[2023-06-13 10:11:14,259] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:11:14,262] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:11:14,262] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c2abe8f-0bbd-4a39-aa0d-d71ad59d825a/dqc_reference
[2023-06-13 10:11:15,567] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:11:15,568] [INFO] Task started: Prodigal
[2023-06-13 10:11:15,568] [INFO] Running command: gunzip -c /var/lib/cwl/stgc662e3da-140f-46b0-9157-43618eea6fac/GCA_022449685.1_ASM2244968v1_genomic.fna.gz | prodigal -d GCA_022449685.1_ASM2244968v1_genomic.fna/cds.fna -a GCA_022449685.1_ASM2244968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:11:23,388] [INFO] Task succeeded: Prodigal
[2023-06-13 10:11:23,388] [INFO] Task started: HMMsearch
[2023-06-13 10:11:23,388] [INFO] Running command: hmmsearch --tblout GCA_022449685.1_ASM2244968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c2abe8f-0bbd-4a39-aa0d-d71ad59d825a/dqc_reference/reference_markers.hmm GCA_022449685.1_ASM2244968v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:11:23,633] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:11:23,634] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc662e3da-140f-46b0-9157-43618eea6fac/GCA_022449685.1_ASM2244968v1_genomic.fna.gz]
[2023-06-13 10:11:23,664] [INFO] Query marker FASTA was written to GCA_022449685.1_ASM2244968v1_genomic.fna/markers.fasta
[2023-06-13 10:11:23,664] [INFO] Task started: Blastn
[2023-06-13 10:11:23,664] [INFO] Running command: blastn -query GCA_022449685.1_ASM2244968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c2abe8f-0bbd-4a39-aa0d-d71ad59d825a/dqc_reference/reference_markers.fasta -out GCA_022449685.1_ASM2244968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:24,271] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:24,275] [INFO] Selected 17 target genomes.
[2023-06-13 10:11:24,276] [INFO] Target genome list was writen to GCA_022449685.1_ASM2244968v1_genomic.fna/target_genomes.txt
[2023-06-13 10:11:24,280] [INFO] Task started: fastANI
[2023-06-13 10:11:24,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgc662e3da-140f-46b0-9157-43618eea6fac/GCA_022449685.1_ASM2244968v1_genomic.fna.gz --refList GCA_022449685.1_ASM2244968v1_genomic.fna/target_genomes.txt --output GCA_022449685.1_ASM2244968v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:11:35,529] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:35,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c2abe8f-0bbd-4a39-aa0d-d71ad59d825a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:11:35,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c2abe8f-0bbd-4a39-aa0d-d71ad59d825a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:11:35,532] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:11:35,532] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 10:11:35,532] [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
--------------------------------------------------------------------------------
[2023-06-13 10:11:35,535] [INFO] DFAST Taxonomy check result was written to GCA_022449685.1_ASM2244968v1_genomic.fna/tc_result.tsv
[2023-06-13 10:11:35,536] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:11:35,536] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:11:35,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c2abe8f-0bbd-4a39-aa0d-d71ad59d825a/dqc_reference/checkm_data
[2023-06-13 10:11:35,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:11:35,572] [INFO] Task started: CheckM
[2023-06-13 10:11:35,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022449685.1_ASM2244968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022449685.1_ASM2244968v1_genomic.fna/checkm_input GCA_022449685.1_ASM2244968v1_genomic.fna/checkm_result
[2023-06-13 10:12:03,821] [INFO] Task succeeded: CheckM
[2023-06-13 10:12:03,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:12:03,844] [INFO] ===== Completeness check finished =====
[2023-06-13 10:12:03,845] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:12:03,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022449685.1_ASM2244968v1_genomic.fna/markers.fasta)
[2023-06-13 10:12:03,846] [INFO] Task started: Blastn
[2023-06-13 10:12:03,846] [INFO] Running command: blastn -query GCA_022449685.1_ASM2244968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c2abe8f-0bbd-4a39-aa0d-d71ad59d825a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022449685.1_ASM2244968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:12:04,648] [INFO] Task succeeded: Blastn
[2023-06-13 10:12:04,653] [INFO] Selected 9 target genomes.
[2023-06-13 10:12:04,653] [INFO] Target genome list was writen to GCA_022449685.1_ASM2244968v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:12:04,659] [INFO] Task started: fastANI
[2023-06-13 10:12:04,659] [INFO] Running command: fastANI --query /var/lib/cwl/stgc662e3da-140f-46b0-9157-43618eea6fac/GCA_022449685.1_ASM2244968v1_genomic.fna.gz --refList GCA_022449685.1_ASM2244968v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022449685.1_ASM2244968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:12:09,899] [INFO] Task succeeded: fastANI
[2023-06-13 10:12:09,907] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 10:12:09,908] [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_009392075.1	s__UBA9611 sp009392075	96.5613	494	872	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	96.71	96.71	0.58	0.58	2	inconclusive
GCA_009392095.1	s__UBA9611 sp009391975	95.7194	603	872	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.46	97.52	0.83	0.73	9	inconclusive
GCA_002698265.1	s__UBA9611 sp002698265	81.7389	433	872	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.74	98.13	0.78	0.72	6	-
GCA_002746355.1	s__UBA9611 sp002746355	81.4312	633	872	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	80.9133	621	872	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.06	0.94	0.90	6	-
GCA_002816575.1	s__UBA9611 sp002816575	78.8887	333	872	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002816585.1	s__UBA9611 sp002816585	78.6276	342	872	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730485.1	s__UBA9611 sp002730485	78.4448	311	872	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204585.1	s__UBA9611 sp013204585	78.0519	374	872	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 10:12:09,910] [INFO] GTDB search result was written to GCA_022449685.1_ASM2244968v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:12:09,910] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:12:09,913] [INFO] DFAST_QC result json was written to GCA_022449685.1_ASM2244968v1_genomic.fna/dqc_result.json
[2023-06-13 10:12:09,913] [INFO] DFAST_QC completed!
[2023-06-13 10:12:09,914] [INFO] Total running time: 0h0m56s