[2023-06-30 22:46:23,665] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:46:23,690] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:46:23,690] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fc7850f-e3fc-4a38-b6b8-3cd82eeaca91/dqc_reference
[2023-06-30 22:46:25,638] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:46:25,639] [INFO] Task started: Prodigal
[2023-06-30 22:46:25,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg564f9542-5083-47e5-a303-79cb44faa93c/GCA_016288405.1_ASM1628840v1_genomic.fna.gz | prodigal -d GCA_016288405.1_ASM1628840v1_genomic.fna/cds.fna -a GCA_016288405.1_ASM1628840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:46:29,588] [INFO] Task succeeded: Prodigal
[2023-06-30 22:46:29,589] [INFO] Task started: HMMsearch
[2023-06-30 22:46:29,589] [INFO] Running command: hmmsearch --tblout GCA_016288405.1_ASM1628840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fc7850f-e3fc-4a38-b6b8-3cd82eeaca91/dqc_reference/reference_markers.hmm GCA_016288405.1_ASM1628840v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:46:29,788] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:46:29,790] [INFO] Found 6/6 markers.
[2023-06-30 22:46:29,813] [INFO] Query marker FASTA was written to GCA_016288405.1_ASM1628840v1_genomic.fna/markers.fasta
[2023-06-30 22:46:29,814] [INFO] Task started: Blastn
[2023-06-30 22:46:29,814] [INFO] Running command: blastn -query GCA_016288405.1_ASM1628840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fc7850f-e3fc-4a38-b6b8-3cd82eeaca91/dqc_reference/reference_markers.fasta -out GCA_016288405.1_ASM1628840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:46:30,420] [INFO] Task succeeded: Blastn
[2023-06-30 22:46:30,425] [INFO] Selected 18 target genomes.
[2023-06-30 22:46:30,426] [INFO] Target genome list was writen to GCA_016288405.1_ASM1628840v1_genomic.fna/target_genomes.txt
[2023-06-30 22:46:30,434] [INFO] Task started: fastANI
[2023-06-30 22:46:30,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg564f9542-5083-47e5-a303-79cb44faa93c/GCA_016288405.1_ASM1628840v1_genomic.fna.gz --refList GCA_016288405.1_ASM1628840v1_genomic.fna/target_genomes.txt --output GCA_016288405.1_ASM1628840v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:46:42,135] [INFO] Task succeeded: fastANI
[2023-06-30 22:46:42,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fc7850f-e3fc-4a38-b6b8-3cd82eeaca91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:46:42,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fc7850f-e3fc-4a38-b6b8-3cd82eeaca91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:46:42,139] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:46:42,139] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 22:46:42,139] [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
--------------------------------------------------------------------------------
[2023-06-30 22:46:42,142] [INFO] DFAST Taxonomy check result was written to GCA_016288405.1_ASM1628840v1_genomic.fna/tc_result.tsv
[2023-06-30 22:46:42,142] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:46:42,143] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:46:42,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fc7850f-e3fc-4a38-b6b8-3cd82eeaca91/dqc_reference/checkm_data
[2023-06-30 22:46:42,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:46:42,172] [INFO] Task started: CheckM
[2023-06-30 22:46:42,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016288405.1_ASM1628840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016288405.1_ASM1628840v1_genomic.fna/checkm_input GCA_016288405.1_ASM1628840v1_genomic.fna/checkm_result
[2023-06-30 22:47:01,860] [INFO] Task succeeded: CheckM
[2023-06-30 22:47:01,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.52%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:47:01,894] [INFO] ===== Completeness check finished =====
[2023-06-30 22:47:01,895] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:47:01,895] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016288405.1_ASM1628840v1_genomic.fna/markers.fasta)
[2023-06-30 22:47:01,896] [INFO] Task started: Blastn
[2023-06-30 22:47:01,896] [INFO] Running command: blastn -query GCA_016288405.1_ASM1628840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fc7850f-e3fc-4a38-b6b8-3cd82eeaca91/dqc_reference/reference_markers_gtdb.fasta -out GCA_016288405.1_ASM1628840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:47:02,764] [INFO] Task succeeded: Blastn
[2023-06-30 22:47:02,769] [INFO] Selected 13 target genomes.
[2023-06-30 22:47:02,769] [INFO] Target genome list was writen to GCA_016288405.1_ASM1628840v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:47:02,821] [INFO] Task started: fastANI
[2023-06-30 22:47:02,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg564f9542-5083-47e5-a303-79cb44faa93c/GCA_016288405.1_ASM1628840v1_genomic.fna.gz --refList GCA_016288405.1_ASM1628840v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016288405.1_ASM1628840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:47:08,168] [INFO] Task succeeded: fastANI
[2023-06-30 22:47:08,179] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 22:47:08,179] [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_002309575.1	s__UBA1177 sp002309575	98.0486	466	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	97.91	97.60	0.87	0.84	4	conclusive
GCA_017615095.1	s__UBA1177 sp017615095	85.5359	338	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002310035.1	s__UBA1177 sp002310035	82.7836	157	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774115.1	s__UBA1177 sp902774115	81.1268	196	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	96.80	96.80	0.84	0.84	2	-
GCA_905233945.1	s__UBA1177 sp905233945	80.8443	196	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002310995.1	s__UBA1177 sp002310995	80.7556	159	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	99.84	99.84	0.93	0.93	2	-
GCA_017963125.1	s__UBA1177 sp017963125	80.7377	198	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780365.1	s__UBA1177 sp902780365	80.5717	159	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017405875.1	s__UBA1177 sp017405875	80.2661	166	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	97.50	97.50	0.88	0.88	2	-
GCA_017645765.1	s__UBA1177 sp017645765	80.196	193	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017961325.1	s__UBA1177 sp017961325	80.0491	166	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235605.1	s__UBA1177 sp905235605	79.3124	180	552	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	99.00	99.00	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-30 22:47:08,181] [INFO] GTDB search result was written to GCA_016288405.1_ASM1628840v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:47:08,182] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:47:08,185] [INFO] DFAST_QC result json was written to GCA_016288405.1_ASM1628840v1_genomic.fna/dqc_result.json
[2023-06-30 22:47:08,185] [INFO] DFAST_QC completed!
[2023-06-30 22:47:08,185] [INFO] Total running time: 0h0m45s