[2023-06-28 21:58:07,178] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:58:07,182] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:58:07,182] [INFO] DQC Reference Directory: /var/lib/cwl/stg8926564a-717f-499b-8556-550b32eda508/dqc_reference
[2023-06-28 21:58:08,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:58:08,387] [INFO] Task started: Prodigal
[2023-06-28 21:58:08,387] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a4b3e4d-d4c8-4041-b97e-0bc57c0d3a15/GCA_017435245.1_ASM1743524v1_genomic.fna.gz | prodigal -d GCA_017435245.1_ASM1743524v1_genomic.fna/cds.fna -a GCA_017435245.1_ASM1743524v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:58:12,159] [INFO] Task succeeded: Prodigal
[2023-06-28 21:58:12,159] [INFO] Task started: HMMsearch
[2023-06-28 21:58:12,159] [INFO] Running command: hmmsearch --tblout GCA_017435245.1_ASM1743524v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8926564a-717f-499b-8556-550b32eda508/dqc_reference/reference_markers.hmm GCA_017435245.1_ASM1743524v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:58:12,373] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:58:12,375] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7a4b3e4d-d4c8-4041-b97e-0bc57c0d3a15/GCA_017435245.1_ASM1743524v1_genomic.fna.gz]
[2023-06-28 21:58:12,403] [INFO] Query marker FASTA was written to GCA_017435245.1_ASM1743524v1_genomic.fna/markers.fasta
[2023-06-28 21:58:12,404] [INFO] Task started: Blastn
[2023-06-28 21:58:12,404] [INFO] Running command: blastn -query GCA_017435245.1_ASM1743524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8926564a-717f-499b-8556-550b32eda508/dqc_reference/reference_markers.fasta -out GCA_017435245.1_ASM1743524v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:58:12,915] [INFO] Task succeeded: Blastn
[2023-06-28 21:58:12,921] [INFO] Selected 11 target genomes.
[2023-06-28 21:58:12,922] [INFO] Target genome list was writen to GCA_017435245.1_ASM1743524v1_genomic.fna/target_genomes.txt
[2023-06-28 21:58:12,927] [INFO] Task started: fastANI
[2023-06-28 21:58:12,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a4b3e4d-d4c8-4041-b97e-0bc57c0d3a15/GCA_017435245.1_ASM1743524v1_genomic.fna.gz --refList GCA_017435245.1_ASM1743524v1_genomic.fna/target_genomes.txt --output GCA_017435245.1_ASM1743524v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:58:19,646] [INFO] Task succeeded: fastANI
[2023-06-28 21:58:19,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8926564a-717f-499b-8556-550b32eda508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:58:19,646] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8926564a-717f-499b-8556-550b32eda508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:58:19,648] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:58:19,648] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:58:19,648] [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
--------------------------------------------------------------------------------
[2023-06-28 21:58:19,650] [INFO] DFAST Taxonomy check result was written to GCA_017435245.1_ASM1743524v1_genomic.fna/tc_result.tsv
[2023-06-28 21:58:19,650] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:58:19,651] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:58:19,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8926564a-717f-499b-8556-550b32eda508/dqc_reference/checkm_data
[2023-06-28 21:58:19,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:58:19,672] [INFO] Task started: CheckM
[2023-06-28 21:58:19,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017435245.1_ASM1743524v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017435245.1_ASM1743524v1_genomic.fna/checkm_input GCA_017435245.1_ASM1743524v1_genomic.fna/checkm_result
[2023-06-28 21:58:38,553] [INFO] Task succeeded: CheckM
[2023-06-28 21:58:38,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 32.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:58:38,576] [INFO] ===== Completeness check finished =====
[2023-06-28 21:58:38,576] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:58:38,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017435245.1_ASM1743524v1_genomic.fna/markers.fasta)
[2023-06-28 21:58:38,577] [INFO] Task started: Blastn
[2023-06-28 21:58:38,577] [INFO] Running command: blastn -query GCA_017435245.1_ASM1743524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8926564a-717f-499b-8556-550b32eda508/dqc_reference/reference_markers_gtdb.fasta -out GCA_017435245.1_ASM1743524v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:58:39,078] [INFO] Task succeeded: Blastn
[2023-06-28 21:58:39,083] [INFO] Selected 15 target genomes.
[2023-06-28 21:58:39,083] [INFO] Target genome list was writen to GCA_017435245.1_ASM1743524v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:58:39,094] [INFO] Task started: fastANI
[2023-06-28 21:58:39,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a4b3e4d-d4c8-4041-b97e-0bc57c0d3a15/GCA_017435245.1_ASM1743524v1_genomic.fna.gz --refList GCA_017435245.1_ASM1743524v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017435245.1_ASM1743524v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:58:44,103] [INFO] Task succeeded: fastANI
[2023-06-28 21:58:44,116] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:58:44,117] [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_017435245.1	s__Faecousia sp017435245	100.0	403	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015068125.1	s__Faecousia sp015068125	78.3438	79	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435525.1	s__Faecousia sp017435525	78.2953	94	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017466215.1	s__Faecousia sp017466215	78.1432	80	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017381835.1	s__Faecousia sp017381835	78.1349	95	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017555395.1	s__Faecousia sp017555395	77.9645	60	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436955.1	s__Faecousia sp017436955	77.8991	82	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.69	98.69	0.93	0.93	2	-
GCA_017521485.1	s__Faecousia sp017521485	77.7659	101	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549125.1	s__Faecousia sp017549125	77.7521	74	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017473225.1	s__Faecousia sp017473225	77.7497	75	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936985.1	s__Faecousia sp017936985	77.6983	66	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017624645.1	s__Faecousia sp017624645	77.5166	66	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068495.1	s__Faecousia sp015068495	77.419	77	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540635.1	s__Faecousia sp900540635	77.1372	62	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.77	97.74	0.82	0.81	3	-
GCA_017436035.1	s__Faecousia sp017436035	77.0184	62	411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:58:44,120] [INFO] GTDB search result was written to GCA_017435245.1_ASM1743524v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:58:44,120] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:58:44,123] [INFO] DFAST_QC result json was written to GCA_017435245.1_ASM1743524v1_genomic.fna/dqc_result.json
[2023-06-28 21:58:44,123] [INFO] DFAST_QC completed!
[2023-06-28 21:58:44,123] [INFO] Total running time: 0h0m37s