[2023-06-28 08:29:36,340] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:29:36,351] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:29:36,351] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc146389-4010-4aaa-b3d6-9b2bf8d8e347/dqc_reference
[2023-06-28 08:29:37,546] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:29:37,547] [INFO] Task started: Prodigal
[2023-06-28 08:29:37,547] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2fb4584-a087-4b9f-a368-4bf0cb4059d3/GCA_017848335.1_ASM1784833v1_genomic.fna.gz | prodigal -d GCA_017848335.1_ASM1784833v1_genomic.fna/cds.fna -a GCA_017848335.1_ASM1784833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:29:43,179] [INFO] Task succeeded: Prodigal
[2023-06-28 08:29:43,180] [INFO] Task started: HMMsearch
[2023-06-28 08:29:43,180] [INFO] Running command: hmmsearch --tblout GCA_017848335.1_ASM1784833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc146389-4010-4aaa-b3d6-9b2bf8d8e347/dqc_reference/reference_markers.hmm GCA_017848335.1_ASM1784833v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:29:43,415] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:29:43,416] [INFO] Found 6/6 markers.
[2023-06-28 08:29:43,438] [INFO] Query marker FASTA was written to GCA_017848335.1_ASM1784833v1_genomic.fna/markers.fasta
[2023-06-28 08:29:43,438] [INFO] Task started: Blastn
[2023-06-28 08:29:43,438] [INFO] Running command: blastn -query GCA_017848335.1_ASM1784833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc146389-4010-4aaa-b3d6-9b2bf8d8e347/dqc_reference/reference_markers.fasta -out GCA_017848335.1_ASM1784833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:29:44,088] [INFO] Task succeeded: Blastn
[2023-06-28 08:29:44,105] [INFO] Selected 26 target genomes.
[2023-06-28 08:29:44,105] [INFO] Target genome list was writen to GCA_017848335.1_ASM1784833v1_genomic.fna/target_genomes.txt
[2023-06-28 08:29:44,111] [INFO] Task started: fastANI
[2023-06-28 08:29:44,111] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2fb4584-a087-4b9f-a368-4bf0cb4059d3/GCA_017848335.1_ASM1784833v1_genomic.fna.gz --refList GCA_017848335.1_ASM1784833v1_genomic.fna/target_genomes.txt --output GCA_017848335.1_ASM1784833v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:30:03,350] [INFO] Task succeeded: fastANI
[2023-06-28 08:30:03,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc146389-4010-4aaa-b3d6-9b2bf8d8e347/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:30:03,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc146389-4010-4aaa-b3d6-9b2bf8d8e347/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:30:03,353] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:30:03,353] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 08:30:03,353] [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 08:30:03,357] [INFO] DFAST Taxonomy check result was written to GCA_017848335.1_ASM1784833v1_genomic.fna/tc_result.tsv
[2023-06-28 08:30:03,358] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:30:03,358] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:30:03,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc146389-4010-4aaa-b3d6-9b2bf8d8e347/dqc_reference/checkm_data
[2023-06-28 08:30:03,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:30:03,390] [INFO] Task started: CheckM
[2023-06-28 08:30:03,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017848335.1_ASM1784833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017848335.1_ASM1784833v1_genomic.fna/checkm_input GCA_017848335.1_ASM1784833v1_genomic.fna/checkm_result
[2023-06-28 08:30:26,251] [INFO] Task succeeded: CheckM
[2023-06-28 08:30:26,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:30:26,276] [INFO] ===== Completeness check finished =====
[2023-06-28 08:30:26,276] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:30:26,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017848335.1_ASM1784833v1_genomic.fna/markers.fasta)
[2023-06-28 08:30:26,277] [INFO] Task started: Blastn
[2023-06-28 08:30:26,277] [INFO] Running command: blastn -query GCA_017848335.1_ASM1784833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc146389-4010-4aaa-b3d6-9b2bf8d8e347/dqc_reference/reference_markers_gtdb.fasta -out GCA_017848335.1_ASM1784833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:30:27,340] [INFO] Task succeeded: Blastn
[2023-06-28 08:30:27,345] [INFO] Selected 22 target genomes.
[2023-06-28 08:30:27,345] [INFO] Target genome list was writen to GCA_017848335.1_ASM1784833v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:30:27,355] [INFO] Task started: fastANI
[2023-06-28 08:30:27,355] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2fb4584-a087-4b9f-a368-4bf0cb4059d3/GCA_017848335.1_ASM1784833v1_genomic.fna.gz --refList GCA_017848335.1_ASM1784833v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017848335.1_ASM1784833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:30:37,726] [INFO] Task succeeded: fastANI
[2023-06-28 08:30:37,736] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:30:37,737] [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_017848335.1	s__UBA1212 sp017848335	100.0	706	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1212;f__UBA1212;g__UBA1212	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002309655.1	s__UBA1212 sp002309655	77.3631	146	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1212;f__UBA1212;g__UBA1212	95.0	97.68	97.40	0.94	0.92	8	-
GCA_902792515.1	s__UBA1212 sp902792515	77.2715	134	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1212;f__UBA1212;g__UBA1212	95.0	96.82	96.30	0.96	0.96	3	-
GCA_002308595.1	s__UBA1212 sp002308595	77.0255	64	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1212;f__UBA1212;g__UBA1212	95.0	96.60	96.60	0.80	0.80	2	-
GCA_902782645.1	s__UBA1212 sp902782645	76.5771	70	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1212;f__UBA1212;g__UBA1212	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017959965.1	s__UBA1212 sp017959965	76.5677	81	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1212;f__UBA1212;g__UBA1212	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:30:37,743] [INFO] GTDB search result was written to GCA_017848335.1_ASM1784833v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:30:37,744] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:30:37,747] [INFO] DFAST_QC result json was written to GCA_017848335.1_ASM1784833v1_genomic.fna/dqc_result.json
[2023-06-28 08:30:37,747] [INFO] DFAST_QC completed!
[2023-06-28 08:30:37,747] [INFO] Total running time: 0h1m1s