[2023-06-13 03:03:02,955] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:03:02,958] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:03:02,958] [INFO] DQC Reference Directory: /var/lib/cwl/stgf07bd5b2-4ebd-4202-a78b-827c31c9f140/dqc_reference
[2023-06-13 03:03:04,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:03:04,276] [INFO] Task started: Prodigal
[2023-06-13 03:03:04,276] [INFO] Running command: gunzip -c /var/lib/cwl/stgce3897a4-6310-45b0-ba09-ec7d63b30394/GCA_022764005.1_ASM2276400v1_genomic.fna.gz | prodigal -d GCA_022764005.1_ASM2276400v1_genomic.fna/cds.fna -a GCA_022764005.1_ASM2276400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:03:07,999] [INFO] Task succeeded: Prodigal
[2023-06-13 03:03:07,999] [INFO] Task started: HMMsearch
[2023-06-13 03:03:07,999] [INFO] Running command: hmmsearch --tblout GCA_022764005.1_ASM2276400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf07bd5b2-4ebd-4202-a78b-827c31c9f140/dqc_reference/reference_markers.hmm GCA_022764005.1_ASM2276400v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:03:08,278] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:03:08,280] [INFO] Found 6/6 markers.
[2023-06-13 03:03:08,329] [INFO] Query marker FASTA was written to GCA_022764005.1_ASM2276400v1_genomic.fna/markers.fasta
[2023-06-13 03:03:08,329] [INFO] Task started: Blastn
[2023-06-13 03:03:08,329] [INFO] Running command: blastn -query GCA_022764005.1_ASM2276400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf07bd5b2-4ebd-4202-a78b-827c31c9f140/dqc_reference/reference_markers.fasta -out GCA_022764005.1_ASM2276400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:03:09,039] [INFO] Task succeeded: Blastn
[2023-06-13 03:03:09,043] [INFO] Selected 28 target genomes.
[2023-06-13 03:03:09,043] [INFO] Target genome list was writen to GCA_022764005.1_ASM2276400v1_genomic.fna/target_genomes.txt
[2023-06-13 03:03:09,085] [INFO] Task started: fastANI
[2023-06-13 03:03:09,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgce3897a4-6310-45b0-ba09-ec7d63b30394/GCA_022764005.1_ASM2276400v1_genomic.fna.gz --refList GCA_022764005.1_ASM2276400v1_genomic.fna/target_genomes.txt --output GCA_022764005.1_ASM2276400v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:03:28,239] [INFO] Task succeeded: fastANI
[2023-06-13 03:03:28,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf07bd5b2-4ebd-4202-a78b-827c31c9f140/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:03:28,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf07bd5b2-4ebd-4202-a78b-827c31c9f140/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:03:28,242] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 03:03:28,242] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 03:03:28,242] [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 03:03:28,244] [INFO] DFAST Taxonomy check result was written to GCA_022764005.1_ASM2276400v1_genomic.fna/tc_result.tsv
[2023-06-13 03:03:28,245] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:03:28,245] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:03:28,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf07bd5b2-4ebd-4202-a78b-827c31c9f140/dqc_reference/checkm_data
[2023-06-13 03:03:28,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:03:28,273] [INFO] Task started: CheckM
[2023-06-13 03:03:28,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022764005.1_ASM2276400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022764005.1_ASM2276400v1_genomic.fna/checkm_input GCA_022764005.1_ASM2276400v1_genomic.fna/checkm_result
[2023-06-13 03:03:48,410] [INFO] Task succeeded: CheckM
[2023-06-13 03:03:48,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:03:48,433] [INFO] ===== Completeness check finished =====
[2023-06-13 03:03:48,433] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:03:48,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022764005.1_ASM2276400v1_genomic.fna/markers.fasta)
[2023-06-13 03:03:48,434] [INFO] Task started: Blastn
[2023-06-13 03:03:48,434] [INFO] Running command: blastn -query GCA_022764005.1_ASM2276400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf07bd5b2-4ebd-4202-a78b-827c31c9f140/dqc_reference/reference_markers_gtdb.fasta -out GCA_022764005.1_ASM2276400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:03:49,506] [INFO] Task succeeded: Blastn
[2023-06-13 03:03:49,512] [INFO] Selected 18 target genomes.
[2023-06-13 03:03:49,512] [INFO] Target genome list was writen to GCA_022764005.1_ASM2276400v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:03:49,520] [INFO] Task started: fastANI
[2023-06-13 03:03:49,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgce3897a4-6310-45b0-ba09-ec7d63b30394/GCA_022764005.1_ASM2276400v1_genomic.fna.gz --refList GCA_022764005.1_ASM2276400v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022764005.1_ASM2276400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:03:53,790] [INFO] Task succeeded: fastANI
[2023-06-13 03:03:53,805] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 03:03:53,806] [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_900542055.1	s__51-20 sp900542055	98.8771	409	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	99.99	99.97	0.96	0.95	3	conclusive
GCA_900762565.1	s__51-20 sp900762565	79.2167	193	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017546885.1	s__51-20 sp017546885	78.6675	76	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465405.1	s__51-20 sp017465405	78.3997	176	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761715.1	s__51-20 sp902761715	78.3851	152	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937705.1	s__51-20 sp017937705	78.1891	174	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795665.1	s__51-20 sp902795665	77.8154	100	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470585.1	s__51-20 sp017470585	77.8151	108	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288295.1	s__51-20 sp016288295	77.78	142	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017961285.1	s__51-20 sp017961285	77.7062	103	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017650255.1	s__51-20 sp017650255	77.4084	66	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626035.1	s__JAGAJR01 sp017626035	76.9538	71	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__JAGAJR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900767645.1	s__CAAFZY01 sp900767645	76.6721	63	496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAAFZY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 03:03:53,808] [INFO] GTDB search result was written to GCA_022764005.1_ASM2276400v1_genomic.fna/result_gtdb.tsv
[2023-06-13 03:03:53,809] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:03:53,812] [INFO] DFAST_QC result json was written to GCA_022764005.1_ASM2276400v1_genomic.fna/dqc_result.json
[2023-06-13 03:03:53,812] [INFO] DFAST_QC completed!
[2023-06-13 03:03:53,812] [INFO] Total running time: 0h0m51s