[2023-06-19 09:52:27,670] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:52:27,674] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:52:27,674] [INFO] DQC Reference Directory: /var/lib/cwl/stg689061a1-8b16-4ea7-aca6-ef5356d87474/dqc_reference
[2023-06-19 09:52:29,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:52:29,102] [INFO] Task started: Prodigal
[2023-06-19 09:52:29,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg32789055-4aeb-4036-ba1c-933d83d12dcb/GCA_013202445.1_ASM1320244v1_genomic.fna.gz | prodigal -d GCA_013202445.1_ASM1320244v1_genomic.fna/cds.fna -a GCA_013202445.1_ASM1320244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:52:31,728] [INFO] Task succeeded: Prodigal
[2023-06-19 09:52:31,729] [INFO] Task started: HMMsearch
[2023-06-19 09:52:31,729] [INFO] Running command: hmmsearch --tblout GCA_013202445.1_ASM1320244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg689061a1-8b16-4ea7-aca6-ef5356d87474/dqc_reference/reference_markers.hmm GCA_013202445.1_ASM1320244v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:52:31,910] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:52:31,913] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg32789055-4aeb-4036-ba1c-933d83d12dcb/GCA_013202445.1_ASM1320244v1_genomic.fna.gz]
[2023-06-19 09:52:31,936] [INFO] Query marker FASTA was written to GCA_013202445.1_ASM1320244v1_genomic.fna/markers.fasta
[2023-06-19 09:52:31,936] [INFO] Task started: Blastn
[2023-06-19 09:52:31,936] [INFO] Running command: blastn -query GCA_013202445.1_ASM1320244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg689061a1-8b16-4ea7-aca6-ef5356d87474/dqc_reference/reference_markers.fasta -out GCA_013202445.1_ASM1320244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:52:32,522] [INFO] Task succeeded: Blastn
[2023-06-19 09:52:32,539] [INFO] Selected 17 target genomes.
[2023-06-19 09:52:32,540] [INFO] Target genome list was writen to GCA_013202445.1_ASM1320244v1_genomic.fna/target_genomes.txt
[2023-06-19 09:52:32,550] [INFO] Task started: fastANI
[2023-06-19 09:52:32,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg32789055-4aeb-4036-ba1c-933d83d12dcb/GCA_013202445.1_ASM1320244v1_genomic.fna.gz --refList GCA_013202445.1_ASM1320244v1_genomic.fna/target_genomes.txt --output GCA_013202445.1_ASM1320244v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:52:43,614] [INFO] Task succeeded: fastANI
[2023-06-19 09:52:43,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg689061a1-8b16-4ea7-aca6-ef5356d87474/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:52:43,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg689061a1-8b16-4ea7-aca6-ef5356d87474/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:52:43,616] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:52:43,617] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 09:52:43,617] [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
--------------------------------------------------------------------------------
[2023-06-19 09:52:43,621] [INFO] DFAST Taxonomy check result was written to GCA_013202445.1_ASM1320244v1_genomic.fna/tc_result.tsv
[2023-06-19 09:52:43,621] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:52:43,622] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:52:43,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg689061a1-8b16-4ea7-aca6-ef5356d87474/dqc_reference/checkm_data
[2023-06-19 09:52:43,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:52:43,646] [INFO] Task started: CheckM
[2023-06-19 09:52:43,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013202445.1_ASM1320244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013202445.1_ASM1320244v1_genomic.fna/checkm_input GCA_013202445.1_ASM1320244v1_genomic.fna/checkm_result
[2023-06-19 09:52:59,855] [INFO] Task succeeded: CheckM
[2023-06-19 09:52:59,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:52:59,880] [INFO] ===== Completeness check finished =====
[2023-06-19 09:52:59,881] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:52:59,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013202445.1_ASM1320244v1_genomic.fna/markers.fasta)
[2023-06-19 09:52:59,882] [INFO] Task started: Blastn
[2023-06-19 09:52:59,882] [INFO] Running command: blastn -query GCA_013202445.1_ASM1320244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg689061a1-8b16-4ea7-aca6-ef5356d87474/dqc_reference/reference_markers_gtdb.fasta -out GCA_013202445.1_ASM1320244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:53:00,706] [INFO] Task succeeded: Blastn
[2023-06-19 09:53:00,711] [INFO] Selected 18 target genomes.
[2023-06-19 09:53:00,712] [INFO] Target genome list was writen to GCA_013202445.1_ASM1320244v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:53:00,772] [INFO] Task started: fastANI
[2023-06-19 09:53:00,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg32789055-4aeb-4036-ba1c-933d83d12dcb/GCA_013202445.1_ASM1320244v1_genomic.fna.gz --refList GCA_013202445.1_ASM1320244v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013202445.1_ASM1320244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:53:07,520] [INFO] Task succeeded: fastANI
[2023-06-19 09:53:07,530] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:53:07,530] [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_013202445.1	s__E44-bin88 sp013202445	100.0	357	360	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__E44-bin88;g__E44-bin88	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011176635.1	s__E44-bin88 sp011176635	79.9429	160	360	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__E44-bin88;g__E44-bin88	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004375675.1	s__E44-bin88 sp004375675	79.4885	122	360	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__E44-bin88;g__E44-bin88	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011191985.1	s__W111 sp011191985	76.7001	63	360	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__W111;g__W111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931015.1	s__UBA5760 sp016931015	76.3159	52	360	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__UBA5760;g__UBA5760	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 09:53:07,532] [INFO] GTDB search result was written to GCA_013202445.1_ASM1320244v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:53:07,533] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:53:07,538] [INFO] DFAST_QC result json was written to GCA_013202445.1_ASM1320244v1_genomic.fna/dqc_result.json
[2023-06-19 09:53:07,538] [INFO] DFAST_QC completed!
[2023-06-19 09:53:07,539] [INFO] Total running time: 0h0m40s