[2023-06-08 10:59:37,051] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:59:37,053] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:59:37,053] [INFO] DQC Reference Directory: /var/lib/cwl/stge6100d2c-bf2c-4c3c-ab45-2f9792ae3230/dqc_reference
[2023-06-08 10:59:38,272] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:59:38,272] [INFO] Task started: Prodigal
[2023-06-08 10:59:38,273] [INFO] Running command: gunzip -c /var/lib/cwl/stg54123555-e0bf-4d9d-949f-81e0fc69c4d8/GCA_945866355.1_MiE-16apr19-361_genomic.fna.gz | prodigal -d GCA_945866355.1_MiE-16apr19-361_genomic.fna/cds.fna -a GCA_945866355.1_MiE-16apr19-361_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:59:55,462] [INFO] Task succeeded: Prodigal
[2023-06-08 10:59:55,463] [INFO] Task started: HMMsearch
[2023-06-08 10:59:55,463] [INFO] Running command: hmmsearch --tblout GCA_945866355.1_MiE-16apr19-361_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6100d2c-bf2c-4c3c-ab45-2f9792ae3230/dqc_reference/reference_markers.hmm GCA_945866355.1_MiE-16apr19-361_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:59:55,692] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:59:55,694] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg54123555-e0bf-4d9d-949f-81e0fc69c4d8/GCA_945866355.1_MiE-16apr19-361_genomic.fna.gz]
[2023-06-08 10:59:55,728] [INFO] Query marker FASTA was written to GCA_945866355.1_MiE-16apr19-361_genomic.fna/markers.fasta
[2023-06-08 10:59:55,729] [INFO] Task started: Blastn
[2023-06-08 10:59:55,729] [INFO] Running command: blastn -query GCA_945866355.1_MiE-16apr19-361_genomic.fna/markers.fasta -db /var/lib/cwl/stge6100d2c-bf2c-4c3c-ab45-2f9792ae3230/dqc_reference/reference_markers.fasta -out GCA_945866355.1_MiE-16apr19-361_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:59:56,360] [INFO] Task succeeded: Blastn
[2023-06-08 10:59:56,365] [INFO] Selected 25 target genomes.
[2023-06-08 10:59:56,365] [INFO] Target genome list was writen to GCA_945866355.1_MiE-16apr19-361_genomic.fna/target_genomes.txt
[2023-06-08 10:59:56,370] [INFO] Task started: fastANI
[2023-06-08 10:59:56,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg54123555-e0bf-4d9d-949f-81e0fc69c4d8/GCA_945866355.1_MiE-16apr19-361_genomic.fna.gz --refList GCA_945866355.1_MiE-16apr19-361_genomic.fna/target_genomes.txt --output GCA_945866355.1_MiE-16apr19-361_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:00:15,539] [INFO] Task succeeded: fastANI
[2023-06-08 11:00:15,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6100d2c-bf2c-4c3c-ab45-2f9792ae3230/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:00:15,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6100d2c-bf2c-4c3c-ab45-2f9792ae3230/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:00:15,543] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:00:15,543] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:00:15,543] [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
--------------------------------------------------------------------------------
[2023-06-08 11:00:15,546] [INFO] DFAST Taxonomy check result was written to GCA_945866355.1_MiE-16apr19-361_genomic.fna/tc_result.tsv
[2023-06-08 11:00:15,546] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:00:15,547] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:00:15,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6100d2c-bf2c-4c3c-ab45-2f9792ae3230/dqc_reference/checkm_data
[2023-06-08 11:00:15,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:00:15,583] [INFO] Task started: CheckM
[2023-06-08 11:00:15,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945866355.1_MiE-16apr19-361_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945866355.1_MiE-16apr19-361_genomic.fna/checkm_input GCA_945866355.1_MiE-16apr19-361_genomic.fna/checkm_result
[2023-06-08 11:01:06,242] [INFO] Task succeeded: CheckM
[2023-06-08 11:01:06,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:01:06,268] [INFO] ===== Completeness check finished =====
[2023-06-08 11:01:06,268] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:01:06,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945866355.1_MiE-16apr19-361_genomic.fna/markers.fasta)
[2023-06-08 11:01:06,269] [INFO] Task started: Blastn
[2023-06-08 11:01:06,269] [INFO] Running command: blastn -query GCA_945866355.1_MiE-16apr19-361_genomic.fna/markers.fasta -db /var/lib/cwl/stge6100d2c-bf2c-4c3c-ab45-2f9792ae3230/dqc_reference/reference_markers_gtdb.fasta -out GCA_945866355.1_MiE-16apr19-361_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:01:07,230] [INFO] Task succeeded: Blastn
[2023-06-08 11:01:07,235] [INFO] Selected 20 target genomes.
[2023-06-08 11:01:07,235] [INFO] Target genome list was writen to GCA_945866355.1_MiE-16apr19-361_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:01:07,243] [INFO] Task started: fastANI
[2023-06-08 11:01:07,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg54123555-e0bf-4d9d-949f-81e0fc69c4d8/GCA_945866355.1_MiE-16apr19-361_genomic.fna.gz --refList GCA_945866355.1_MiE-16apr19-361_genomic.fna/target_genomes_gtdb.txt --output GCA_945866355.1_MiE-16apr19-361_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:01:21,750] [INFO] Task succeeded: fastANI
[2023-06-08 11:01:21,757] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:01:21,757] [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_903954065.1	s__CAJBME01 sp903954065	97.0947	713	766	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__V1-33;g__CAJBME01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903936775.1	s__CAIZWU01 sp903936775	78.1145	50	766	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__V1-33;g__CAIZWU01	95.0	99.53	99.53	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-08 11:01:21,759] [INFO] GTDB search result was written to GCA_945866355.1_MiE-16apr19-361_genomic.fna/result_gtdb.tsv
[2023-06-08 11:01:21,760] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:01:21,763] [INFO] DFAST_QC result json was written to GCA_945866355.1_MiE-16apr19-361_genomic.fna/dqc_result.json
[2023-06-08 11:01:21,763] [INFO] DFAST_QC completed!
[2023-06-08 11:01:21,763] [INFO] Total running time: 0h1m45s