[2024-01-24 13:36:45,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,396] [INFO] DQC Reference Directory: /var/lib/cwl/stgb64efd96-1cf0-484d-af30-3f153343d257/dqc_reference
[2024-01-24 13:36:46,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,663] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,663] [INFO] Running command: gunzip -c /var/lib/cwl/stgead04170-5ba6-4a62-b99d-bbc774a8fd31/GCF_022758235.1_ASM2275823v1_genomic.fna.gz | prodigal -d GCF_022758235.1_ASM2275823v1_genomic.fna/cds.fna -a GCF_022758235.1_ASM2275823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:12,500] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:12,500] [INFO] Task started: HMMsearch
[2024-01-24 13:37:12,501] [INFO] Running command: hmmsearch --tblout GCF_022758235.1_ASM2275823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb64efd96-1cf0-484d-af30-3f153343d257/dqc_reference/reference_markers.hmm GCF_022758235.1_ASM2275823v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:12,822] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:12,824] [INFO] Found 6/6 markers.
[2024-01-24 13:37:12,869] [INFO] Query marker FASTA was written to GCF_022758235.1_ASM2275823v1_genomic.fna/markers.fasta
[2024-01-24 13:37:12,870] [INFO] Task started: Blastn
[2024-01-24 13:37:12,870] [INFO] Running command: blastn -query GCF_022758235.1_ASM2275823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb64efd96-1cf0-484d-af30-3f153343d257/dqc_reference/reference_markers.fasta -out GCF_022758235.1_ASM2275823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:13,605] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:13,608] [INFO] Selected 20 target genomes.
[2024-01-24 13:37:13,609] [INFO] Target genome list was writen to GCF_022758235.1_ASM2275823v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:13,620] [INFO] Task started: fastANI
[2024-01-24 13:37:13,620] [INFO] Running command: fastANI --query /var/lib/cwl/stgead04170-5ba6-4a62-b99d-bbc774a8fd31/GCF_022758235.1_ASM2275823v1_genomic.fna.gz --refList GCF_022758235.1_ASM2275823v1_genomic.fna/target_genomes.txt --output GCF_022758235.1_ASM2275823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:31,729] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:31,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb64efd96-1cf0-484d-af30-3f153343d257/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:31,730] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb64efd96-1cf0-484d-af30-3f153343d257/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:31,745] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:31,746] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:31,746] [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 ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.9882	557	1637	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.7841	646	1637	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	78.6018	575	1637	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	78.5283	578	1637	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	78.5126	610	1637	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	78.4444	586	1637	95	below_threshold
Pontibacter akesuensis	strain=DSM 18820	GCA_900116885.1	388950	388950	type	True	78.4059	535	1637	95	below_threshold
Pontibacter russatus	strain=BT326	GCA_009931655.1	2694929	2694929	type	True	78.4053	563	1637	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	78.3663	387	1637	95	below_threshold
Pontibacter amylolyticus	strain=CGMCC 1.12749	GCA_014638845.1	1424080	1424080	type	True	78.3053	483	1637	95	below_threshold
Pontibacter oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	78.2828	450	1637	95	below_threshold
Pontibacter ramchanderi	strain=LP43	GCA_002846395.1	1179743	1179743	type	True	78.1068	471	1637	95	below_threshold
Pontibacter beigongshangensis	strain=T6-1	GCA_014332515.1	2574733	2574733	type	True	78.0143	409	1637	95	below_threshold
Pontibacter lucknowensis	strain=DM9	GCA_900156415.1	1077936	1077936	type	True	78.0118	417	1637	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_900188175.1	1610492	1610492	type	True	78.0076	443	1637	95	below_threshold
Botryobacter ruber	strain=SYSU D60016	GCA_003347595.2	2171629	2171629	type	True	77.9889	411	1637	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	77.9805	400	1637	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_003002015.1	1610492	1610492	type	True	77.9305	447	1637	95	below_threshold
Pontibacter roseus	strain=DSM 17521	GCA_000373265.1	336989	336989	type	True	77.9075	460	1637	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	77.8786	388	1637	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:31,748] [INFO] DFAST Taxonomy check result was written to GCF_022758235.1_ASM2275823v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:31,748] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:31,748] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:31,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb64efd96-1cf0-484d-af30-3f153343d257/dqc_reference/checkm_data
[2024-01-24 13:37:31,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:31,796] [INFO] Task started: CheckM
[2024-01-24 13:37:31,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022758235.1_ASM2275823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022758235.1_ASM2275823v1_genomic.fna/checkm_input GCF_022758235.1_ASM2275823v1_genomic.fna/checkm_result
[2024-01-24 13:38:41,355] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:41,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:41,378] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:41,379] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:41,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022758235.1_ASM2275823v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:41,379] [INFO] Task started: Blastn
[2024-01-24 13:38:41,380] [INFO] Running command: blastn -query GCF_022758235.1_ASM2275823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb64efd96-1cf0-484d-af30-3f153343d257/dqc_reference/reference_markers_gtdb.fasta -out GCF_022758235.1_ASM2275823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:42,295] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:42,300] [INFO] Selected 18 target genomes.
[2024-01-24 13:38:42,301] [INFO] Target genome list was writen to GCF_022758235.1_ASM2275823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:42,326] [INFO] Task started: fastANI
[2024-01-24 13:38:42,327] [INFO] Running command: fastANI --query /var/lib/cwl/stgead04170-5ba6-4a62-b99d-bbc774a8fd31/GCF_022758235.1_ASM2275823v1_genomic.fna.gz --refList GCF_022758235.1_ASM2275823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022758235.1_ASM2275823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:58,096] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:58,117] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:38:58,117] [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
GCF_015694705.1	s__Pontibacter sp015694705	79.2302	761	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907195.1	s__Pontibacter sp001907195	78.894	652	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385705.1	s__Pontibacter sp006385705	78.7907	645	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003585765.1	s__Pontibacter actiniarum	78.5848	578	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003054055.1	s__Pontibacter mucosus	78.5188	609	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113285.1	s__Pontibacter chinhatensis	78.4511	585	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931655.1	s__Pontibacter russatus	78.4055	563	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611675.1	s__Pontibacter akesuensis	78.3744	539	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900156345.1	s__Pontibacter indicus	78.3295	485	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638845.1	s__Pontibacter amylolyticus	78.2975	484	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576375.1	s__Pontibacter oryzae	78.2663	452	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212495.1	s__Pontibacter sp014212495	78.2017	503	1637	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	78.1144	470	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014332515.1	s__Botryobacter beigongshangensis	78.0412	407	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156415.1	s__Pontibacter lucknowensis	78.0199	416	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	98.51	98.51	0.92	0.92	2	-
GCF_900188175.1	s__Pontibacter ummariensis	78.0076	443	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003347595.2	s__Botryobacter ruber	77.9872	410	1637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373265.1	s__Pontibacter roseus	77.9075	460	1637	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 13:38:58,120] [INFO] GTDB search result was written to GCF_022758235.1_ASM2275823v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:58,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:58,129] [INFO] DFAST_QC result json was written to GCF_022758235.1_ASM2275823v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:58,130] [INFO] DFAST_QC completed!
[2024-01-24 13:38:58,130] [INFO] Total running time: 0h2m13s