[2023-06-30 00:56:10,803] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:56:10,806] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:56:10,806] [INFO] DQC Reference Directory: /var/lib/cwl/stg71a40f65-0519-4387-ba60-25875fd923e7/dqc_reference
[2023-06-30 00:56:12,044] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:56:12,045] [INFO] Task started: Prodigal
[2023-06-30 00:56:12,045] [INFO] Running command: gunzip -c /var/lib/cwl/stgabaf5ab0-eadc-4b18-9839-787393abf269/GCA_019187565.1_ASM1918756v1_genomic.fna.gz | prodigal -d GCA_019187565.1_ASM1918756v1_genomic.fna/cds.fna -a GCA_019187565.1_ASM1918756v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:56:19,609] [INFO] Task succeeded: Prodigal
[2023-06-30 00:56:19,610] [INFO] Task started: HMMsearch
[2023-06-30 00:56:19,610] [INFO] Running command: hmmsearch --tblout GCA_019187565.1_ASM1918756v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71a40f65-0519-4387-ba60-25875fd923e7/dqc_reference/reference_markers.hmm GCA_019187565.1_ASM1918756v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:56:19,861] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:56:19,863] [INFO] Found 6/6 markers.
[2023-06-30 00:56:19,911] [INFO] Query marker FASTA was written to GCA_019187565.1_ASM1918756v1_genomic.fna/markers.fasta
[2023-06-30 00:56:19,911] [INFO] Task started: Blastn
[2023-06-30 00:56:19,911] [INFO] Running command: blastn -query GCA_019187565.1_ASM1918756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71a40f65-0519-4387-ba60-25875fd923e7/dqc_reference/reference_markers.fasta -out GCA_019187565.1_ASM1918756v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:56:20,486] [INFO] Task succeeded: Blastn
[2023-06-30 00:56:20,497] [INFO] Selected 20 target genomes.
[2023-06-30 00:56:20,498] [INFO] Target genome list was writen to GCA_019187565.1_ASM1918756v1_genomic.fna/target_genomes.txt
[2023-06-30 00:56:20,505] [INFO] Task started: fastANI
[2023-06-30 00:56:20,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgabaf5ab0-eadc-4b18-9839-787393abf269/GCA_019187565.1_ASM1918756v1_genomic.fna.gz --refList GCA_019187565.1_ASM1918756v1_genomic.fna/target_genomes.txt --output GCA_019187565.1_ASM1918756v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:56:29,914] [INFO] Task succeeded: fastANI
[2023-06-30 00:56:29,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71a40f65-0519-4387-ba60-25875fd923e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:56:29,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71a40f65-0519-4387-ba60-25875fd923e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:56:29,921] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:56:29,921] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:56:29,922] [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
Ignavibacterium album	strain=JCM 16511	GCA_000258405.1	591197	591197	type	True	76.2258	139	1315	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:56:29,924] [INFO] DFAST Taxonomy check result was written to GCA_019187565.1_ASM1918756v1_genomic.fna/tc_result.tsv
[2023-06-30 00:56:29,925] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:56:29,925] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:56:29,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71a40f65-0519-4387-ba60-25875fd923e7/dqc_reference/checkm_data
[2023-06-30 00:56:29,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:56:29,966] [INFO] Task started: CheckM
[2023-06-30 00:56:29,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019187565.1_ASM1918756v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019187565.1_ASM1918756v1_genomic.fna/checkm_input GCA_019187565.1_ASM1918756v1_genomic.fna/checkm_result
[2023-06-30 00:56:58,842] [INFO] Task succeeded: CheckM
[2023-06-30 00:56:58,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:56:58,867] [INFO] ===== Completeness check finished =====
[2023-06-30 00:56:58,867] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:56:58,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019187565.1_ASM1918756v1_genomic.fna/markers.fasta)
[2023-06-30 00:56:58,868] [INFO] Task started: Blastn
[2023-06-30 00:56:58,869] [INFO] Running command: blastn -query GCA_019187565.1_ASM1918756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71a40f65-0519-4387-ba60-25875fd923e7/dqc_reference/reference_markers_gtdb.fasta -out GCA_019187565.1_ASM1918756v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:56:59,697] [INFO] Task succeeded: Blastn
[2023-06-30 00:56:59,702] [INFO] Selected 12 target genomes.
[2023-06-30 00:56:59,702] [INFO] Target genome list was writen to GCA_019187565.1_ASM1918756v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:56:59,709] [INFO] Task started: fastANI
[2023-06-30 00:56:59,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgabaf5ab0-eadc-4b18-9839-787393abf269/GCA_019187565.1_ASM1918756v1_genomic.fna.gz --refList GCA_019187565.1_ASM1918756v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019187565.1_ASM1918756v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:57:07,556] [INFO] Task succeeded: fastANI
[2023-06-30 00:57:07,570] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 00:57:07,571] [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_013285405.1	s__IGN2 sp013285405	98.1979	1116	1315	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	99.60	98.20	0.96	0.86	8	conclusive
GCA_016716565.1	s__IGN2 sp016716565	79.6525	654	1315	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050295.1	s__IGN3 sp002050295	78.8007	211	1315	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	99.89	99.89	0.88	0.88	2	-
GCA_014860115.1	s__IGN2 sp014860115	78.4417	472	1315	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388525.1	s__IGN2 sp013388525	78.1083	377	1315	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001802865.1	s__RBG-16-34-14 sp001802865	76.5136	77	1315	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__RBG-16-34-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011329055.1	s__Ignavibacterium album_B	76.2497	120	1315	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__Ignavibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258405.1	s__Ignavibacterium album	76.2411	135	1315	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__Ignavibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042995.1	s__IGN2 sp013042995	76.1688	146	1315	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN2	95.0	99.79	99.74	0.93	0.91	5	-
GCA_011368355.1	s__Ignavibacterium album_A	76.1498	166	1315	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__Ignavibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:57:07,573] [INFO] GTDB search result was written to GCA_019187565.1_ASM1918756v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:57:07,573] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:57:07,576] [INFO] DFAST_QC result json was written to GCA_019187565.1_ASM1918756v1_genomic.fna/dqc_result.json
[2023-06-30 00:57:07,576] [INFO] DFAST_QC completed!
[2023-06-30 00:57:07,576] [INFO] Total running time: 0h0m57s