[2023-06-28 23:08:22,737] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:08:22,740] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:08:22,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgdde84748-6827-49f8-8b0d-944aa6ebd4ab/dqc_reference
[2023-06-28 23:08:24,138] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:08:24,148] [INFO] Task started: Prodigal
[2023-06-28 23:08:24,149] [INFO] Running command: gunzip -c /var/lib/cwl/stg431a458c-8bb3-4f8b-83b4-50a53c8c69c4/GCA_017445865.1_ASM1744586v1_genomic.fna.gz | prodigal -d GCA_017445865.1_ASM1744586v1_genomic.fna/cds.fna -a GCA_017445865.1_ASM1744586v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:08:32,575] [INFO] Task succeeded: Prodigal
[2023-06-28 23:08:32,575] [INFO] Task started: HMMsearch
[2023-06-28 23:08:32,575] [INFO] Running command: hmmsearch --tblout GCA_017445865.1_ASM1744586v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdde84748-6827-49f8-8b0d-944aa6ebd4ab/dqc_reference/reference_markers.hmm GCA_017445865.1_ASM1744586v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:08:32,847] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:08:32,848] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg431a458c-8bb3-4f8b-83b4-50a53c8c69c4/GCA_017445865.1_ASM1744586v1_genomic.fna.gz]
[2023-06-28 23:08:32,871] [INFO] Query marker FASTA was written to GCA_017445865.1_ASM1744586v1_genomic.fna/markers.fasta
[2023-06-28 23:08:32,872] [INFO] Task started: Blastn
[2023-06-28 23:08:32,872] [INFO] Running command: blastn -query GCA_017445865.1_ASM1744586v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdde84748-6827-49f8-8b0d-944aa6ebd4ab/dqc_reference/reference_markers.fasta -out GCA_017445865.1_ASM1744586v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:08:33,582] [INFO] Task succeeded: Blastn
[2023-06-28 23:08:33,587] [INFO] Selected 24 target genomes.
[2023-06-28 23:08:33,587] [INFO] Target genome list was writen to GCA_017445865.1_ASM1744586v1_genomic.fna/target_genomes.txt
[2023-06-28 23:08:33,590] [INFO] Task started: fastANI
[2023-06-28 23:08:33,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg431a458c-8bb3-4f8b-83b4-50a53c8c69c4/GCA_017445865.1_ASM1744586v1_genomic.fna.gz --refList GCA_017445865.1_ASM1744586v1_genomic.fna/target_genomes.txt --output GCA_017445865.1_ASM1744586v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:08:49,492] [INFO] Task succeeded: fastANI
[2023-06-28 23:08:49,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdde84748-6827-49f8-8b0d-944aa6ebd4ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:08:49,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdde84748-6827-49f8-8b0d-944aa6ebd4ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:08:49,494] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:08:49,494] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:08:49,495] [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 23:08:49,501] [INFO] DFAST Taxonomy check result was written to GCA_017445865.1_ASM1744586v1_genomic.fna/tc_result.tsv
[2023-06-28 23:08:49,503] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:08:49,503] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:08:49,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdde84748-6827-49f8-8b0d-944aa6ebd4ab/dqc_reference/checkm_data
[2023-06-28 23:08:49,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:08:49,530] [INFO] Task started: CheckM
[2023-06-28 23:08:49,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017445865.1_ASM1744586v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017445865.1_ASM1744586v1_genomic.fna/checkm_input GCA_017445865.1_ASM1744586v1_genomic.fna/checkm_result
[2023-06-28 23:09:19,230] [INFO] Task succeeded: CheckM
[2023-06-28 23:09:19,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 12.50%
Strain heterogeneity: 53.85%
--------------------------------------------------------------------------------
[2023-06-28 23:09:19,261] [INFO] ===== Completeness check finished =====
[2023-06-28 23:09:19,262] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:09:19,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017445865.1_ASM1744586v1_genomic.fna/markers.fasta)
[2023-06-28 23:09:19,262] [INFO] Task started: Blastn
[2023-06-28 23:09:19,263] [INFO] Running command: blastn -query GCA_017445865.1_ASM1744586v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdde84748-6827-49f8-8b0d-944aa6ebd4ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_017445865.1_ASM1744586v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:09:20,230] [INFO] Task succeeded: Blastn
[2023-06-28 23:09:20,234] [INFO] Selected 25 target genomes.
[2023-06-28 23:09:20,235] [INFO] Target genome list was writen to GCA_017445865.1_ASM1744586v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:09:20,266] [INFO] Task started: fastANI
[2023-06-28 23:09:20,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg431a458c-8bb3-4f8b-83b4-50a53c8c69c4/GCA_017445865.1_ASM1744586v1_genomic.fna.gz --refList GCA_017445865.1_ASM1744586v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017445865.1_ASM1744586v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:09:28,879] [INFO] Task succeeded: fastANI
[2023-06-28 23:09:28,898] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:09:28,898] [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_018066175.1	s__RF16 sp018066175	78.3749	55	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902771935.1	s__RF16 sp902771935	77.908	58	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	95.09	95.09	0.89	0.89	2	-
GCA_017439235.1	s__RF16 sp017439235	77.8722	78	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017443145.1	s__RF16 sp017443145	77.8622	77	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002315745.1	s__RF16 sp002315745	77.6406	61	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234025.1	s__RF16 sp905234025	77.5532	57	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785605.1	s__RF16 sp902785605	77.4778	85	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.88	96.82	0.84	0.82	4	-
GCA_900316005.1	s__RF16 sp900316005	77.3953	84	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.46	95.78	0.88	0.80	13	-
GCA_905233415.1	s__RF16 sp905233415	77.3901	78	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780495.1	s__RF16 sp902780495	77.3573	54	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551025.1	s__RF16 sp017551025	77.3375	82	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017964045.1	s__RF16 sp017964045	77.3212	53	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.97	97.34	0.74	0.68	3	-
GCA_905234835.1	s__RF16 sp905234835	77.1819	58	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.79	96.79	0.85	0.85	2	-
GCA_902799705.1	s__RF16 sp902799705	77.1419	77	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016297215.1	s__RF16 sp016297215	77.1417	57	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319645.1	s__RF16 sp900319645	76.7877	80	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.68	95.36	0.92	0.85	3	-
GCA_905233375.1	s__RF16 sp905233375	76.5904	79	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:09:28,900] [INFO] GTDB search result was written to GCA_017445865.1_ASM1744586v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:09:28,901] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:09:28,904] [INFO] DFAST_QC result json was written to GCA_017445865.1_ASM1744586v1_genomic.fna/dqc_result.json
[2023-06-28 23:09:28,905] [INFO] DFAST_QC completed!
[2023-06-28 23:09:28,905] [INFO] Total running time: 0h1m6s