[2023-06-16 22:23:16,758] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:23:16,761] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:23:16,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bc697e1-c8b9-49b7-bb5f-ebb32f2efa64/dqc_reference
[2023-06-16 22:23:18,168] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:23:18,170] [INFO] Task started: Prodigal
[2023-06-16 22:23:18,170] [INFO] Running command: gunzip -c /var/lib/cwl/stg580c4545-41dc-47cb-9c80-16cd714c4984/GCA_009391445.1_ASM939144v1_genomic.fna.gz | prodigal -d GCA_009391445.1_ASM939144v1_genomic.fna/cds.fna -a GCA_009391445.1_ASM939144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:23:24,514] [INFO] Task succeeded: Prodigal
[2023-06-16 22:23:24,514] [INFO] Task started: HMMsearch
[2023-06-16 22:23:24,515] [INFO] Running command: hmmsearch --tblout GCA_009391445.1_ASM939144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bc697e1-c8b9-49b7-bb5f-ebb32f2efa64/dqc_reference/reference_markers.hmm GCA_009391445.1_ASM939144v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:23:24,729] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:23:24,731] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg580c4545-41dc-47cb-9c80-16cd714c4984/GCA_009391445.1_ASM939144v1_genomic.fna.gz]
[2023-06-16 22:23:24,762] [INFO] Query marker FASTA was written to GCA_009391445.1_ASM939144v1_genomic.fna/markers.fasta
[2023-06-16 22:23:24,763] [INFO] Task started: Blastn
[2023-06-16 22:23:24,763] [INFO] Running command: blastn -query GCA_009391445.1_ASM939144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bc697e1-c8b9-49b7-bb5f-ebb32f2efa64/dqc_reference/reference_markers.fasta -out GCA_009391445.1_ASM939144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:23:25,246] [INFO] Task succeeded: Blastn
[2023-06-16 22:23:25,249] [INFO] Selected 12 target genomes.
[2023-06-16 22:23:25,250] [INFO] Target genome list was writen to GCA_009391445.1_ASM939144v1_genomic.fna/target_genomes.txt
[2023-06-16 22:23:25,252] [INFO] Task started: fastANI
[2023-06-16 22:23:25,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg580c4545-41dc-47cb-9c80-16cd714c4984/GCA_009391445.1_ASM939144v1_genomic.fna.gz --refList GCA_009391445.1_ASM939144v1_genomic.fna/target_genomes.txt --output GCA_009391445.1_ASM939144v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:23:32,357] [INFO] Task succeeded: fastANI
[2023-06-16 22:23:32,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bc697e1-c8b9-49b7-bb5f-ebb32f2efa64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:23:32,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bc697e1-c8b9-49b7-bb5f-ebb32f2efa64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:23:32,360] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:23:32,360] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 22:23:32,361] [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
--------------------------------------------------------------------------------
[2023-06-16 22:23:32,363] [INFO] DFAST Taxonomy check result was written to GCA_009391445.1_ASM939144v1_genomic.fna/tc_result.tsv
[2023-06-16 22:23:32,364] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:23:32,364] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:23:32,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bc697e1-c8b9-49b7-bb5f-ebb32f2efa64/dqc_reference/checkm_data
[2023-06-16 22:23:32,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:23:32,398] [INFO] Task started: CheckM
[2023-06-16 22:23:32,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009391445.1_ASM939144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009391445.1_ASM939144v1_genomic.fna/checkm_input GCA_009391445.1_ASM939144v1_genomic.fna/checkm_result
[2023-06-16 22:23:57,086] [INFO] Task succeeded: CheckM
[2023-06-16 22:23:57,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:23:57,110] [INFO] ===== Completeness check finished =====
[2023-06-16 22:23:57,111] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:23:57,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009391445.1_ASM939144v1_genomic.fna/markers.fasta)
[2023-06-16 22:23:57,112] [INFO] Task started: Blastn
[2023-06-16 22:23:57,112] [INFO] Running command: blastn -query GCA_009391445.1_ASM939144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bc697e1-c8b9-49b7-bb5f-ebb32f2efa64/dqc_reference/reference_markers_gtdb.fasta -out GCA_009391445.1_ASM939144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:23:57,578] [INFO] Task succeeded: Blastn
[2023-06-16 22:23:57,583] [INFO] Selected 7 target genomes.
[2023-06-16 22:23:57,583] [INFO] Target genome list was writen to GCA_009391445.1_ASM939144v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:23:57,586] [INFO] Task started: fastANI
[2023-06-16 22:23:57,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg580c4545-41dc-47cb-9c80-16cd714c4984/GCA_009391445.1_ASM939144v1_genomic.fna.gz --refList GCA_009391445.1_ASM939144v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009391445.1_ASM939144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:24:01,568] [INFO] Task succeeded: fastANI
[2023-06-16 22:24:01,579] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:24:01,579] [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_009392095.1	s__UBA9611 sp009391975	98.6262	581	705	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.46	97.52	0.83	0.73	9	conclusive
GCA_009392075.1	s__UBA9611 sp009392075	94.7199	459	705	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	96.71	96.71	0.58	0.58	2	-
GCA_002328185.1	s__UBA9611 sp002328185	80.7171	518	705	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.06	0.94	0.90	6	-
GCA_002746355.1	s__UBA9611 sp002746355	80.4511	534	705	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_002698265.1	s__UBA9611 sp002698265	79.8127	379	705	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.74	98.13	0.78	0.72	6	-
GCA_002816585.1	s__UBA9611 sp002816585	78.2288	292	705	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	78.0325	252	705	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 22:24:01,581] [INFO] GTDB search result was written to GCA_009391445.1_ASM939144v1_genomic.fna/result_gtdb.tsv
[2023-06-16 22:24:01,582] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:24:01,585] [INFO] DFAST_QC result json was written to GCA_009391445.1_ASM939144v1_genomic.fna/dqc_result.json
[2023-06-16 22:24:01,585] [INFO] DFAST_QC completed!
[2023-06-16 22:24:01,585] [INFO] Total running time: 0h0m45s