[2023-06-29 09:02:46,255] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:02:46,266] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:02:46,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e6df41f-882f-4115-9be6-8d3f298b80d2/dqc_reference
[2023-06-29 09:02:47,557] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:02:47,558] [INFO] Task started: Prodigal
[2023-06-29 09:02:47,558] [INFO] Running command: gunzip -c /var/lib/cwl/stg77a9533d-32e5-4082-8e3c-18c781e512b1/GCA_020852225.1_ASM2085222v1_genomic.fna.gz | prodigal -d GCA_020852225.1_ASM2085222v1_genomic.fna/cds.fna -a GCA_020852225.1_ASM2085222v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:03:08,145] [INFO] Task succeeded: Prodigal
[2023-06-29 09:03:08,146] [INFO] Task started: HMMsearch
[2023-06-29 09:03:08,146] [INFO] Running command: hmmsearch --tblout GCA_020852225.1_ASM2085222v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e6df41f-882f-4115-9be6-8d3f298b80d2/dqc_reference/reference_markers.hmm GCA_020852225.1_ASM2085222v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:03:08,457] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:03:08,458] [INFO] Found 6/6 markers.
[2023-06-29 09:03:08,495] [INFO] Query marker FASTA was written to GCA_020852225.1_ASM2085222v1_genomic.fna/markers.fasta
[2023-06-29 09:03:08,495] [INFO] Task started: Blastn
[2023-06-29 09:03:08,496] [INFO] Running command: blastn -query GCA_020852225.1_ASM2085222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e6df41f-882f-4115-9be6-8d3f298b80d2/dqc_reference/reference_markers.fasta -out GCA_020852225.1_ASM2085222v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:03:09,079] [INFO] Task succeeded: Blastn
[2023-06-29 09:03:09,084] [INFO] Selected 26 target genomes.
[2023-06-29 09:03:09,085] [INFO] Target genome list was writen to GCA_020852225.1_ASM2085222v1_genomic.fna/target_genomes.txt
[2023-06-29 09:03:09,114] [INFO] Task started: fastANI
[2023-06-29 09:03:09,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a9533d-32e5-4082-8e3c-18c781e512b1/GCA_020852225.1_ASM2085222v1_genomic.fna.gz --refList GCA_020852225.1_ASM2085222v1_genomic.fna/target_genomes.txt --output GCA_020852225.1_ASM2085222v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:03:31,408] [INFO] Task succeeded: fastANI
[2023-06-29 09:03:31,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e6df41f-882f-4115-9be6-8d3f298b80d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:03:31,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e6df41f-882f-4115-9be6-8d3f298b80d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:03:31,411] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:03:31,411] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 09:03:31,412] [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
--------------------------------------------------------------------------------
[2023-06-29 09:03:31,414] [INFO] DFAST Taxonomy check result was written to GCA_020852225.1_ASM2085222v1_genomic.fna/tc_result.tsv
[2023-06-29 09:03:31,417] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:03:31,417] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:03:31,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e6df41f-882f-4115-9be6-8d3f298b80d2/dqc_reference/checkm_data
[2023-06-29 09:03:31,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:03:31,467] [INFO] Task started: CheckM
[2023-06-29 09:03:31,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020852225.1_ASM2085222v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020852225.1_ASM2085222v1_genomic.fna/checkm_input GCA_020852225.1_ASM2085222v1_genomic.fna/checkm_result
[2023-06-29 09:04:27,589] [INFO] Task succeeded: CheckM
[2023-06-29 09:04:27,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:04:27,617] [INFO] ===== Completeness check finished =====
[2023-06-29 09:04:27,617] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:04:27,617] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020852225.1_ASM2085222v1_genomic.fna/markers.fasta)
[2023-06-29 09:04:27,618] [INFO] Task started: Blastn
[2023-06-29 09:04:27,618] [INFO] Running command: blastn -query GCA_020852225.1_ASM2085222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e6df41f-882f-4115-9be6-8d3f298b80d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_020852225.1_ASM2085222v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:04:28,323] [INFO] Task succeeded: Blastn
[2023-06-29 09:04:28,329] [INFO] Selected 28 target genomes.
[2023-06-29 09:04:28,329] [INFO] Target genome list was writen to GCA_020852225.1_ASM2085222v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:04:28,343] [INFO] Task started: fastANI
[2023-06-29 09:04:28,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a9533d-32e5-4082-8e3c-18c781e512b1/GCA_020852225.1_ASM2085222v1_genomic.fna.gz --refList GCA_020852225.1_ASM2085222v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020852225.1_ASM2085222v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:04:51,281] [INFO] Task succeeded: fastANI
[2023-06-29 09:04:51,288] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 09:04:51,288] [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_016711295.1	s__JADJTE01 sp016711295	99.3412	1214	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__UBA2359;g__JADJTE01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016718845.1	s__JAEUUX01 sp016718845	75.2561	88	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__UBA2359;g__JAEUUX01	95.0	98.81	98.81	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-29 09:04:51,290] [INFO] GTDB search result was written to GCA_020852225.1_ASM2085222v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:04:51,291] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:04:51,293] [INFO] DFAST_QC result json was written to GCA_020852225.1_ASM2085222v1_genomic.fna/dqc_result.json
[2023-06-29 09:04:51,293] [INFO] DFAST_QC completed!
[2023-06-29 09:04:51,293] [INFO] Total running time: 0h2m5s