[2023-06-19 00:58:11,093] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:58:11,095] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:58:11,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg89771aec-693c-4b66-8817-f12c6d1ff539/dqc_reference
[2023-06-19 00:58:12,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:58:12,543] [INFO] Task started: Prodigal
[2023-06-19 00:58:12,543] [INFO] Running command: gunzip -c /var/lib/cwl/stg3de1b96b-e3eb-480b-a977-04957004879d/GCA_018651285.1_ASM1865128v1_genomic.fna.gz | prodigal -d GCA_018651285.1_ASM1865128v1_genomic.fna/cds.fna -a GCA_018651285.1_ASM1865128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:58:18,208] [INFO] Task succeeded: Prodigal
[2023-06-19 00:58:18,209] [INFO] Task started: HMMsearch
[2023-06-19 00:58:18,209] [INFO] Running command: hmmsearch --tblout GCA_018651285.1_ASM1865128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89771aec-693c-4b66-8817-f12c6d1ff539/dqc_reference/reference_markers.hmm GCA_018651285.1_ASM1865128v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:58:18,363] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:58:18,365] [INFO] Found 6/6 markers.
[2023-06-19 00:58:18,383] [INFO] Query marker FASTA was written to GCA_018651285.1_ASM1865128v1_genomic.fna/markers.fasta
[2023-06-19 00:58:18,384] [INFO] Task started: Blastn
[2023-06-19 00:58:18,384] [INFO] Running command: blastn -query GCA_018651285.1_ASM1865128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89771aec-693c-4b66-8817-f12c6d1ff539/dqc_reference/reference_markers.fasta -out GCA_018651285.1_ASM1865128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:58:18,963] [INFO] Task succeeded: Blastn
[2023-06-19 00:58:18,968] [INFO] Selected 32 target genomes.
[2023-06-19 00:58:18,968] [INFO] Target genome list was writen to GCA_018651285.1_ASM1865128v1_genomic.fna/target_genomes.txt
[2023-06-19 00:58:18,972] [INFO] Task started: fastANI
[2023-06-19 00:58:18,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg3de1b96b-e3eb-480b-a977-04957004879d/GCA_018651285.1_ASM1865128v1_genomic.fna.gz --refList GCA_018651285.1_ASM1865128v1_genomic.fna/target_genomes.txt --output GCA_018651285.1_ASM1865128v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:58:35,514] [INFO] Task succeeded: fastANI
[2023-06-19 00:58:35,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89771aec-693c-4b66-8817-f12c6d1ff539/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:58:35,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89771aec-693c-4b66-8817-f12c6d1ff539/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:58:35,516] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:58:35,516] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 00:58:35,517] [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
--------------------------------------------------------------------------------
[2023-06-19 00:58:35,520] [INFO] DFAST Taxonomy check result was written to GCA_018651285.1_ASM1865128v1_genomic.fna/tc_result.tsv
[2023-06-19 00:58:35,520] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:58:35,520] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:58:35,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89771aec-693c-4b66-8817-f12c6d1ff539/dqc_reference/checkm_data
[2023-06-19 00:58:35,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:58:35,544] [INFO] Task started: CheckM
[2023-06-19 00:58:35,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018651285.1_ASM1865128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018651285.1_ASM1865128v1_genomic.fna/checkm_input GCA_018651285.1_ASM1865128v1_genomic.fna/checkm_result
[2023-06-19 00:58:58,758] [INFO] Task succeeded: CheckM
[2023-06-19 00:58:58,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 17.99%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:58:58,794] [INFO] ===== Completeness check finished =====
[2023-06-19 00:58:58,794] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:58:58,794] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018651285.1_ASM1865128v1_genomic.fna/markers.fasta)
[2023-06-19 00:58:58,794] [INFO] Task started: Blastn
[2023-06-19 00:58:58,795] [INFO] Running command: blastn -query GCA_018651285.1_ASM1865128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89771aec-693c-4b66-8817-f12c6d1ff539/dqc_reference/reference_markers_gtdb.fasta -out GCA_018651285.1_ASM1865128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:58:59,658] [INFO] Task succeeded: Blastn
[2023-06-19 00:58:59,661] [INFO] Selected 16 target genomes.
[2023-06-19 00:58:59,661] [INFO] Target genome list was writen to GCA_018651285.1_ASM1865128v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:58:59,669] [INFO] Task started: fastANI
[2023-06-19 00:58:59,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg3de1b96b-e3eb-480b-a977-04957004879d/GCA_018651285.1_ASM1865128v1_genomic.fna.gz --refList GCA_018651285.1_ASM1865128v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018651285.1_ASM1865128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:59:06,730] [INFO] Task succeeded: fastANI
[2023-06-19 00:59:06,736] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:59:06,736] [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_003045825.1	s__UBA10364 sp003045825	97.6757	248	271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.67	96.47	0.88	0.80	20	conclusive
GCA_905478295.1	s__UBA10364 sp002387615	82.7749	225	271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.55	99.11	0.94	0.89	10	-
GCA_002685435.1	s__UBA10364 sp002685435	82.5682	170	271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402665.1	s__UBA10364 sp018402665	82.5448	220	271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	96.42	96.42	0.92	0.92	2	-
GCA_012269745.1	s__UBA10364 sp012269745	78.3022	61	271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:59:06,739] [INFO] GTDB search result was written to GCA_018651285.1_ASM1865128v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:59:06,739] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:59:06,741] [INFO] DFAST_QC result json was written to GCA_018651285.1_ASM1865128v1_genomic.fna/dqc_result.json
[2023-06-19 00:59:06,742] [INFO] DFAST_QC completed!
[2023-06-19 00:59:06,742] [INFO] Total running time: 0h0m56s