[2023-06-28 08:10:50,739] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:10:50,741] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:10:50,741] [INFO] DQC Reference Directory: /var/lib/cwl/stg6267be18-25b1-4fac-9b33-2ac9309b3cab/dqc_reference
[2023-06-28 08:10:51,927] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:10:51,927] [INFO] Task started: Prodigal
[2023-06-28 08:10:51,928] [INFO] Running command: gunzip -c /var/lib/cwl/stg87e4ec54-c37b-49c2-abf8-d5abd7974af2/GCA_017856775.1_ASM1785677v1_genomic.fna.gz | prodigal -d GCA_017856775.1_ASM1785677v1_genomic.fna/cds.fna -a GCA_017856775.1_ASM1785677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:10:58,723] [INFO] Task succeeded: Prodigal
[2023-06-28 08:10:58,723] [INFO] Task started: HMMsearch
[2023-06-28 08:10:58,723] [INFO] Running command: hmmsearch --tblout GCA_017856775.1_ASM1785677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6267be18-25b1-4fac-9b33-2ac9309b3cab/dqc_reference/reference_markers.hmm GCA_017856775.1_ASM1785677v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:10:58,906] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:10:58,907] [INFO] Found 6/6 markers.
[2023-06-28 08:10:58,923] [INFO] Query marker FASTA was written to GCA_017856775.1_ASM1785677v1_genomic.fna/markers.fasta
[2023-06-28 08:10:58,924] [INFO] Task started: Blastn
[2023-06-28 08:10:58,924] [INFO] Running command: blastn -query GCA_017856775.1_ASM1785677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6267be18-25b1-4fac-9b33-2ac9309b3cab/dqc_reference/reference_markers.fasta -out GCA_017856775.1_ASM1785677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:10:59,472] [INFO] Task succeeded: Blastn
[2023-06-28 08:10:59,475] [INFO] Selected 26 target genomes.
[2023-06-28 08:10:59,476] [INFO] Target genome list was writen to GCA_017856775.1_ASM1785677v1_genomic.fna/target_genomes.txt
[2023-06-28 08:10:59,476] [INFO] Task started: fastANI
[2023-06-28 08:10:59,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg87e4ec54-c37b-49c2-abf8-d5abd7974af2/GCA_017856775.1_ASM1785677v1_genomic.fna.gz --refList GCA_017856775.1_ASM1785677v1_genomic.fna/target_genomes.txt --output GCA_017856775.1_ASM1785677v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:11:17,087] [INFO] Task succeeded: fastANI
[2023-06-28 08:11:17,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6267be18-25b1-4fac-9b33-2ac9309b3cab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:11:17,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6267be18-25b1-4fac-9b33-2ac9309b3cab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:11:17,089] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:11:17,089] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 08:11:17,089] [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 08:11:17,091] [INFO] DFAST Taxonomy check result was written to GCA_017856775.1_ASM1785677v1_genomic.fna/tc_result.tsv
[2023-06-28 08:11:17,092] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:11:17,092] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:11:17,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6267be18-25b1-4fac-9b33-2ac9309b3cab/dqc_reference/checkm_data
[2023-06-28 08:11:17,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:11:17,113] [INFO] Task started: CheckM
[2023-06-28 08:11:17,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017856775.1_ASM1785677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017856775.1_ASM1785677v1_genomic.fna/checkm_input GCA_017856775.1_ASM1785677v1_genomic.fna/checkm_result
[2023-06-28 08:11:42,075] [INFO] Task succeeded: CheckM
[2023-06-28 08:11:42,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:11:42,089] [INFO] ===== Completeness check finished =====
[2023-06-28 08:11:42,089] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:11:42,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017856775.1_ASM1785677v1_genomic.fna/markers.fasta)
[2023-06-28 08:11:42,089] [INFO] Task started: Blastn
[2023-06-28 08:11:42,089] [INFO] Running command: blastn -query GCA_017856775.1_ASM1785677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6267be18-25b1-4fac-9b33-2ac9309b3cab/dqc_reference/reference_markers_gtdb.fasta -out GCA_017856775.1_ASM1785677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:11:42,828] [INFO] Task succeeded: Blastn
[2023-06-28 08:11:42,832] [INFO] Selected 15 target genomes.
[2023-06-28 08:11:42,832] [INFO] Target genome list was writen to GCA_017856775.1_ASM1785677v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:11:42,834] [INFO] Task started: fastANI
[2023-06-28 08:11:42,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg87e4ec54-c37b-49c2-abf8-d5abd7974af2/GCA_017856775.1_ASM1785677v1_genomic.fna.gz --refList GCA_017856775.1_ASM1785677v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017856775.1_ASM1785677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:11:49,422] [INFO] Task succeeded: fastANI
[2023-06-28 08:11:49,431] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:11:49,432] [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_005791465.1	s__JJ008 sp005791465	97.4615	340	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	96.68	95.07	0.75	0.71	5	conclusive
GCA_014190475.1	s__JJ008 sp014190475	84.5544	365	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	97.91	97.91	0.83	0.83	2	-
GCA_903879995.1	s__JJ008 sp903879995	81.2534	267	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.65	98.57	0.79	0.77	3	-
GCA_016866355.1	s__JJ008 sp016866355	80.9413	336	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868585.1	s__JJ008 sp016868585	80.0658	291	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868475.1	s__JJ008 sp016868475	79.7056	262	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872155.1	s__JJ008 sp016872155	76.2701	59	494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:11:49,433] [INFO] GTDB search result was written to GCA_017856775.1_ASM1785677v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:11:49,434] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:11:49,436] [INFO] DFAST_QC result json was written to GCA_017856775.1_ASM1785677v1_genomic.fna/dqc_result.json
[2023-06-28 08:11:49,436] [INFO] DFAST_QC completed!
[2023-06-28 08:11:49,436] [INFO] Total running time: 0h0m59s