[2023-06-30 19:31:48,900] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:31:48,910] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:31:48,911] [INFO] DQC Reference Directory: /var/lib/cwl/stgacb7a942-df4c-481a-9d70-41ad76a4ff8d/dqc_reference
[2023-06-30 19:31:50,245] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:31:50,246] [INFO] Task started: Prodigal
[2023-06-30 19:31:50,246] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0a3ec65-3b6e-4163-9b15-bd3ed99c4fde/GCA_016866415.1_JGI_2017-08-21_genomic.fna.gz | prodigal -d GCA_016866415.1_JGI_2017-08-21_genomic.fna/cds.fna -a GCA_016866415.1_JGI_2017-08-21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:31:59,540] [INFO] Task succeeded: Prodigal
[2023-06-30 19:31:59,541] [INFO] Task started: HMMsearch
[2023-06-30 19:31:59,541] [INFO] Running command: hmmsearch --tblout GCA_016866415.1_JGI_2017-08-21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacb7a942-df4c-481a-9d70-41ad76a4ff8d/dqc_reference/reference_markers.hmm GCA_016866415.1_JGI_2017-08-21_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:31:59,824] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:31:59,825] [INFO] Found 6/6 markers.
[2023-06-30 19:31:59,851] [INFO] Query marker FASTA was written to GCA_016866415.1_JGI_2017-08-21_genomic.fna/markers.fasta
[2023-06-30 19:31:59,851] [INFO] Task started: Blastn
[2023-06-30 19:31:59,851] [INFO] Running command: blastn -query GCA_016866415.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stgacb7a942-df4c-481a-9d70-41ad76a4ff8d/dqc_reference/reference_markers.fasta -out GCA_016866415.1_JGI_2017-08-21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:32:00,471] [INFO] Task succeeded: Blastn
[2023-06-30 19:32:00,475] [INFO] Selected 33 target genomes.
[2023-06-30 19:32:00,476] [INFO] Target genome list was writen to GCA_016866415.1_JGI_2017-08-21_genomic.fna/target_genomes.txt
[2023-06-30 19:32:00,482] [INFO] Task started: fastANI
[2023-06-30 19:32:00,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0a3ec65-3b6e-4163-9b15-bd3ed99c4fde/GCA_016866415.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016866415.1_JGI_2017-08-21_genomic.fna/target_genomes.txt --output GCA_016866415.1_JGI_2017-08-21_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:32:22,481] [INFO] Task succeeded: fastANI
[2023-06-30 19:32:22,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacb7a942-df4c-481a-9d70-41ad76a4ff8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:32:22,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacb7a942-df4c-481a-9d70-41ad76a4ff8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:32:22,484] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:32:22,485] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 19:32:22,485] [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 19:32:22,490] [INFO] DFAST Taxonomy check result was written to GCA_016866415.1_JGI_2017-08-21_genomic.fna/tc_result.tsv
[2023-06-30 19:32:22,491] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:32:22,491] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:32:22,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacb7a942-df4c-481a-9d70-41ad76a4ff8d/dqc_reference/checkm_data
[2023-06-30 19:32:22,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:32:22,528] [INFO] Task started: CheckM
[2023-06-30 19:32:22,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016866415.1_JGI_2017-08-21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016866415.1_JGI_2017-08-21_genomic.fna/checkm_input GCA_016866415.1_JGI_2017-08-21_genomic.fna/checkm_result
[2023-06-30 19:32:55,548] [INFO] Task succeeded: CheckM
[2023-06-30 19:32:55,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:32:55,571] [INFO] ===== Completeness check finished =====
[2023-06-30 19:32:55,571] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:32:55,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016866415.1_JGI_2017-08-21_genomic.fna/markers.fasta)
[2023-06-30 19:32:55,572] [INFO] Task started: Blastn
[2023-06-30 19:32:55,572] [INFO] Running command: blastn -query GCA_016866415.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stgacb7a942-df4c-481a-9d70-41ad76a4ff8d/dqc_reference/reference_markers_gtdb.fasta -out GCA_016866415.1_JGI_2017-08-21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:32:56,465] [INFO] Task succeeded: Blastn
[2023-06-30 19:32:56,471] [INFO] Selected 26 target genomes.
[2023-06-30 19:32:56,471] [INFO] Target genome list was writen to GCA_016866415.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:32:56,483] [INFO] Task started: fastANI
[2023-06-30 19:32:56,483] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0a3ec65-3b6e-4163-9b15-bd3ed99c4fde/GCA_016866415.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016866415.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt --output GCA_016866415.1_JGI_2017-08-21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:33:08,372] [INFO] Task succeeded: fastANI
[2023-06-30 19:33:08,383] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:33:08,383] [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_016866415.1	s__UBA952 sp016866415	100.0	615	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016866375.1	s__UBA952 sp016866375	77.0904	65	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983465.1	s__UBA952 sp017983465	77.0788	63	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.99	99.99	0.99	0.99	2	-
GCA_903860985.1	s__UBA952 sp903860985	77.0203	57	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.77	99.68	0.93	0.92	3	-
GCA_018883325.1	s__UBA952 sp018883325	76.9875	125	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903935095.1	s__UBA952 sp903935095	76.7742	68	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.97	99.95	0.99	0.98	5	-
GCA_009926905.1	s__UBA952 sp009926905	76.553	73	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178305.1	s__CAIUKX01 sp016178305	75.9838	55	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 19:33:08,385] [INFO] GTDB search result was written to GCA_016866415.1_JGI_2017-08-21_genomic.fna/result_gtdb.tsv
[2023-06-30 19:33:08,386] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:33:08,389] [INFO] DFAST_QC result json was written to GCA_016866415.1_JGI_2017-08-21_genomic.fna/dqc_result.json
[2023-06-30 19:33:08,389] [INFO] DFAST_QC completed!
[2023-06-30 19:33:08,389] [INFO] Total running time: 0h1m19s