[2023-06-29 00:04:01,360] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:04:01,366] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:04:01,366] [INFO] DQC Reference Directory: /var/lib/cwl/stge09360e2-2134-4cb4-be20-6ae5bac8722c/dqc_reference
[2023-06-29 00:04:02,794] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:04:02,795] [INFO] Task started: Prodigal
[2023-06-29 00:04:02,795] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ffdc28b-e5b2-4fbf-83b4-693f58458879/GCA_012964995.1_ASM1296499v1_genomic.fna.gz | prodigal -d GCA_012964995.1_ASM1296499v1_genomic.fna/cds.fna -a GCA_012964995.1_ASM1296499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:04:11,972] [INFO] Task succeeded: Prodigal
[2023-06-29 00:04:11,972] [INFO] Task started: HMMsearch
[2023-06-29 00:04:11,972] [INFO] Running command: hmmsearch --tblout GCA_012964995.1_ASM1296499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge09360e2-2134-4cb4-be20-6ae5bac8722c/dqc_reference/reference_markers.hmm GCA_012964995.1_ASM1296499v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:04:12,221] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:04:12,223] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3ffdc28b-e5b2-4fbf-83b4-693f58458879/GCA_012964995.1_ASM1296499v1_genomic.fna.gz]
[2023-06-29 00:04:12,259] [INFO] Query marker FASTA was written to GCA_012964995.1_ASM1296499v1_genomic.fna/markers.fasta
[2023-06-29 00:04:12,260] [INFO] Task started: Blastn
[2023-06-29 00:04:12,260] [INFO] Running command: blastn -query GCA_012964995.1_ASM1296499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge09360e2-2134-4cb4-be20-6ae5bac8722c/dqc_reference/reference_markers.fasta -out GCA_012964995.1_ASM1296499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:04:12,812] [INFO] Task succeeded: Blastn
[2023-06-29 00:04:12,820] [INFO] Selected 10 target genomes.
[2023-06-29 00:04:12,821] [INFO] Target genome list was writen to GCA_012964995.1_ASM1296499v1_genomic.fna/target_genomes.txt
[2023-06-29 00:04:12,826] [INFO] Task started: fastANI
[2023-06-29 00:04:12,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ffdc28b-e5b2-4fbf-83b4-693f58458879/GCA_012964995.1_ASM1296499v1_genomic.fna.gz --refList GCA_012964995.1_ASM1296499v1_genomic.fna/target_genomes.txt --output GCA_012964995.1_ASM1296499v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:04:18,264] [INFO] Task succeeded: fastANI
[2023-06-29 00:04:18,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge09360e2-2134-4cb4-be20-6ae5bac8722c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:04:18,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge09360e2-2134-4cb4-be20-6ae5bac8722c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:04:18,269] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:04:18,269] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 00:04:18,270] [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
--------------------------------------------------------------------------------
[2023-06-29 00:04:18,272] [INFO] DFAST Taxonomy check result was written to GCA_012964995.1_ASM1296499v1_genomic.fna/tc_result.tsv
[2023-06-29 00:04:18,273] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:04:18,273] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:04:18,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge09360e2-2134-4cb4-be20-6ae5bac8722c/dqc_reference/checkm_data
[2023-06-29 00:04:18,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:04:18,317] [INFO] Task started: CheckM
[2023-06-29 00:04:18,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012964995.1_ASM1296499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012964995.1_ASM1296499v1_genomic.fna/checkm_input GCA_012964995.1_ASM1296499v1_genomic.fna/checkm_result
[2023-06-29 00:04:49,347] [INFO] Task succeeded: CheckM
[2023-06-29 00:04:49,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 1.74%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-29 00:04:49,400] [INFO] ===== Completeness check finished =====
[2023-06-29 00:04:49,400] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:04:49,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012964995.1_ASM1296499v1_genomic.fna/markers.fasta)
[2023-06-29 00:04:49,401] [INFO] Task started: Blastn
[2023-06-29 00:04:49,401] [INFO] Running command: blastn -query GCA_012964995.1_ASM1296499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge09360e2-2134-4cb4-be20-6ae5bac8722c/dqc_reference/reference_markers_gtdb.fasta -out GCA_012964995.1_ASM1296499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:04:50,108] [INFO] Task succeeded: Blastn
[2023-06-29 00:04:50,115] [INFO] Selected 17 target genomes.
[2023-06-29 00:04:50,115] [INFO] Target genome list was writen to GCA_012964995.1_ASM1296499v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:04:50,128] [INFO] Task started: fastANI
[2023-06-29 00:04:50,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ffdc28b-e5b2-4fbf-83b4-693f58458879/GCA_012964995.1_ASM1296499v1_genomic.fna.gz --refList GCA_012964995.1_ASM1296499v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012964995.1_ASM1296499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:04:59,352] [INFO] Task succeeded: fastANI
[2023-06-29 00:04:59,367] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:04:59,368] [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_002710215.1	s__UBA11650 sp002710215	99.03	730	1008	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	99.22	99.06	0.76	0.73	3	conclusive
GCA_002401285.1	s__UBA11650 sp002401285	91.1231	647	1008	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	98.75	98.75	0.80	0.80	2	-
GCA_002708395.1	s__UBA11650 sp002708395	80.2712	405	1008	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	98.39	98.39	0.67	0.67	2	-
GCA_002746355.1	s__UBA9611 sp002746355	78.5218	139	1008	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_002328185.1	s__UBA9611 sp002328185	77.4126	134	1008	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.06	0.94	0.90	6	-
GCA_013204585.1	s__UBA9611 sp013204585	76.3241	84	1008	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840175.1	s__VXOI01 sp009840175	76.2479	94	1008	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__VXOI01	95.0	99.70	99.70	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-29 00:04:59,372] [INFO] GTDB search result was written to GCA_012964995.1_ASM1296499v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:04:59,373] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:04:59,377] [INFO] DFAST_QC result json was written to GCA_012964995.1_ASM1296499v1_genomic.fna/dqc_result.json
[2023-06-29 00:04:59,377] [INFO] DFAST_QC completed!
[2023-06-29 00:04:59,377] [INFO] Total running time: 0h0m58s