[2023-06-28 22:10:09,612] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:10:09,614] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:10:09,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdd31095-0f58-43e0-bde6-c94fdcc25804/dqc_reference
[2023-06-28 22:10:10,820] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:10:10,821] [INFO] Task started: Prodigal
[2023-06-28 22:10:10,821] [INFO] Running command: gunzip -c /var/lib/cwl/stgb943a10c-0749-412e-8f37-3bd109f7c94c/GCA_002708495.1_ASM270849v1_genomic.fna.gz | prodigal -d GCA_002708495.1_ASM270849v1_genomic.fna/cds.fna -a GCA_002708495.1_ASM270849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:10:13,820] [INFO] Task succeeded: Prodigal
[2023-06-28 22:10:13,821] [INFO] Task started: HMMsearch
[2023-06-28 22:10:13,821] [INFO] Running command: hmmsearch --tblout GCA_002708495.1_ASM270849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdd31095-0f58-43e0-bde6-c94fdcc25804/dqc_reference/reference_markers.hmm GCA_002708495.1_ASM270849v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:10:14,015] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:10:14,017] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb943a10c-0749-412e-8f37-3bd109f7c94c/GCA_002708495.1_ASM270849v1_genomic.fna.gz]
[2023-06-28 22:10:14,040] [INFO] Query marker FASTA was written to GCA_002708495.1_ASM270849v1_genomic.fna/markers.fasta
[2023-06-28 22:10:14,041] [INFO] Task started: Blastn
[2023-06-28 22:10:14,041] [INFO] Running command: blastn -query GCA_002708495.1_ASM270849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdd31095-0f58-43e0-bde6-c94fdcc25804/dqc_reference/reference_markers.fasta -out GCA_002708495.1_ASM270849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:10:14,567] [INFO] Task succeeded: Blastn
[2023-06-28 22:10:14,571] [INFO] Selected 0 target genomes.
[2023-06-28 22:10:14,572] [INFO] Target genome list was writen to GCA_002708495.1_ASM270849v1_genomic.fna/target_genomes.txt
[2023-06-28 22:10:14,572] [ERROR] File is empty. [GCA_002708495.1_ASM270849v1_genomic.fna/target_genomes.txt]
[2023-06-28 22:10:14,572] [ERROR] Task failed. No target genome found.
[2023-06-28 22:10:14,573] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:10:14,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdd31095-0f58-43e0-bde6-c94fdcc25804/dqc_reference/checkm_data
[2023-06-28 22:10:14,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:10:14,594] [INFO] Task started: CheckM
[2023-06-28 22:10:14,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708495.1_ASM270849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708495.1_ASM270849v1_genomic.fna/checkm_input GCA_002708495.1_ASM270849v1_genomic.fna/checkm_result
[2023-06-28 22:10:31,027] [INFO] Task succeeded: CheckM
[2023-06-28 22:10:31,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:10:31,049] [INFO] ===== Completeness check finished =====
[2023-06-28 22:10:31,049] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:10:31,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708495.1_ASM270849v1_genomic.fna/markers.fasta)
[2023-06-28 22:10:31,050] [INFO] Task started: Blastn
[2023-06-28 22:10:31,050] [INFO] Running command: blastn -query GCA_002708495.1_ASM270849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdd31095-0f58-43e0-bde6-c94fdcc25804/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708495.1_ASM270849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:10:31,679] [INFO] Task succeeded: Blastn
[2023-06-28 22:10:31,684] [INFO] Selected 5 target genomes.
[2023-06-28 22:10:31,684] [INFO] Target genome list was writen to GCA_002708495.1_ASM270849v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:10:31,688] [INFO] Task started: fastANI
[2023-06-28 22:10:31,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgb943a10c-0749-412e-8f37-3bd109f7c94c/GCA_002708495.1_ASM270849v1_genomic.fna.gz --refList GCA_002708495.1_ASM270849v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708495.1_ASM270849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:10:33,643] [INFO] Task succeeded: fastANI
[2023-06-28 22:10:33,650] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:10:33,651] [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_009392675.1	s__UBA11996 sp009392675	95.4598	254	447	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	95.66	95.66	0.60	0.60	2	conclusive
GCA_002500485.1	s__UBA11996 sp002500485	89.0577	345	447	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435305.1	s__UBA11996 sp002435305	88.5835	331	447	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	99.14	98.93	0.85	0.82	4	-
GCA_003228105.1	s__UBA11996 sp003228105	88.0554	292	447	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012965485.1	s__UBA11996 sp012965485	88.033	202	447	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:10:33,652] [INFO] GTDB search result was written to GCA_002708495.1_ASM270849v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:10:33,653] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:10:33,655] [INFO] DFAST_QC result json was written to GCA_002708495.1_ASM270849v1_genomic.fna/dqc_result.json
[2023-06-28 22:10:33,656] [INFO] DFAST_QC completed!
[2023-06-28 22:10:33,656] [INFO] Total running time: 0h0m24s