[2023-06-29 06:53:51,332] [INFO] DFAST_QC pipeline started.
[2023-06-29 06:53:51,339] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 06:53:51,339] [INFO] DQC Reference Directory: /var/lib/cwl/stga1d86a4b-a624-40f1-9d8c-1d88d07ac1b6/dqc_reference
[2023-06-29 06:53:53,648] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 06:53:53,649] [INFO] Task started: Prodigal
[2023-06-29 06:53:53,649] [INFO] Running command: gunzip -c /var/lib/cwl/stg49be1fc8-301c-4608-b7ab-860e56429db4/GCA_020635735.1_ASM2063573v1_genomic.fna.gz | prodigal -d GCA_020635735.1_ASM2063573v1_genomic.fna/cds.fna -a GCA_020635735.1_ASM2063573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 06:54:10,127] [INFO] Task succeeded: Prodigal
[2023-06-29 06:54:10,127] [INFO] Task started: HMMsearch
[2023-06-29 06:54:10,128] [INFO] Running command: hmmsearch --tblout GCA_020635735.1_ASM2063573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1d86a4b-a624-40f1-9d8c-1d88d07ac1b6/dqc_reference/reference_markers.hmm GCA_020635735.1_ASM2063573v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 06:54:10,380] [INFO] Task succeeded: HMMsearch
[2023-06-29 06:54:10,382] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg49be1fc8-301c-4608-b7ab-860e56429db4/GCA_020635735.1_ASM2063573v1_genomic.fna.gz]
[2023-06-29 06:54:10,416] [INFO] Query marker FASTA was written to GCA_020635735.1_ASM2063573v1_genomic.fna/markers.fasta
[2023-06-29 06:54:10,416] [INFO] Task started: Blastn
[2023-06-29 06:54:10,416] [INFO] Running command: blastn -query GCA_020635735.1_ASM2063573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1d86a4b-a624-40f1-9d8c-1d88d07ac1b6/dqc_reference/reference_markers.fasta -out GCA_020635735.1_ASM2063573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:54:11,003] [INFO] Task succeeded: Blastn
[2023-06-29 06:54:11,008] [INFO] Selected 15 target genomes.
[2023-06-29 06:54:11,009] [INFO] Target genome list was writen to GCA_020635735.1_ASM2063573v1_genomic.fna/target_genomes.txt
[2023-06-29 06:54:11,011] [INFO] Task started: fastANI
[2023-06-29 06:54:11,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg49be1fc8-301c-4608-b7ab-860e56429db4/GCA_020635735.1_ASM2063573v1_genomic.fna.gz --refList GCA_020635735.1_ASM2063573v1_genomic.fna/target_genomes.txt --output GCA_020635735.1_ASM2063573v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 06:54:19,181] [INFO] Task succeeded: fastANI
[2023-06-29 06:54:19,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1d86a4b-a624-40f1-9d8c-1d88d07ac1b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 06:54:19,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1d86a4b-a624-40f1-9d8c-1d88d07ac1b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 06:54:19,184] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 06:54:19,184] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 06:54:19,184] [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 06:54:19,186] [INFO] DFAST Taxonomy check result was written to GCA_020635735.1_ASM2063573v1_genomic.fna/tc_result.tsv
[2023-06-29 06:54:19,187] [INFO] ===== Taxonomy check completed =====
[2023-06-29 06:54:19,188] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 06:54:19,188] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1d86a4b-a624-40f1-9d8c-1d88d07ac1b6/dqc_reference/checkm_data
[2023-06-29 06:54:19,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 06:54:19,219] [INFO] Task started: CheckM
[2023-06-29 06:54:19,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020635735.1_ASM2063573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020635735.1_ASM2063573v1_genomic.fna/checkm_input GCA_020635735.1_ASM2063573v1_genomic.fna/checkm_result
[2023-06-29 06:55:08,124] [INFO] Task succeeded: CheckM
[2023-06-29 06:55:08,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.62%
Contamintation: 8.33%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-29 06:55:08,148] [INFO] ===== Completeness check finished =====
[2023-06-29 06:55:08,148] [INFO] ===== Start GTDB Search =====
[2023-06-29 06:55:08,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020635735.1_ASM2063573v1_genomic.fna/markers.fasta)
[2023-06-29 06:55:08,149] [INFO] Task started: Blastn
[2023-06-29 06:55:08,149] [INFO] Running command: blastn -query GCA_020635735.1_ASM2063573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1d86a4b-a624-40f1-9d8c-1d88d07ac1b6/dqc_reference/reference_markers_gtdb.fasta -out GCA_020635735.1_ASM2063573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:55:08,943] [INFO] Task succeeded: Blastn
[2023-06-29 06:55:08,948] [INFO] Selected 16 target genomes.
[2023-06-29 06:55:08,948] [INFO] Target genome list was writen to GCA_020635735.1_ASM2063573v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 06:55:08,952] [INFO] Task started: fastANI
[2023-06-29 06:55:08,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg49be1fc8-301c-4608-b7ab-860e56429db4/GCA_020635735.1_ASM2063573v1_genomic.fna.gz --refList GCA_020635735.1_ASM2063573v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020635735.1_ASM2063573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 06:55:18,905] [INFO] Task succeeded: fastANI
[2023-06-29 06:55:18,919] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 06:55:18,919] [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_008016945.1	s__PHOS-HE28 sp008016945	80.9623	297	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788205.1	s__PHOS-HE28 sp016788205	80.9403	311	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787985.1	s__PHOS-HE28 sp016787985	80.2013	255	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482775.1	s__PHOS-HE28 sp002482775	80.0789	313	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787995.1	s__PHOS-HE28 sp016787995	80.0479	240	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713875.1	s__PHOS-HE28 sp016713875	79.7557	247	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.66	99.38	0.97	0.94	4	-
GCA_016715895.1	s__PHOS-HE28 sp016715895	79.7458	266	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788295.1	s__PHOS-HE28 sp016788295	79.6	228	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342985.1	s__PHOS-HE28 sp002342985	79.3242	230	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788285.1	s__PHOS-HE28 sp016788285	79.2629	220	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718655.1	s__PHOS-HE28 sp016718655	79.2342	236	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	98.66	98.64	0.87	0.86	3	-
GCA_016716605.1	s__PHOS-HE28 sp016716605	79.1688	236	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702645.1	s__PHOS-HE28 sp016702645	79.0906	215	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788635.1	s__PHOS-HE28 sp016788635	79.0122	210	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705955.1	s__PHOS-HE28 sp016705955	78.9836	210	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712025.1	s__PHOS-HE28 sp016712025	78.7659	170	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 06:55:18,921] [INFO] GTDB search result was written to GCA_020635735.1_ASM2063573v1_genomic.fna/result_gtdb.tsv
[2023-06-29 06:55:18,922] [INFO] ===== GTDB Search completed =====
[2023-06-29 06:55:18,926] [INFO] DFAST_QC result json was written to GCA_020635735.1_ASM2063573v1_genomic.fna/dqc_result.json
[2023-06-29 06:55:18,926] [INFO] DFAST_QC completed!
[2023-06-29 06:55:18,927] [INFO] Total running time: 0h1m28s