[2024-01-24 14:39:45,823] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,827] [INFO] DQC Reference Directory: /var/lib/cwl/stg20dcb21e-88f2-47c2-af2a-455c8ee56ec8/dqc_reference
[2024-01-24 14:39:48,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:48,366] [INFO] Task started: Prodigal
[2024-01-24 14:39:48,367] [INFO] Running command: gunzip -c /var/lib/cwl/stge03e3160-b0ec-4860-8177-ea9c984d36d6/GCF_010092985.1_ASM1009298v1_genomic.fna.gz | prodigal -d GCF_010092985.1_ASM1009298v1_genomic.fna/cds.fna -a GCF_010092985.1_ASM1009298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:06,554] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:06,555] [INFO] Task started: HMMsearch
[2024-01-24 14:40:06,555] [INFO] Running command: hmmsearch --tblout GCF_010092985.1_ASM1009298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20dcb21e-88f2-47c2-af2a-455c8ee56ec8/dqc_reference/reference_markers.hmm GCF_010092985.1_ASM1009298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:06,860] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:06,862] [INFO] Found 6/6 markers.
[2024-01-24 14:40:06,906] [INFO] Query marker FASTA was written to GCF_010092985.1_ASM1009298v1_genomic.fna/markers.fasta
[2024-01-24 14:40:06,906] [INFO] Task started: Blastn
[2024-01-24 14:40:06,906] [INFO] Running command: blastn -query GCF_010092985.1_ASM1009298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20dcb21e-88f2-47c2-af2a-455c8ee56ec8/dqc_reference/reference_markers.fasta -out GCF_010092985.1_ASM1009298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:07,556] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:07,559] [INFO] Selected 14 target genomes.
[2024-01-24 14:40:07,560] [INFO] Target genome list was writen to GCF_010092985.1_ASM1009298v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:07,568] [INFO] Task started: fastANI
[2024-01-24 14:40:07,568] [INFO] Running command: fastANI --query /var/lib/cwl/stge03e3160-b0ec-4860-8177-ea9c984d36d6/GCF_010092985.1_ASM1009298v1_genomic.fna.gz --refList GCF_010092985.1_ASM1009298v1_genomic.fna/target_genomes.txt --output GCF_010092985.1_ASM1009298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:24,442] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:24,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20dcb21e-88f2-47c2-af2a-455c8ee56ec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:24,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20dcb21e-88f2-47c2-af2a-455c8ee56ec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:24,454] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:24,454] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:24,454] [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 pudoricolor	strain=BT214	GCA_010092985.1	2694930	2694930	type	True	100.0	1447	1448	95	conclusive
Pontibacter fetidus	strain=BT213	GCA_010119545.1	2700082	2700082	type	True	83.1906	948	1448	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	81.9318	871	1448	95	below_threshold
Pontibacter burrus	strain=BT327	GCA_010686685.1	2704466	2704466	type	True	81.4983	840	1448	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.634	487	1448	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	78.3762	438	1448	95	below_threshold
Pontibacter amylolyticus	strain=CGMCC 1.12749	GCA_014638845.1	1424080	1424080	type	True	78.1123	392	1448	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	78.0673	404	1448	95	below_threshold
Pontibacter korlensis	strain=X14-1T	GCA_000973725.1	400092	400092	type	True	78.0408	321	1448	95	below_threshold
Pontibacter oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	78.0285	367	1448	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	77.9773	343	1448	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	77.9649	386	1448	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	77.8532	378	1448	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.0693	241	1448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:24,457] [INFO] DFAST Taxonomy check result was written to GCF_010092985.1_ASM1009298v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:24,457] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:24,458] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:24,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20dcb21e-88f2-47c2-af2a-455c8ee56ec8/dqc_reference/checkm_data
[2024-01-24 14:40:24,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:24,514] [INFO] Task started: CheckM
[2024-01-24 14:40:24,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010092985.1_ASM1009298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010092985.1_ASM1009298v1_genomic.fna/checkm_input GCF_010092985.1_ASM1009298v1_genomic.fna/checkm_result
[2024-01-24 14:41:17,091] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:17,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:17,113] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:17,114] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:17,114] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010092985.1_ASM1009298v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:17,115] [INFO] Task started: Blastn
[2024-01-24 14:41:17,115] [INFO] Running command: blastn -query GCF_010092985.1_ASM1009298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20dcb21e-88f2-47c2-af2a-455c8ee56ec8/dqc_reference/reference_markers_gtdb.fasta -out GCF_010092985.1_ASM1009298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:17,890] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:17,893] [INFO] Selected 6 target genomes.
[2024-01-24 14:41:17,893] [INFO] Target genome list was writen to GCF_010092985.1_ASM1009298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:17,922] [INFO] Task started: fastANI
[2024-01-24 14:41:17,923] [INFO] Running command: fastANI --query /var/lib/cwl/stge03e3160-b0ec-4860-8177-ea9c984d36d6/GCF_010092985.1_ASM1009298v1_genomic.fna.gz --refList GCF_010092985.1_ASM1009298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010092985.1_ASM1009298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:27,458] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:27,469] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:27,469] [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_010092985.1	s__Pontibacter pudoricolor	100.0	1447	1448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018122615.1	s__Pontibacter sp018122615	89.2394	1233	1448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010119545.1	s__Pontibacter fetidus	83.2192	945	1448	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	82.4326	940	1448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297265.1	s__Pontibacter sp014297265	81.9322	872	1448	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	81.5252	837	1448	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 14:41:27,471] [INFO] GTDB search result was written to GCF_010092985.1_ASM1009298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:27,472] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:27,475] [INFO] DFAST_QC result json was written to GCF_010092985.1_ASM1009298v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:27,475] [INFO] DFAST_QC completed!
[2024-01-24 14:41:27,475] [INFO] Total running time: 0h1m42s