[2024-01-24 12:13:05,899] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:05,900] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:05,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg34ed8411-aa56-4570-b5c1-22f155dc9db1/dqc_reference
[2024-01-24 12:13:07,078] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:07,079] [INFO] Task started: Prodigal
[2024-01-24 12:13:07,079] [INFO] Running command: gunzip -c /var/lib/cwl/stg331c70a5-8fe6-475e-9631-09bb53ba9c6d/GCF_022758145.1_ASM2275814v1_genomic.fna.gz | prodigal -d GCF_022758145.1_ASM2275814v1_genomic.fna/cds.fna -a GCF_022758145.1_ASM2275814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:24,327] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:24,327] [INFO] Task started: HMMsearch
[2024-01-24 12:13:24,327] [INFO] Running command: hmmsearch --tblout GCF_022758145.1_ASM2275814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34ed8411-aa56-4570-b5c1-22f155dc9db1/dqc_reference/reference_markers.hmm GCF_022758145.1_ASM2275814v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:24,537] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:24,538] [INFO] Found 6/6 markers.
[2024-01-24 12:13:24,569] [INFO] Query marker FASTA was written to GCF_022758145.1_ASM2275814v1_genomic.fna/markers.fasta
[2024-01-24 12:13:24,569] [INFO] Task started: Blastn
[2024-01-24 12:13:24,569] [INFO] Running command: blastn -query GCF_022758145.1_ASM2275814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34ed8411-aa56-4570-b5c1-22f155dc9db1/dqc_reference/reference_markers.fasta -out GCF_022758145.1_ASM2275814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:25,159] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:25,162] [INFO] Selected 19 target genomes.
[2024-01-24 12:13:25,162] [INFO] Target genome list was writen to GCF_022758145.1_ASM2275814v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:25,172] [INFO] Task started: fastANI
[2024-01-24 12:13:25,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg331c70a5-8fe6-475e-9631-09bb53ba9c6d/GCF_022758145.1_ASM2275814v1_genomic.fna.gz --refList GCF_022758145.1_ASM2275814v1_genomic.fna/target_genomes.txt --output GCF_022758145.1_ASM2275814v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:39,582] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:39,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34ed8411-aa56-4570-b5c1-22f155dc9db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:39,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34ed8411-aa56-4570-b5c1-22f155dc9db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:39,598] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:13:39,599] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:13:39,599] [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 deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	80.4917	598	1380	95	below_threshold
Pontibacter fetidus	strain=BT213	GCA_010119545.1	2700082	2700082	type	True	80.2365	614	1380	95	below_threshold
Pontibacter pudoricolor	strain=BT214	GCA_010092985.1	2694930	2694930	type	True	79.7753	562	1380	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	79.5929	652	1380	95	below_threshold
Pontibacter burrus	strain=BT327	GCA_010686685.1	2704466	2704466	type	True	79.0735	499	1380	95	below_threshold
Pontibacter cellulosilyticus	strain=SD6	GCA_014306105.1	1720253	1720253	type	True	78.564	467	1380	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	78.4641	462	1380	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	78.359	352	1380	95	below_threshold
Pontibacter ramchanderi	strain=LP43	GCA_002846395.1	1179743	1179743	type	True	78.2039	355	1380	95	below_threshold
Pontibacter roseus	strain=DSM 17521	GCA_000373265.1	336989	336989	type	True	78.1231	326	1380	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.1179	393	1380	95	below_threshold
Pontibacter virosus	strain=DSM 100231	GCA_003096355.1	1765052	1765052	type	True	78.1073	370	1380	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	77.9862	395	1380	95	below_threshold
Pontibacter indicus	strain=LP100	GCA_900156345.1	1317125	1317125	type	True	77.891	368	1380	95	below_threshold
Pontibacter beigongshangensis	strain=T6-1	GCA_014332515.1	2574733	2574733	type	True	77.7336	296	1380	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.6486	269	1380	95	below_threshold
Pontibacter akesuensis	strain=AKS 1T	GCA_001611675.1	388950	388950	type	True	77.6412	375	1380	95	below_threshold
Pontibacter akesuensis	strain=KCTC 12758	GCA_014651555.1	388950	388950	type	True	77.6312	378	1380	95	below_threshold
Pontibacter akesuensis	strain=DSM 18820	GCA_900116885.1	388950	388950	type	True	77.6056	382	1380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:39,601] [INFO] DFAST Taxonomy check result was written to GCF_022758145.1_ASM2275814v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:39,602] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:39,602] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:39,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34ed8411-aa56-4570-b5c1-22f155dc9db1/dqc_reference/checkm_data
[2024-01-24 12:13:39,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:39,644] [INFO] Task started: CheckM
[2024-01-24 12:13:39,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022758145.1_ASM2275814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022758145.1_ASM2275814v1_genomic.fna/checkm_input GCF_022758145.1_ASM2275814v1_genomic.fna/checkm_result
[2024-01-24 12:14:27,698] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:27,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:27,721] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:27,721] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:27,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022758145.1_ASM2275814v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:27,722] [INFO] Task started: Blastn
[2024-01-24 12:14:27,722] [INFO] Running command: blastn -query GCF_022758145.1_ASM2275814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34ed8411-aa56-4570-b5c1-22f155dc9db1/dqc_reference/reference_markers_gtdb.fasta -out GCF_022758145.1_ASM2275814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:28,504] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:28,507] [INFO] Selected 18 target genomes.
[2024-01-24 12:14:28,507] [INFO] Target genome list was writen to GCF_022758145.1_ASM2275814v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:28,518] [INFO] Task started: fastANI
[2024-01-24 12:14:28,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg331c70a5-8fe6-475e-9631-09bb53ba9c6d/GCF_022758145.1_ASM2275814v1_genomic.fna.gz --refList GCF_022758145.1_ASM2275814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022758145.1_ASM2275814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:43,568] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:43,583] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:14:43,583] [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_014297265.1	s__Pontibacter sp014297265	80.5296	591	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119545.1	s__Pontibacter fetidus	80.2457	613	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010092985.1	s__Pontibacter pudoricolor	79.7753	562	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018122615.1	s__Pontibacter sp018122615	79.4928	557	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014212495.1	s__Pontibacter sp014212495	79.3856	553	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010686685.1	s__Pontibacter burrus	79.0641	500	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284895.1	s__Pontibacter sp003284895	78.4509	464	1380	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	78.3259	354	1380	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	78.193	355	1380	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	78.1274	392	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373265.1	s__Pontibacter roseus	78.1245	327	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096355.1	s__Pontibacter virosus	78.1084	371	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015686655.1	s__Pontibacter sp015686655	78.0067	383	1380	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	77.9659	398	1380	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	77.8801	368	1380	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	77.7336	296	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611675.1	s__Pontibacter akesuensis	77.6412	375	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_008017455.1	s__Botryobacter sp008017455	77.4777	301	1380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:43,585] [INFO] GTDB search result was written to GCF_022758145.1_ASM2275814v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:43,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:43,590] [INFO] DFAST_QC result json was written to GCF_022758145.1_ASM2275814v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:43,591] [INFO] DFAST_QC completed!
[2024-01-24 12:14:43,591] [INFO] Total running time: 0h1m38s