[2023-06-28 22:24:54,158] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:24:54,160] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:24:54,161] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ed821a0-a55d-417f-8407-b5626cfa3905/dqc_reference
[2023-06-28 22:24:55,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:24:55,599] [INFO] Task started: Prodigal
[2023-06-28 22:24:55,599] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ff6b474-0f75-49ec-8192-9ce3d2583222/GCA_020722705.1_ASM2072270v1_genomic.fna.gz | prodigal -d GCA_020722705.1_ASM2072270v1_genomic.fna/cds.fna -a GCA_020722705.1_ASM2072270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:25:08,929] [INFO] Task succeeded: Prodigal
[2023-06-28 22:25:08,930] [INFO] Task started: HMMsearch
[2023-06-28 22:25:08,930] [INFO] Running command: hmmsearch --tblout GCA_020722705.1_ASM2072270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ed821a0-a55d-417f-8407-b5626cfa3905/dqc_reference/reference_markers.hmm GCA_020722705.1_ASM2072270v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:25:09,249] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:25:09,250] [INFO] Found 6/6 markers.
[2023-06-28 22:25:09,303] [INFO] Query marker FASTA was written to GCA_020722705.1_ASM2072270v1_genomic.fna/markers.fasta
[2023-06-28 22:25:09,303] [INFO] Task started: Blastn
[2023-06-28 22:25:09,304] [INFO] Running command: blastn -query GCA_020722705.1_ASM2072270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ed821a0-a55d-417f-8407-b5626cfa3905/dqc_reference/reference_markers.fasta -out GCA_020722705.1_ASM2072270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:25:09,961] [INFO] Task succeeded: Blastn
[2023-06-28 22:25:09,966] [INFO] Selected 20 target genomes.
[2023-06-28 22:25:09,966] [INFO] Target genome list was writen to GCA_020722705.1_ASM2072270v1_genomic.fna/target_genomes.txt
[2023-06-28 22:25:09,970] [INFO] Task started: fastANI
[2023-06-28 22:25:09,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ff6b474-0f75-49ec-8192-9ce3d2583222/GCA_020722705.1_ASM2072270v1_genomic.fna.gz --refList GCA_020722705.1_ASM2072270v1_genomic.fna/target_genomes.txt --output GCA_020722705.1_ASM2072270v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:25:25,511] [INFO] Task succeeded: fastANI
[2023-06-28 22:25:25,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ed821a0-a55d-417f-8407-b5626cfa3905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:25:25,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ed821a0-a55d-417f-8407-b5626cfa3905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:25:25,518] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:25:25,519] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:25:25,519] [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
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	74.6795	50	1348	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:25:25,521] [INFO] DFAST Taxonomy check result was written to GCA_020722705.1_ASM2072270v1_genomic.fna/tc_result.tsv
[2023-06-28 22:25:25,521] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:25:25,521] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:25:25,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ed821a0-a55d-417f-8407-b5626cfa3905/dqc_reference/checkm_data
[2023-06-28 22:25:25,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:25:25,570] [INFO] Task started: CheckM
[2023-06-28 22:25:25,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020722705.1_ASM2072270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020722705.1_ASM2072270v1_genomic.fna/checkm_input GCA_020722705.1_ASM2072270v1_genomic.fna/checkm_result
[2023-06-28 22:26:06,348] [INFO] Task succeeded: CheckM
[2023-06-28 22:26:06,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:26:06,371] [INFO] ===== Completeness check finished =====
[2023-06-28 22:26:06,371] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:26:06,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020722705.1_ASM2072270v1_genomic.fna/markers.fasta)
[2023-06-28 22:26:06,372] [INFO] Task started: Blastn
[2023-06-28 22:26:06,372] [INFO] Running command: blastn -query GCA_020722705.1_ASM2072270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ed821a0-a55d-417f-8407-b5626cfa3905/dqc_reference/reference_markers_gtdb.fasta -out GCA_020722705.1_ASM2072270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:26:07,161] [INFO] Task succeeded: Blastn
[2023-06-28 22:26:07,166] [INFO] Selected 23 target genomes.
[2023-06-28 22:26:07,167] [INFO] Target genome list was writen to GCA_020722705.1_ASM2072270v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:26:07,181] [INFO] Task started: fastANI
[2023-06-28 22:26:07,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ff6b474-0f75-49ec-8192-9ce3d2583222/GCA_020722705.1_ASM2072270v1_genomic.fna.gz --refList GCA_020722705.1_ASM2072270v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020722705.1_ASM2072270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:26:22,023] [INFO] Task succeeded: fastANI
[2023-06-28 22:26:22,034] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 22:26:22,035] [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_012517255.1	s__JAAYVH01 sp012517255	77.7534	443	1348	d__Bacteria;p__Armatimonadota;c__Chthonomonadetes;o__Chthonomonadales;f__CAJBBX01;g__JAAYVH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885605.1	s__CAJBBX01 sp903885605	76.3086	177	1348	d__Bacteria;p__Armatimonadota;c__Chthonomonadetes;o__Chthonomonadales;f__CAJBBX01;g__CAJBBX01	95.0	99.86	99.85	0.97	0.97	5	-
GCA_903951425.1	s__CAJBBX01 sp903951425	75.9552	178	1348	d__Bacteria;p__Armatimonadota;c__Chthonomonadetes;o__Chthonomonadales;f__CAJBBX01;g__CAJBBX01	95.0	99.93	99.86	0.97	0.95	8	-
GCA_013360745.1	s__JABWBA01 sp013360745	75.9405	134	1348	d__Bacteria;p__Armatimonadota;c__Chthonomonadetes;o__Chthonomonadales;f__CAJBBX01;g__JABWBA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011047005.1	s__DSOM01 sp011047005	75.2794	55	1348	d__Bacteria;p__Armatimonadota;c__Chthonomonadetes;o__Chthonomonadales;f__CAJBBX01;g__DSOM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:26:22,037] [INFO] GTDB search result was written to GCA_020722705.1_ASM2072270v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:26:22,037] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:26:22,041] [INFO] DFAST_QC result json was written to GCA_020722705.1_ASM2072270v1_genomic.fna/dqc_result.json
[2023-06-28 22:26:22,041] [INFO] DFAST_QC completed!
[2023-06-28 22:26:22,041] [INFO] Total running time: 0h1m28s