[2023-06-05 09:37:29,472] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:37:29,484] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:37:29,484] [INFO] DQC Reference Directory: /var/lib/cwl/stg321a5b1e-2d2b-4fa4-8340-3c6403bc8b78/dqc_reference
[2023-06-05 09:37:31,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:37:31,896] [INFO] Task started: Prodigal
[2023-06-05 09:37:31,896] [INFO] Running command: gunzip -c /var/lib/cwl/stg0226206e-9055-4727-8237-091cd859e239/GCA_902525895.1_AG-895-P14_genomic.fna.gz | prodigal -d GCA_902525895.1_AG-895-P14_genomic.fna/cds.fna -a GCA_902525895.1_AG-895-P14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:37:34,330] [INFO] Task succeeded: Prodigal
[2023-06-05 09:37:34,330] [INFO] Task started: HMMsearch
[2023-06-05 09:37:34,331] [INFO] Running command: hmmsearch --tblout GCA_902525895.1_AG-895-P14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg321a5b1e-2d2b-4fa4-8340-3c6403bc8b78/dqc_reference/reference_markers.hmm GCA_902525895.1_AG-895-P14_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:37:34,548] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:37:34,550] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0226206e-9055-4727-8237-091cd859e239/GCA_902525895.1_AG-895-P14_genomic.fna.gz]
[2023-06-05 09:37:34,573] [INFO] Query marker FASTA was written to GCA_902525895.1_AG-895-P14_genomic.fna/markers.fasta
[2023-06-05 09:37:34,574] [INFO] Task started: Blastn
[2023-06-05 09:37:34,574] [INFO] Running command: blastn -query GCA_902525895.1_AG-895-P14_genomic.fna/markers.fasta -db /var/lib/cwl/stg321a5b1e-2d2b-4fa4-8340-3c6403bc8b78/dqc_reference/reference_markers.fasta -out GCA_902525895.1_AG-895-P14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:37:36,281] [INFO] Task succeeded: Blastn
[2023-06-05 09:37:36,286] [INFO] Selected 15 target genomes.
[2023-06-05 09:37:36,287] [INFO] Target genome list was writen to GCA_902525895.1_AG-895-P14_genomic.fna/target_genomes.txt
[2023-06-05 09:37:36,297] [INFO] Task started: fastANI
[2023-06-05 09:37:36,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg0226206e-9055-4727-8237-091cd859e239/GCA_902525895.1_AG-895-P14_genomic.fna.gz --refList GCA_902525895.1_AG-895-P14_genomic.fna/target_genomes.txt --output GCA_902525895.1_AG-895-P14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:37:42,237] [INFO] Task succeeded: fastANI
[2023-06-05 09:37:42,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg321a5b1e-2d2b-4fa4-8340-3c6403bc8b78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:37:42,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg321a5b1e-2d2b-4fa4-8340-3c6403bc8b78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:37:42,240] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:37:42,240] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 09:37:42,241] [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
--------------------------------------------------------------------------------
[2023-06-05 09:37:42,243] [INFO] DFAST Taxonomy check result was written to GCA_902525895.1_AG-895-P14_genomic.fna/tc_result.tsv
[2023-06-05 09:37:42,243] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:37:42,243] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:37:42,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg321a5b1e-2d2b-4fa4-8340-3c6403bc8b78/dqc_reference/checkm_data
[2023-06-05 09:37:42,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:37:42,268] [INFO] Task started: CheckM
[2023-06-05 09:37:42,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902525895.1_AG-895-P14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902525895.1_AG-895-P14_genomic.fna/checkm_input GCA_902525895.1_AG-895-P14_genomic.fna/checkm_result
[2023-06-05 09:37:57,600] [INFO] Task succeeded: CheckM
[2023-06-05 09:37:57,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:37:57,629] [INFO] ===== Completeness check finished =====
[2023-06-05 09:37:57,629] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:37:57,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902525895.1_AG-895-P14_genomic.fna/markers.fasta)
[2023-06-05 09:37:57,630] [INFO] Task started: Blastn
[2023-06-05 09:37:57,630] [INFO] Running command: blastn -query GCA_902525895.1_AG-895-P14_genomic.fna/markers.fasta -db /var/lib/cwl/stg321a5b1e-2d2b-4fa4-8340-3c6403bc8b78/dqc_reference/reference_markers_gtdb.fasta -out GCA_902525895.1_AG-895-P14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:37:58,515] [INFO] Task succeeded: Blastn
[2023-06-05 09:37:58,519] [INFO] Selected 14 target genomes.
[2023-06-05 09:37:58,519] [INFO] Target genome list was writen to GCA_902525895.1_AG-895-P14_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:37:58,520] [INFO] Task started: fastANI
[2023-06-05 09:37:58,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg0226206e-9055-4727-8237-091cd859e239/GCA_902525895.1_AG-895-P14_genomic.fna.gz --refList GCA_902525895.1_AG-895-P14_genomic.fna/target_genomes_gtdb.txt --output GCA_902525895.1_AG-895-P14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:38:02,985] [INFO] Task succeeded: fastANI
[2023-06-05 09:38:03,000] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:38:03,001] [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_902543145.1	s__AAA536-G10 sp902543145	99.7285	386	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	99.74	99.74	0.81	0.81	2	conclusive
GCA_902619485.1	s__AAA536-G10 sp902619485	94.1479	291	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529515.1	s__AAA536-G10 sp902529515	93.7147	239	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.18	97.18	0.52	0.52	2	-
GCA_902539895.1	s__AAA536-G10 sp902539895	93.5248	247	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902542765.1	s__AAA536-G10 sp902542765	93.2356	194	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619805.1	s__AAA536-G10 sp902619805	92.4368	374	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517815.1	s__AAA536-G10 sp902517815	91.9651	356	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623995.1	s__AAA536-G10 sp902623995	91.2128	393	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	98.83	98.83	0.84	0.84	2	-
GCA_902595145.1	s__AAA536-G10 sp902595145	91.0459	255	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589185.1	s__AAA536-G10 sp902589185	90.7762	260	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583415.1	s__AAA536-G10 sp902583415	90.6907	266	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592615.1	s__AAA536-G10 sp902592615	89.7419	304	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558885.1	s__AAA536-G10 sp902558885	89.2799	290	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578805.1	s__AAA536-G10 sp902578805	88.6201	283	478	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 09:38:03,002] [INFO] GTDB search result was written to GCA_902525895.1_AG-895-P14_genomic.fna/result_gtdb.tsv
[2023-06-05 09:38:03,003] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:38:03,006] [INFO] DFAST_QC result json was written to GCA_902525895.1_AG-895-P14_genomic.fna/dqc_result.json
[2023-06-05 09:38:03,006] [INFO] DFAST_QC completed!
[2023-06-05 09:38:03,006] [INFO] Total running time: 0h0m34s