[2024-01-24 12:13:28,911] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,913] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,913] [INFO] DQC Reference Directory: /var/lib/cwl/stg54ab2bab-0eac-4a83-8694-075746d0ef1d/dqc_reference
[2024-01-24 12:13:30,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,420] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,421] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a31ebbc-d340-4701-84ff-488814056e40/GCF_009931655.1_ASM993165v1_genomic.fna.gz | prodigal -d GCF_009931655.1_ASM993165v1_genomic.fna/cds.fna -a GCF_009931655.1_ASM993165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:59,181] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:59,181] [INFO] Task started: HMMsearch
[2024-01-24 12:13:59,181] [INFO] Running command: hmmsearch --tblout GCF_009931655.1_ASM993165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54ab2bab-0eac-4a83-8694-075746d0ef1d/dqc_reference/reference_markers.hmm GCF_009931655.1_ASM993165v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:59,479] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:59,481] [INFO] Found 6/6 markers.
[2024-01-24 12:13:59,532] [INFO] Query marker FASTA was written to GCF_009931655.1_ASM993165v1_genomic.fna/markers.fasta
[2024-01-24 12:13:59,533] [INFO] Task started: Blastn
[2024-01-24 12:13:59,533] [INFO] Running command: blastn -query GCF_009931655.1_ASM993165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54ab2bab-0eac-4a83-8694-075746d0ef1d/dqc_reference/reference_markers.fasta -out GCF_009931655.1_ASM993165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:00,274] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:00,277] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:00,277] [INFO] Target genome list was writen to GCF_009931655.1_ASM993165v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:00,289] [INFO] Task started: fastANI
[2024-01-24 12:14:00,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a31ebbc-d340-4701-84ff-488814056e40/GCF_009931655.1_ASM993165v1_genomic.fna.gz --refList GCF_009931655.1_ASM993165v1_genomic.fna/target_genomes.txt --output GCF_009931655.1_ASM993165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:13,151] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:13,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54ab2bab-0eac-4a83-8694-075746d0ef1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:13,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54ab2bab-0eac-4a83-8694-075746d0ef1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:13,165] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:13,165] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:13,166] [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 russatus	strain=BT326	GCA_009931655.1	2694929	2694929	type	True	100.0	1654	1655	95	conclusive
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	79.6549	697	1655	95	below_threshold
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	79.5815	735	1655	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	79.1802	663	1655	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	79.1464	659	1655	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	79.0727	750	1655	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	79.0079	659	1655	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	78.7852	630	1655	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.1491	466	1655	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_900188175.1	1610492	1610492	type	True	78.1053	517	1655	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_003002015.1	1610492	1610492	type	True	78.0594	521	1655	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	77.8357	375	1655	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	77.4095	247	1655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:13,167] [INFO] DFAST Taxonomy check result was written to GCF_009931655.1_ASM993165v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:13,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:13,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:13,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54ab2bab-0eac-4a83-8694-075746d0ef1d/dqc_reference/checkm_data
[2024-01-24 12:14:13,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:13,217] [INFO] Task started: CheckM
[2024-01-24 12:14:13,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009931655.1_ASM993165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009931655.1_ASM993165v1_genomic.fna/checkm_input GCF_009931655.1_ASM993165v1_genomic.fna/checkm_result
[2024-01-24 12:15:30,711] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:30,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:30,727] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:30,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:30,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009931655.1_ASM993165v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:30,729] [INFO] Task started: Blastn
[2024-01-24 12:15:30,729] [INFO] Running command: blastn -query GCF_009931655.1_ASM993165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54ab2bab-0eac-4a83-8694-075746d0ef1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009931655.1_ASM993165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:31,693] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:31,696] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:31,696] [INFO] Target genome list was writen to GCF_009931655.1_ASM993165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:31,707] [INFO] Task started: fastANI
[2024-01-24 12:15:31,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a31ebbc-d340-4701-84ff-488814056e40/GCF_009931655.1_ASM993165v1_genomic.fna.gz --refList GCF_009931655.1_ASM993165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009931655.1_ASM993165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:41,636] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:41,648] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:41,648] [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_009931655.1	s__Pontibacter russatus	100.0	1655	1655	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_006385705.1	s__Pontibacter sp006385705	79.6592	696	1655	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	79.5743	736	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367245.1	s__Pontibacter diazotrophicus	79.1624	750	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054055.1	s__Pontibacter mucosus	79.1511	669	1655	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	79.1305	658	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010015475.1	s__Pontibacter sp010015475	79.0629	750	1655	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	78.7783	631	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188175.1	s__Pontibacter ummariensis	78.1053	517	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,649] [INFO] GTDB search result was written to GCF_009931655.1_ASM993165v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:41,650] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:41,655] [INFO] DFAST_QC result json was written to GCF_009931655.1_ASM993165v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:41,655] [INFO] DFAST_QC completed!
[2024-01-24 12:15:41,655] [INFO] Total running time: 0h2m13s