[2023-06-29 09:20:16,492] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:20:16,495] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:20:16,496] [INFO] DQC Reference Directory: /var/lib/cwl/stg061364e0-af22-443d-a6e0-c62d24d42534/dqc_reference
[2023-06-29 09:20:17,722] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:20:17,723] [INFO] Task started: Prodigal
[2023-06-29 09:20:17,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ac2c3f3-ff0b-48e4-8db8-798607cd585a/GCA_020056285.1_ASM2005628v1_genomic.fna.gz | prodigal -d GCA_020056285.1_ASM2005628v1_genomic.fna/cds.fna -a GCA_020056285.1_ASM2005628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:20:20,913] [INFO] Task succeeded: Prodigal
[2023-06-29 09:20:20,913] [INFO] Task started: HMMsearch
[2023-06-29 09:20:20,913] [INFO] Running command: hmmsearch --tblout GCA_020056285.1_ASM2005628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg061364e0-af22-443d-a6e0-c62d24d42534/dqc_reference/reference_markers.hmm GCA_020056285.1_ASM2005628v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:20:21,102] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:20:21,103] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4ac2c3f3-ff0b-48e4-8db8-798607cd585a/GCA_020056285.1_ASM2005628v1_genomic.fna.gz]
[2023-06-29 09:20:21,121] [INFO] Query marker FASTA was written to GCA_020056285.1_ASM2005628v1_genomic.fna/markers.fasta
[2023-06-29 09:20:21,121] [INFO] Task started: Blastn
[2023-06-29 09:20:21,121] [INFO] Running command: blastn -query GCA_020056285.1_ASM2005628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg061364e0-af22-443d-a6e0-c62d24d42534/dqc_reference/reference_markers.fasta -out GCA_020056285.1_ASM2005628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:20:23,335] [INFO] Task succeeded: Blastn
[2023-06-29 09:20:23,355] [INFO] Selected 5 target genomes.
[2023-06-29 09:20:23,356] [INFO] Target genome list was writen to GCA_020056285.1_ASM2005628v1_genomic.fna/target_genomes.txt
[2023-06-29 09:20:23,390] [INFO] Task started: fastANI
[2023-06-29 09:20:23,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ac2c3f3-ff0b-48e4-8db8-798607cd585a/GCA_020056285.1_ASM2005628v1_genomic.fna.gz --refList GCA_020056285.1_ASM2005628v1_genomic.fna/target_genomes.txt --output GCA_020056285.1_ASM2005628v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:20:28,071] [INFO] Task succeeded: fastANI
[2023-06-29 09:20:28,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg061364e0-af22-443d-a6e0-c62d24d42534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:20:28,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg061364e0-af22-443d-a6e0-c62d24d42534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:20:28,074] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:20:28,074] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 09:20:28,074] [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 09:20:28,077] [INFO] DFAST Taxonomy check result was written to GCA_020056285.1_ASM2005628v1_genomic.fna/tc_result.tsv
[2023-06-29 09:20:28,078] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:20:28,078] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:20:28,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg061364e0-af22-443d-a6e0-c62d24d42534/dqc_reference/checkm_data
[2023-06-29 09:20:28,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:20:28,101] [INFO] Task started: CheckM
[2023-06-29 09:20:28,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020056285.1_ASM2005628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020056285.1_ASM2005628v1_genomic.fna/checkm_input GCA_020056285.1_ASM2005628v1_genomic.fna/checkm_result
[2023-06-29 09:20:45,670] [INFO] Task succeeded: CheckM
[2023-06-29 09:20:45,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.12%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:20:45,693] [INFO] ===== Completeness check finished =====
[2023-06-29 09:20:45,693] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:20:45,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020056285.1_ASM2005628v1_genomic.fna/markers.fasta)
[2023-06-29 09:20:45,694] [INFO] Task started: Blastn
[2023-06-29 09:20:45,694] [INFO] Running command: blastn -query GCA_020056285.1_ASM2005628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg061364e0-af22-443d-a6e0-c62d24d42534/dqc_reference/reference_markers_gtdb.fasta -out GCA_020056285.1_ASM2005628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:20:46,207] [INFO] Task succeeded: Blastn
[2023-06-29 09:20:46,211] [INFO] Selected 6 target genomes.
[2023-06-29 09:20:46,212] [INFO] Target genome list was writen to GCA_020056285.1_ASM2005628v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:20:46,219] [INFO] Task started: fastANI
[2023-06-29 09:20:46,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ac2c3f3-ff0b-48e4-8db8-798607cd585a/GCA_020056285.1_ASM2005628v1_genomic.fna.gz --refList GCA_020056285.1_ASM2005628v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020056285.1_ASM2005628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:20:48,075] [INFO] Task succeeded: fastANI
[2023-06-29 09:20:48,081] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:20:48,081] [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_018814355.1	s__COMBO-56-21 sp018814355	80.1641	129	305	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA10834;f__UBA10834;g__COMBO-56-21	95.0	99.71	99.71	0.97	0.97	2	-
GCA_001800675.1	s__COMBO-56-21 sp001800675	77.9461	71	305	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA10834;f__UBA10834;g__COMBO-56-21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013329135.1	s__UBA9653 sp9653u	77.3297	59	305	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA10834;f__UBA10834;g__UBA9653	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016930135.1	s__COMBO-56-21 sp016930135	77.1644	74	305	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA10834;f__UBA10834;g__COMBO-56-21	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 09:20:48,084] [INFO] GTDB search result was written to GCA_020056285.1_ASM2005628v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:20:48,085] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:20:48,087] [INFO] DFAST_QC result json was written to GCA_020056285.1_ASM2005628v1_genomic.fna/dqc_result.json
[2023-06-29 09:20:48,088] [INFO] DFAST_QC completed!
[2023-06-29 09:20:48,088] [INFO] Total running time: 0h0m32s