[2023-06-05 09:56:15,191] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:56:15,195] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:56:15,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg38e919da-0f7c-4200-ad4d-fae382fcdb84/dqc_reference
[2023-06-05 09:56:17,609] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:56:17,610] [INFO] Task started: Prodigal
[2023-06-05 09:56:17,610] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a49be8e-61ad-4e00-aa02-f21a34068745/GCA_902628385.1_AH-324-A14_genomic.fna.gz | prodigal -d GCA_902628385.1_AH-324-A14_genomic.fna/cds.fna -a GCA_902628385.1_AH-324-A14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:56:20,701] [INFO] Task succeeded: Prodigal
[2023-06-05 09:56:20,701] [INFO] Task started: HMMsearch
[2023-06-05 09:56:20,702] [INFO] Running command: hmmsearch --tblout GCA_902628385.1_AH-324-A14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38e919da-0f7c-4200-ad4d-fae382fcdb84/dqc_reference/reference_markers.hmm GCA_902628385.1_AH-324-A14_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:56:20,905] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:56:20,906] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1a49be8e-61ad-4e00-aa02-f21a34068745/GCA_902628385.1_AH-324-A14_genomic.fna.gz]
[2023-06-05 09:56:20,930] [INFO] Query marker FASTA was written to GCA_902628385.1_AH-324-A14_genomic.fna/markers.fasta
[2023-06-05 09:56:20,931] [INFO] Task started: Blastn
[2023-06-05 09:56:20,931] [INFO] Running command: blastn -query GCA_902628385.1_AH-324-A14_genomic.fna/markers.fasta -db /var/lib/cwl/stg38e919da-0f7c-4200-ad4d-fae382fcdb84/dqc_reference/reference_markers.fasta -out GCA_902628385.1_AH-324-A14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:56:21,505] [INFO] Task succeeded: Blastn
[2023-06-05 09:56:21,509] [INFO] Selected 6 target genomes.
[2023-06-05 09:56:21,510] [INFO] Target genome list was writen to GCA_902628385.1_AH-324-A14_genomic.fna/target_genomes.txt
[2023-06-05 09:56:21,513] [INFO] Task started: fastANI
[2023-06-05 09:56:21,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a49be8e-61ad-4e00-aa02-f21a34068745/GCA_902628385.1_AH-324-A14_genomic.fna.gz --refList GCA_902628385.1_AH-324-A14_genomic.fna/target_genomes.txt --output GCA_902628385.1_AH-324-A14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:56:23,645] [INFO] Task succeeded: fastANI
[2023-06-05 09:56:23,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38e919da-0f7c-4200-ad4d-fae382fcdb84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:56:23,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38e919da-0f7c-4200-ad4d-fae382fcdb84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:56:23,649] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:56:23,649] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 09:56:23,649] [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 09:56:23,652] [INFO] DFAST Taxonomy check result was written to GCA_902628385.1_AH-324-A14_genomic.fna/tc_result.tsv
[2023-06-05 09:56:23,653] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:56:23,653] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:56:23,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38e919da-0f7c-4200-ad4d-fae382fcdb84/dqc_reference/checkm_data
[2023-06-05 09:56:23,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:56:23,680] [INFO] Task started: CheckM
[2023-06-05 09:56:23,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902628385.1_AH-324-A14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902628385.1_AH-324-A14_genomic.fna/checkm_input GCA_902628385.1_AH-324-A14_genomic.fna/checkm_result
[2023-06-05 09:56:40,854] [INFO] Task succeeded: CheckM
[2023-06-05 09:56:40,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:56:40,876] [INFO] ===== Completeness check finished =====
[2023-06-05 09:56:40,877] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:56:40,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902628385.1_AH-324-A14_genomic.fna/markers.fasta)
[2023-06-05 09:56:40,878] [INFO] Task started: Blastn
[2023-06-05 09:56:40,878] [INFO] Running command: blastn -query GCA_902628385.1_AH-324-A14_genomic.fna/markers.fasta -db /var/lib/cwl/stg38e919da-0f7c-4200-ad4d-fae382fcdb84/dqc_reference/reference_markers_gtdb.fasta -out GCA_902628385.1_AH-324-A14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:56:41,602] [INFO] Task succeeded: Blastn
[2023-06-05 09:56:41,606] [INFO] Selected 9 target genomes.
[2023-06-05 09:56:41,607] [INFO] Target genome list was writen to GCA_902628385.1_AH-324-A14_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:56:41,637] [INFO] Task started: fastANI
[2023-06-05 09:56:41,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a49be8e-61ad-4e00-aa02-f21a34068745/GCA_902628385.1_AH-324-A14_genomic.fna.gz --refList GCA_902628385.1_AH-324-A14_genomic.fna/target_genomes_gtdb.txt --output GCA_902628385.1_AH-324-A14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:56:44,200] [INFO] Task succeeded: fastANI
[2023-06-05 09:56:44,211] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 09:56:44,211] [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_002295705.1	s__UBA8592 sp002295705	90.7623	305	438	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.20	99.08	0.80	0.73	4	-
GCA_011523005.1	s__UBA8592 sp002380145	87.6255	320	438	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	97.37	95.83	0.82	0.81	6	-
GCA_002713605.1	s__UBA8592 sp002713605	87.011	124	438	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.46	99.46	0.60	0.60	2	-
GCA_002712415.1	s__UBA8592 sp002712415	86.4376	261	438	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	97.66	97.33	0.73	0.67	3	-
GCA_002712325.1	s__UBA8592 sp002712325	83.2446	191	438	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.19	99.19	0.77	0.77	2	-
GCA_002341185.1	s__UBA8592 sp002341185	80.5091	234	438	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.95	99.95	0.96	0.96	2	-
GCA_002713485.1	s__UBA8592 sp002713485	80.0454	112	438	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	97.04	97.04	0.72	0.72	2	-
--------------------------------------------------------------------------------
[2023-06-05 09:56:44,227] [INFO] GTDB search result was written to GCA_902628385.1_AH-324-A14_genomic.fna/result_gtdb.tsv
[2023-06-05 09:56:44,228] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:56:44,232] [INFO] DFAST_QC result json was written to GCA_902628385.1_AH-324-A14_genomic.fna/dqc_result.json
[2023-06-05 09:56:44,232] [INFO] DFAST_QC completed!
[2023-06-05 09:56:44,233] [INFO] Total running time: 0h0m29s