[2023-06-18 13:03:41,775] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:03:41,777] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:03:41,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg9803f758-5a14-4fd3-a53b-efd0a1bba38b/dqc_reference
[2023-06-18 13:03:42,984] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:03:42,985] [INFO] Task started: Prodigal
[2023-06-18 13:03:42,985] [INFO] Running command: gunzip -c /var/lib/cwl/stgd09122a3-9296-4508-99da-a5809da07bf2/GCA_018901175.1_ASM1890117v1_genomic.fna.gz | prodigal -d GCA_018901175.1_ASM1890117v1_genomic.fna/cds.fna -a GCA_018901175.1_ASM1890117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:03:47,374] [INFO] Task succeeded: Prodigal
[2023-06-18 13:03:47,374] [INFO] Task started: HMMsearch
[2023-06-18 13:03:47,374] [INFO] Running command: hmmsearch --tblout GCA_018901175.1_ASM1890117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9803f758-5a14-4fd3-a53b-efd0a1bba38b/dqc_reference/reference_markers.hmm GCA_018901175.1_ASM1890117v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:03:47,556] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:03:47,559] [INFO] Found 6/6 markers.
[2023-06-18 13:03:47,586] [INFO] Query marker FASTA was written to GCA_018901175.1_ASM1890117v1_genomic.fna/markers.fasta
[2023-06-18 13:03:47,587] [INFO] Task started: Blastn
[2023-06-18 13:03:47,587] [INFO] Running command: blastn -query GCA_018901175.1_ASM1890117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9803f758-5a14-4fd3-a53b-efd0a1bba38b/dqc_reference/reference_markers.fasta -out GCA_018901175.1_ASM1890117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:03:48,153] [INFO] Task succeeded: Blastn
[2023-06-18 13:03:48,159] [INFO] Selected 20 target genomes.
[2023-06-18 13:03:48,159] [INFO] Target genome list was writen to GCA_018901175.1_ASM1890117v1_genomic.fna/target_genomes.txt
[2023-06-18 13:03:48,163] [INFO] Task started: fastANI
[2023-06-18 13:03:48,163] [INFO] Running command: fastANI --query /var/lib/cwl/stgd09122a3-9296-4508-99da-a5809da07bf2/GCA_018901175.1_ASM1890117v1_genomic.fna.gz --refList GCA_018901175.1_ASM1890117v1_genomic.fna/target_genomes.txt --output GCA_018901175.1_ASM1890117v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:04:00,445] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:00,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9803f758-5a14-4fd3-a53b-efd0a1bba38b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:04:00,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9803f758-5a14-4fd3-a53b-efd0a1bba38b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:04:00,447] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:04:00,447] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 13:04:00,447] [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
--------------------------------------------------------------------------------
[2023-06-18 13:04:00,452] [INFO] DFAST Taxonomy check result was written to GCA_018901175.1_ASM1890117v1_genomic.fna/tc_result.tsv
[2023-06-18 13:04:00,452] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:04:00,453] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:04:00,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9803f758-5a14-4fd3-a53b-efd0a1bba38b/dqc_reference/checkm_data
[2023-06-18 13:04:00,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:04:00,479] [INFO] Task started: CheckM
[2023-06-18 13:04:00,479] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018901175.1_ASM1890117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018901175.1_ASM1890117v1_genomic.fna/checkm_input GCA_018901175.1_ASM1890117v1_genomic.fna/checkm_result
[2023-06-18 13:04:19,957] [INFO] Task succeeded: CheckM
[2023-06-18 13:04:19,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:04:19,990] [INFO] ===== Completeness check finished =====
[2023-06-18 13:04:19,991] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:04:19,991] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018901175.1_ASM1890117v1_genomic.fna/markers.fasta)
[2023-06-18 13:04:19,991] [INFO] Task started: Blastn
[2023-06-18 13:04:19,991] [INFO] Running command: blastn -query GCA_018901175.1_ASM1890117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9803f758-5a14-4fd3-a53b-efd0a1bba38b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018901175.1_ASM1890117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:04:20,768] [INFO] Task succeeded: Blastn
[2023-06-18 13:04:20,777] [INFO] Selected 10 target genomes.
[2023-06-18 13:04:20,777] [INFO] Target genome list was writen to GCA_018901175.1_ASM1890117v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:04:20,782] [INFO] Task started: fastANI
[2023-06-18 13:04:20,783] [INFO] Running command: fastANI --query /var/lib/cwl/stgd09122a3-9296-4508-99da-a5809da07bf2/GCA_018901175.1_ASM1890117v1_genomic.fna.gz --refList GCA_018901175.1_ASM1890117v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018901175.1_ASM1890117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:04:25,649] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:25,658] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:04:25,658] [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_018819165.1	s__UBA5619 sp018819165	97.459	300	486	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA5619;g__UBA5619	95.0	97.52	97.46	0.68	0.68	4	conclusive
GCA_001830835.1	s__UBA5619 sp001830835	94.5799	373	486	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA5619;g__UBA5619	95.0	99.43	99.43	0.87	0.84	3	-
GCA_018827585.1	s__UBA5619 sp018827585	84.0177	325	486	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA5619;g__UBA5619	95.0	99.31	99.28	0.84	0.83	3	-
GCA_003141195.1	s__UBA5619 sp003141195	81.7953	285	486	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA5619;g__UBA5619	95.0	99.85	99.82	0.92	0.88	5	-
GCA_018896355.1	s__UBA5619 sp018896355	81.3113	253	486	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA5619;g__UBA5619	95.0	97.97	97.39	0.78	0.72	5	-
GCA_001873745.1	s__UBA5619 sp001873745	80.9903	274	486	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA5619;g__UBA5619	95.0	99.43	99.33	0.83	0.81	3	-
GCA_013824905.1	s__UBA5619 sp013824905	79.78	203	486	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA5619;g__UBA5619	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935075.1	s__UBA5619 sp016935075	79.7691	197	486	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA5619;g__UBA5619	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002424545.1	s__UBA5619 sp002424545	78.6658	184	486	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA5619;g__UBA5619	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 13:04:25,662] [INFO] GTDB search result was written to GCA_018901175.1_ASM1890117v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:04:25,665] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:04:25,668] [INFO] DFAST_QC result json was written to GCA_018901175.1_ASM1890117v1_genomic.fna/dqc_result.json
[2023-06-18 13:04:25,668] [INFO] DFAST_QC completed!
[2023-06-18 13:04:25,669] [INFO] Total running time: 0h0m44s