v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:34:27,736] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:34:27,737] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg21ea9a7c-83e1-434a-92db-017c58161605/GCA_017403015.1_ASM1740301v1_genomic.fna.gz]
[2023-06-28 11:34:27,757] [INFO] Query marker FASTA was written to GCA_017403015.1_ASM1740301v1_genomic.fna/markers.fasta
[2023-06-28 11:34:27,758] [INFO] Task started: Blastn
[2023-06-28 11:34:27,758] [INFO] Running command: blastn -query GCA_017403015.1_ASM1740301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg398fc520-c696-41b1-a605-35d366f4e44d/dqc_reference/reference_markers.fasta -out GCA_017403015.1_ASM1740301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:34:28,310] [INFO] Task succeeded: Blastn
[2023-06-28 11:34:28,314] [INFO] Selected 30 target genomes.
[2023-06-28 11:34:28,314] [INFO] Target genome list was writen to GCA_017403015.1_ASM1740301v1_genomic.fna/target_genomes.txt
[2023-06-28 11:34:28,321] [INFO] Task started: fastANI
[2023-06-28 11:34:28,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg21ea9a7c-83e1-434a-92db-017c58161605/GCA_017403015.1_ASM1740301v1_genomic.fna.gz --refList GCA_017403015.1_ASM1740301v1_genomic.fna/target_genomes.txt --output GCA_017403015.1_ASM1740301v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:34:42,776] [INFO] Task succeeded: fastANI
[2023-06-28 11:34:42,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg398fc520-c696-41b1-a605-35d366f4e44d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:34:42,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg398fc520-c696-41b1-a605-35d366f4e44d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:34:42,778] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:34:42,778] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 11:34:42,778] [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 11:34:42,779] [INFO] DFAST Taxonomy check result was written to GCA_017403015.1_ASM1740301v1_genomic.fna/tc_result.tsv
[2023-06-28 11:34:42,780] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:34:42,780] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:34:42,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg398fc520-c696-41b1-a605-35d366f4e44d/dqc_reference/checkm_data
[2023-06-28 11:34:42,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:34:42,812] [INFO] Task started: CheckM
[2023-06-28 11:34:42,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017403015.1_ASM1740301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017403015.1_ASM1740301v1_genomic.fna/checkm_input GCA_017403015.1_ASM1740301v1_genomic.fna/checkm_result
[2023-06-28 11:35:19,897] [INFO] Task succeeded: CheckM
[2023-06-28 11:35:19,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 5.01%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 11:35:19,916] [INFO] ===== Completeness check finished =====
[2023-06-28 11:35:19,916] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:35:19,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017403015.1_ASM1740301v1_genomic.fna/markers.fasta)
[2023-06-28 11:35:19,917] [INFO] Task started: Blastn
[2023-06-28 11:35:19,918] [INFO] Running command: blastn -query GCA_017403015.1_ASM1740301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg398fc520-c696-41b1-a605-35d366f4e44d/dqc_reference/reference_markers_gtdb.fasta -out GCA_017403015.1_ASM1740301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:35:20,810] [INFO] Task succeeded: Blastn
[2023-06-28 11:35:20,813] [INFO] Selected 18 target genomes.
[2023-06-28 11:35:20,813] [INFO] Target genome list was writen to GCA_017403015.1_ASM1740301v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:35:20,820] [INFO] Task started: fastANI
[2023-06-28 11:35:20,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg21ea9a7c-83e1-434a-92db-017c58161605/GCA_017403015.1_ASM1740301v1_genomic.fna.gz --refList GCA_017403015.1_ASM1740301v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017403015.1_ASM1740301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:35:28,425] [INFO] Task succeeded: fastANI
[2023-06-28 11:35:28,430] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:35:28,430] [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_900313845.1	s__UBA3839 sp900313845	96.2278	242	313	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.94	95.74	0.85	0.70	7	conclusive
GCA_902798705.1	s__UBA3839 sp902798705	86.3801	213	313	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.86	96.85	0.82	0.82	3	-
GCA_002393575.1	s__UBA3839 sp002393575	83.1071	205	313	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.72	96.72	0.83	0.83	2	-
GCA_902768125.1	s__UBA4334 sp902768125	77.8051	51	313	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.29	98.29	0.89	0.89	2	-
GCA_017614895.1	s__UBA4334 sp017614895	77.5389	50	313	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234125.1	s__UBA4334 sp905234125	77.2221	51	313	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.16	98.16	0.81	0.81	2	-
GCA_905234555.1	s__UBA3839 sp905234555	77.152	51	313	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 11:35:28,432] [INFO] GTDB search result was written to GCA_017403015.1_ASM1740301v1_genomic.fna/result_gtdb.tsv
[2023-06-28 11:35:28,432] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:35:28,435] [INFO] DFAST_QC result json was written to GCA_017403015.1_ASM1740301v1_genomic.fna/dqc_result.json
[2023-06-28 11:35:28,435] [INFO] DFAST_QC completed!
[2023-06-28 11:35:28,435] [INFO] Total running time: 0h1m14s