[2023-06-08 13:51:46,585] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:51:46,589] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:51:46,590] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9f4c08f-a379-415f-96bc-25801bde8a88/dqc_reference
[2023-06-08 13:51:47,997] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:51:47,998] [INFO] Task started: Prodigal
[2023-06-08 13:51:47,998] [INFO] Running command: gunzip -c /var/lib/cwl/stg4646abf3-0647-4290-81bb-8a63afdb4ac2/GCA_945902885.1_MiH-16apr19-390_genomic.fna.gz | prodigal -d GCA_945902885.1_MiH-16apr19-390_genomic.fna/cds.fna -a GCA_945902885.1_MiH-16apr19-390_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:51:55,864] [INFO] Task succeeded: Prodigal
[2023-06-08 13:51:55,864] [INFO] Task started: HMMsearch
[2023-06-08 13:51:55,865] [INFO] Running command: hmmsearch --tblout GCA_945902885.1_MiH-16apr19-390_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9f4c08f-a379-415f-96bc-25801bde8a88/dqc_reference/reference_markers.hmm GCA_945902885.1_MiH-16apr19-390_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:51:56,079] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:51:56,080] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4646abf3-0647-4290-81bb-8a63afdb4ac2/GCA_945902885.1_MiH-16apr19-390_genomic.fna.gz]
[2023-06-08 13:51:56,117] [INFO] Query marker FASTA was written to GCA_945902885.1_MiH-16apr19-390_genomic.fna/markers.fasta
[2023-06-08 13:51:56,117] [INFO] Task started: Blastn
[2023-06-08 13:51:56,117] [INFO] Running command: blastn -query GCA_945902885.1_MiH-16apr19-390_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9f4c08f-a379-415f-96bc-25801bde8a88/dqc_reference/reference_markers.fasta -out GCA_945902885.1_MiH-16apr19-390_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:51:56,710] [INFO] Task succeeded: Blastn
[2023-06-08 13:51:56,714] [INFO] Selected 35 target genomes.
[2023-06-08 13:51:56,714] [INFO] Target genome list was writen to GCA_945902885.1_MiH-16apr19-390_genomic.fna/target_genomes.txt
[2023-06-08 13:51:56,716] [INFO] Task started: fastANI
[2023-06-08 13:51:56,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg4646abf3-0647-4290-81bb-8a63afdb4ac2/GCA_945902885.1_MiH-16apr19-390_genomic.fna.gz --refList GCA_945902885.1_MiH-16apr19-390_genomic.fna/target_genomes.txt --output GCA_945902885.1_MiH-16apr19-390_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:52:15,438] [INFO] Task succeeded: fastANI
[2023-06-08 13:52:15,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9f4c08f-a379-415f-96bc-25801bde8a88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:52:15,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9f4c08f-a379-415f-96bc-25801bde8a88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:52:15,440] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:52:15,441] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 13:52:15,441] [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
--------------------------------------------------------------------------------
[2023-06-08 13:52:15,443] [INFO] DFAST Taxonomy check result was written to GCA_945902885.1_MiH-16apr19-390_genomic.fna/tc_result.tsv
[2023-06-08 13:52:15,443] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:52:15,443] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:52:15,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9f4c08f-a379-415f-96bc-25801bde8a88/dqc_reference/checkm_data
[2023-06-08 13:52:15,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:52:15,475] [INFO] Task started: CheckM
[2023-06-08 13:52:15,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945902885.1_MiH-16apr19-390_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945902885.1_MiH-16apr19-390_genomic.fna/checkm_input GCA_945902885.1_MiH-16apr19-390_genomic.fna/checkm_result
[2023-06-08 13:52:42,833] [INFO] Task succeeded: CheckM
[2023-06-08 13:52:42,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 13:52:42,854] [INFO] ===== Completeness check finished =====
[2023-06-08 13:52:42,854] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:52:42,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945902885.1_MiH-16apr19-390_genomic.fna/markers.fasta)
[2023-06-08 13:52:42,855] [INFO] Task started: Blastn
[2023-06-08 13:52:42,855] [INFO] Running command: blastn -query GCA_945902885.1_MiH-16apr19-390_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9f4c08f-a379-415f-96bc-25801bde8a88/dqc_reference/reference_markers_gtdb.fasta -out GCA_945902885.1_MiH-16apr19-390_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:52:43,648] [INFO] Task succeeded: Blastn
[2023-06-08 13:52:43,653] [INFO] Selected 8 target genomes.
[2023-06-08 13:52:43,653] [INFO] Target genome list was writen to GCA_945902885.1_MiH-16apr19-390_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:52:43,658] [INFO] Task started: fastANI
[2023-06-08 13:52:43,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg4646abf3-0647-4290-81bb-8a63afdb4ac2/GCA_945902885.1_MiH-16apr19-390_genomic.fna.gz --refList GCA_945902885.1_MiH-16apr19-390_genomic.fna/target_genomes_gtdb.txt --output GCA_945902885.1_MiH-16apr19-390_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:52:49,030] [INFO] Task succeeded: fastANI
[2023-06-08 13:52:49,039] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:52:49,039] [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_903893815.1	s__UBA4416 sp903893815	97.3694	681	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	97.38	96.70	0.85	0.80	6	conclusive
GCA_005800865.1	s__UBA4416 sp005800865	92.3998	430	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708845.1	s__UBA4416 sp016708845	91.9129	604	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711805.1	s__UBA4416 sp016711805	90.4962	633	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002420145.1	s__UBA4416 sp002420145	81.7664	486	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823565.1	s__UBA4416 sp013823565	81.4696	501	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787365.1	s__UBA4416 sp016787365	81.1094	332	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928655.1	s__UBA4416 sp903928655	78.5305	241	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 13:52:49,041] [INFO] GTDB search result was written to GCA_945902885.1_MiH-16apr19-390_genomic.fna/result_gtdb.tsv
[2023-06-08 13:52:49,041] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:52:49,044] [INFO] DFAST_QC result json was written to GCA_945902885.1_MiH-16apr19-390_genomic.fna/dqc_result.json
[2023-06-08 13:52:49,044] [INFO] DFAST_QC completed!
[2023-06-08 13:52:49,044] [INFO] Total running time: 0h1m2s