[2023-06-05 08:38:22,866] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:38:22,876] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:38:22,876] [INFO] DQC Reference Directory: /var/lib/cwl/stgccfb73c8-5830-49e5-8fda-989667c1052f/dqc_reference
[2023-06-05 08:38:24,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:38:24,423] [INFO] Task started: Prodigal
[2023-06-05 08:38:24,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg70ad3302-4080-4c2c-b520-4be2c55c991d/GCA_902524005.1_AG-337-C06_genomic.fna.gz | prodigal -d GCA_902524005.1_AG-337-C06_genomic.fna/cds.fna -a GCA_902524005.1_AG-337-C06_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:38:25,742] [INFO] Task succeeded: Prodigal
[2023-06-05 08:38:25,743] [INFO] Task started: HMMsearch
[2023-06-05 08:38:25,743] [INFO] Running command: hmmsearch --tblout GCA_902524005.1_AG-337-C06_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccfb73c8-5830-49e5-8fda-989667c1052f/dqc_reference/reference_markers.hmm GCA_902524005.1_AG-337-C06_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:38:25,905] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:38:25,906] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg70ad3302-4080-4c2c-b520-4be2c55c991d/GCA_902524005.1_AG-337-C06_genomic.fna.gz]
[2023-06-05 08:38:25,921] [INFO] Query marker FASTA was written to GCA_902524005.1_AG-337-C06_genomic.fna/markers.fasta
[2023-06-05 08:38:25,922] [INFO] Task started: Blastn
[2023-06-05 08:38:25,922] [INFO] Running command: blastn -query GCA_902524005.1_AG-337-C06_genomic.fna/markers.fasta -db /var/lib/cwl/stgccfb73c8-5830-49e5-8fda-989667c1052f/dqc_reference/reference_markers.fasta -out GCA_902524005.1_AG-337-C06_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:38:27,357] [INFO] Task succeeded: Blastn
[2023-06-05 08:38:27,362] [INFO] Selected 5 target genomes.
[2023-06-05 08:38:27,362] [INFO] Target genome list was writen to GCA_902524005.1_AG-337-C06_genomic.fna/target_genomes.txt
[2023-06-05 08:38:27,371] [INFO] Task started: fastANI
[2023-06-05 08:38:27,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ad3302-4080-4c2c-b520-4be2c55c991d/GCA_902524005.1_AG-337-C06_genomic.fna.gz --refList GCA_902524005.1_AG-337-C06_genomic.fna/target_genomes.txt --output GCA_902524005.1_AG-337-C06_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:38:29,148] [INFO] Task succeeded: fastANI
[2023-06-05 08:38:29,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccfb73c8-5830-49e5-8fda-989667c1052f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:38:29,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccfb73c8-5830-49e5-8fda-989667c1052f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:38:29,151] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:38:29,151] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 08:38:29,152] [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 08:38:29,154] [INFO] DFAST Taxonomy check result was written to GCA_902524005.1_AG-337-C06_genomic.fna/tc_result.tsv
[2023-06-05 08:38:29,155] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:38:29,155] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:38:29,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccfb73c8-5830-49e5-8fda-989667c1052f/dqc_reference/checkm_data
[2023-06-05 08:38:29,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:38:29,177] [INFO] Task started: CheckM
[2023-06-05 08:38:29,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902524005.1_AG-337-C06_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902524005.1_AG-337-C06_genomic.fna/checkm_input GCA_902524005.1_AG-337-C06_genomic.fna/checkm_result
[2023-06-05 08:38:42,063] [INFO] Task succeeded: CheckM
[2023-06-05 08:38:42,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 21.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:38:42,083] [INFO] ===== Completeness check finished =====
[2023-06-05 08:38:42,084] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:38:42,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902524005.1_AG-337-C06_genomic.fna/markers.fasta)
[2023-06-05 08:38:42,085] [INFO] Task started: Blastn
[2023-06-05 08:38:42,085] [INFO] Running command: blastn -query GCA_902524005.1_AG-337-C06_genomic.fna/markers.fasta -db /var/lib/cwl/stgccfb73c8-5830-49e5-8fda-989667c1052f/dqc_reference/reference_markers_gtdb.fasta -out GCA_902524005.1_AG-337-C06_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:38:42,671] [INFO] Task succeeded: Blastn
[2023-06-05 08:38:42,678] [INFO] Selected 8 target genomes.
[2023-06-05 08:38:42,678] [INFO] Target genome list was writen to GCA_902524005.1_AG-337-C06_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:38:42,682] [INFO] Task started: fastANI
[2023-06-05 08:38:42,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ad3302-4080-4c2c-b520-4be2c55c991d/GCA_902524005.1_AG-337-C06_genomic.fna.gz --refList GCA_902524005.1_AG-337-C06_genomic.fna/target_genomes_gtdb.txt --output GCA_902524005.1_AG-337-C06_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:38:45,118] [INFO] Task succeeded: fastANI
[2023-06-05 08:38:45,134] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 08:38:45,134] [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_902528415.1	s__AAA536-G10 sp902528415	92.5467	163	243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.26	95.26	0.64	0.64	2	-
GCA_003278095.1	s__AAA536-G10 sp003278095	92.1372	205	243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.84	95.67	0.90	0.81	3	-
GCA_003282435.1	s__AAA536-G10 sp003282435	91.8064	117	243	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_003283875.1	s__AAA536-G10 sp003283875	91.3321	132	243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.33	95.28	0.67	0.61	3	-
GCA_000384615.1	s__AAA536-G10 sp000384615	91.2327	196	243	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_003282885.1	s__AAA536-G10 sp003282885	91.1517	150	243	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	98.48	96.96	0.85	0.72	3	-
GCA_902514865.1	s__AAA536-G10 sp902514865	90.5522	110	243	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_000421325.1	s__AAA536-G10 sp000421325	86.0397	173	243	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 08:38:45,138] [INFO] GTDB search result was written to GCA_902524005.1_AG-337-C06_genomic.fna/result_gtdb.tsv
[2023-06-05 08:38:45,139] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:38:45,143] [INFO] DFAST_QC result json was written to GCA_902524005.1_AG-337-C06_genomic.fna/dqc_result.json
[2023-06-05 08:38:45,143] [INFO] DFAST_QC completed!
[2023-06-05 08:38:45,143] [INFO] Total running time: 0h0m22s