[2023-06-18 22:45:11,337] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:45:11,341] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:45:11,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg456074ef-c114-4d14-bb00-e15919630f49/dqc_reference
[2023-06-18 22:45:13,624] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:45:13,626] [INFO] Task started: Prodigal
[2023-06-18 22:45:13,626] [INFO] Running command: gunzip -c /var/lib/cwl/stg3844ad29-dad6-40aa-8ed0-4e629610542e/GCA_013813905.1_ASM1381390v1_genomic.fna.gz | prodigal -d GCA_013813905.1_ASM1381390v1_genomic.fna/cds.fna -a GCA_013813905.1_ASM1381390v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:45:20,842] [INFO] Task succeeded: Prodigal
[2023-06-18 22:45:20,842] [INFO] Task started: HMMsearch
[2023-06-18 22:45:20,843] [INFO] Running command: hmmsearch --tblout GCA_013813905.1_ASM1381390v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg456074ef-c114-4d14-bb00-e15919630f49/dqc_reference/reference_markers.hmm GCA_013813905.1_ASM1381390v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:45:21,015] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:45:21,017] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3844ad29-dad6-40aa-8ed0-4e629610542e/GCA_013813905.1_ASM1381390v1_genomic.fna.gz]
[2023-06-18 22:45:21,040] [INFO] Query marker FASTA was written to GCA_013813905.1_ASM1381390v1_genomic.fna/markers.fasta
[2023-06-18 22:45:21,041] [INFO] Task started: Blastn
[2023-06-18 22:45:21,041] [INFO] Running command: blastn -query GCA_013813905.1_ASM1381390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg456074ef-c114-4d14-bb00-e15919630f49/dqc_reference/reference_markers.fasta -out GCA_013813905.1_ASM1381390v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:45:21,588] [INFO] Task succeeded: Blastn
[2023-06-18 22:45:21,591] [INFO] Selected 5 target genomes.
[2023-06-18 22:45:21,592] [INFO] Target genome list was writen to GCA_013813905.1_ASM1381390v1_genomic.fna/target_genomes.txt
[2023-06-18 22:45:21,593] [INFO] Task started: fastANI
[2023-06-18 22:45:21,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg3844ad29-dad6-40aa-8ed0-4e629610542e/GCA_013813905.1_ASM1381390v1_genomic.fna.gz --refList GCA_013813905.1_ASM1381390v1_genomic.fna/target_genomes.txt --output GCA_013813905.1_ASM1381390v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:45:25,365] [INFO] Task succeeded: fastANI
[2023-06-18 22:45:25,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg456074ef-c114-4d14-bb00-e15919630f49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:45:25,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg456074ef-c114-4d14-bb00-e15919630f49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:45:25,368] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:45:25,369] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 22:45:25,369] [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 22:45:25,371] [INFO] DFAST Taxonomy check result was written to GCA_013813905.1_ASM1381390v1_genomic.fna/tc_result.tsv
[2023-06-18 22:45:25,371] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:45:25,371] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:45:25,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg456074ef-c114-4d14-bb00-e15919630f49/dqc_reference/checkm_data
[2023-06-18 22:45:25,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:45:25,394] [INFO] Task started: CheckM
[2023-06-18 22:45:25,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013813905.1_ASM1381390v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013813905.1_ASM1381390v1_genomic.fna/checkm_input GCA_013813905.1_ASM1381390v1_genomic.fna/checkm_result
[2023-06-18 22:45:45,694] [INFO] Task succeeded: CheckM
[2023-06-18 22:45:45,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:45:45,719] [INFO] ===== Completeness check finished =====
[2023-06-18 22:45:45,720] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:45:45,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013813905.1_ASM1381390v1_genomic.fna/markers.fasta)
[2023-06-18 22:45:45,720] [INFO] Task started: Blastn
[2023-06-18 22:45:45,721] [INFO] Running command: blastn -query GCA_013813905.1_ASM1381390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg456074ef-c114-4d14-bb00-e15919630f49/dqc_reference/reference_markers_gtdb.fasta -out GCA_013813905.1_ASM1381390v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:45:46,404] [INFO] Task succeeded: Blastn
[2023-06-18 22:45:46,408] [INFO] Selected 11 target genomes.
[2023-06-18 22:45:46,408] [INFO] Target genome list was writen to GCA_013813905.1_ASM1381390v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:45:46,412] [INFO] Task started: fastANI
[2023-06-18 22:45:46,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg3844ad29-dad6-40aa-8ed0-4e629610542e/GCA_013813905.1_ASM1381390v1_genomic.fna.gz --refList GCA_013813905.1_ASM1381390v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013813905.1_ASM1381390v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:45:50,561] [INFO] Task succeeded: fastANI
[2023-06-18 22:45:50,575] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:45:50,575] [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_013813905.1	s__Palsa-1032 sp013813905	100.0	344	346	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Palsa-1032	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003169735.1	s__Palsa-1032 sp003169735	77.9462	132	346	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Palsa-1032	95.0	99.71	99.69	0.92	0.92	3	-
GCA_001443375.1	s__CSP1-4 sp001443375	77.822	120	346	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CSP1-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696945.1	s__Palsa-1032 sp013696945	77.5317	79	346	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Palsa-1032	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694835.1	s__JACDBP01 sp013694835	77.2786	58	346	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__JACDBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881985.1	s__CTSoil-043 sp017881985	76.8644	58	346	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CTSoil-043	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781485.1	s__YB3-1 sp016781485	76.5235	59	346	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__YB3-1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 22:45:50,578] [INFO] GTDB search result was written to GCA_013813905.1_ASM1381390v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:45:50,578] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:45:50,582] [INFO] DFAST_QC result json was written to GCA_013813905.1_ASM1381390v1_genomic.fna/dqc_result.json
[2023-06-18 22:45:50,582] [INFO] DFAST_QC completed!
[2023-06-18 22:45:50,583] [INFO] Total running time: 0h0m39s