[2024-01-24 11:05:49,403] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,405] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,405] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4085779-5387-4b7b-b4ab-b10201d7cfb2/dqc_reference
[2024-01-24 11:05:51,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,279] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,279] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a3d8c07-22c1-4cb9-89bf-395ad5aaba69/GCF_003096355.1_ASM309635v1_genomic.fna.gz | prodigal -d GCF_003096355.1_ASM309635v1_genomic.fna/cds.fna -a GCF_003096355.1_ASM309635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:16,318] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:16,319] [INFO] Task started: HMMsearch
[2024-01-24 11:06:16,319] [INFO] Running command: hmmsearch --tblout GCF_003096355.1_ASM309635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4085779-5387-4b7b-b4ab-b10201d7cfb2/dqc_reference/reference_markers.hmm GCF_003096355.1_ASM309635v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:16,543] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:16,544] [INFO] Found 6/6 markers.
[2024-01-24 11:06:16,584] [INFO] Query marker FASTA was written to GCF_003096355.1_ASM309635v1_genomic.fna/markers.fasta
[2024-01-24 11:06:16,585] [INFO] Task started: Blastn
[2024-01-24 11:06:16,585] [INFO] Running command: blastn -query GCF_003096355.1_ASM309635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4085779-5387-4b7b-b4ab-b10201d7cfb2/dqc_reference/reference_markers.fasta -out GCF_003096355.1_ASM309635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:17,160] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:17,163] [INFO] Selected 10 target genomes.
[2024-01-24 11:06:17,163] [INFO] Target genome list was writen to GCF_003096355.1_ASM309635v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:17,167] [INFO] Task started: fastANI
[2024-01-24 11:06:17,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a3d8c07-22c1-4cb9-89bf-395ad5aaba69/GCF_003096355.1_ASM309635v1_genomic.fna.gz --refList GCF_003096355.1_ASM309635v1_genomic.fna/target_genomes.txt --output GCF_003096355.1_ASM309635v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:26,909] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:26,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4085779-5387-4b7b-b4ab-b10201d7cfb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:26,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4085779-5387-4b7b-b4ab-b10201d7cfb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:26,920] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:26,920] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:26,920] [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
Pontibacter virosus	strain=DSM 100231	GCA_003096355.1	1765052	1765052	type	True	100.0	1604	1608	95	conclusive
Pontibacter amylolyticus	strain=CGMCC 1.12749	GCA_014638845.1	1424080	1424080	type	True	86.9971	1250	1608	95	below_threshold
Pontibacter indicus	strain=LP100	GCA_900156345.1	1317125	1317125	type	True	84.3105	1185	1608	95	below_threshold
Pontibacter lucknowensis	strain=DM9	GCA_900156415.1	1077936	1077936	type	True	84.0783	1171	1608	95	below_threshold
Pontibacter ramchanderi	strain=LP43	GCA_002846395.1	1179743	1179743	type	True	83.8197	1182	1608	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	81.0944	836	1608	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.9174	566	1608	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.7677	538	1608	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	78.1918	311	1608	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	78.1724	321	1608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:26,922] [INFO] DFAST Taxonomy check result was written to GCF_003096355.1_ASM309635v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:26,923] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:26,923] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:26,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4085779-5387-4b7b-b4ab-b10201d7cfb2/dqc_reference/checkm_data
[2024-01-24 11:06:26,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:26,968] [INFO] Task started: CheckM
[2024-01-24 11:06:26,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003096355.1_ASM309635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003096355.1_ASM309635v1_genomic.fna/checkm_input GCF_003096355.1_ASM309635v1_genomic.fna/checkm_result
[2024-01-24 11:07:33,659] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:33,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:33,677] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:33,677] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:33,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003096355.1_ASM309635v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:33,678] [INFO] Task started: Blastn
[2024-01-24 11:07:33,678] [INFO] Running command: blastn -query GCF_003096355.1_ASM309635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4085779-5387-4b7b-b4ab-b10201d7cfb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003096355.1_ASM309635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:34,435] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:34,438] [INFO] Selected 7 target genomes.
[2024-01-24 11:07:34,438] [INFO] Target genome list was writen to GCF_003096355.1_ASM309635v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:34,442] [INFO] Task started: fastANI
[2024-01-24 11:07:34,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a3d8c07-22c1-4cb9-89bf-395ad5aaba69/GCF_003096355.1_ASM309635v1_genomic.fna.gz --refList GCF_003096355.1_ASM309635v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003096355.1_ASM309635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:42,551] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:42,559] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:42,559] [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
GCF_003096355.1	s__Pontibacter virosus	100.0	1604	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014638845.1	s__Pontibacter amylolyticus	87.0054	1249	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156345.1	s__Pontibacter indicus	84.3078	1186	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156415.1	s__Pontibacter lucknowensis	84.0946	1169	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	98.51	98.51	0.92	0.92	2	-
GCF_015686655.1	s__Pontibacter sp015686655	84.0869	1198	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846395.1	s__Pontibacter ramchanderi	83.8174	1182	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773225.1	s__Pontibacter sp014773225	81.0864	837	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:42,561] [INFO] GTDB search result was written to GCF_003096355.1_ASM309635v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:42,561] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:42,564] [INFO] DFAST_QC result json was written to GCF_003096355.1_ASM309635v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:42,564] [INFO] DFAST_QC completed!
[2024-01-24 11:07:42,564] [INFO] Total running time: 0h1m53s