[2024-01-24 13:35:24,987] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:24,989] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:24,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg6df48d3f-ec55-4606-9db9-71f9e4c5a18c/dqc_reference
[2024-01-24 13:35:26,215] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:26,216] [INFO] Task started: Prodigal
[2024-01-24 13:35:26,216] [INFO] Running command: gunzip -c /var/lib/cwl/stg75c90ce9-63af-4371-b14b-b5ce4b17acd3/GCF_010015475.1_ASM1001547v1_genomic.fna.gz | prodigal -d GCF_010015475.1_ASM1001547v1_genomic.fna/cds.fna -a GCF_010015475.1_ASM1001547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:57,149] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:57,150] [INFO] Task started: HMMsearch
[2024-01-24 13:35:57,150] [INFO] Running command: hmmsearch --tblout GCF_010015475.1_ASM1001547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6df48d3f-ec55-4606-9db9-71f9e4c5a18c/dqc_reference/reference_markers.hmm GCF_010015475.1_ASM1001547v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:57,469] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:57,471] [INFO] Found 6/6 markers.
[2024-01-24 13:35:57,522] [INFO] Query marker FASTA was written to GCF_010015475.1_ASM1001547v1_genomic.fna/markers.fasta
[2024-01-24 13:35:57,522] [INFO] Task started: Blastn
[2024-01-24 13:35:57,523] [INFO] Running command: blastn -query GCF_010015475.1_ASM1001547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6df48d3f-ec55-4606-9db9-71f9e4c5a18c/dqc_reference/reference_markers.fasta -out GCF_010015475.1_ASM1001547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:58,134] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:58,138] [INFO] Selected 14 target genomes.
[2024-01-24 13:35:58,139] [INFO] Target genome list was writen to GCF_010015475.1_ASM1001547v1_genomic.fna/target_genomes.txt
[2024-01-24 13:35:58,162] [INFO] Task started: fastANI
[2024-01-24 13:35:58,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c90ce9-63af-4371-b14b-b5ce4b17acd3/GCF_010015475.1_ASM1001547v1_genomic.fna.gz --refList GCF_010015475.1_ASM1001547v1_genomic.fna/target_genomes.txt --output GCF_010015475.1_ASM1001547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:12,343] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:12,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6df48d3f-ec55-4606-9db9-71f9e4c5a18c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:12,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6df48d3f-ec55-4606-9db9-71f9e4c5a18c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:12,358] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:12,358] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:12,358] [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 pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	100.0	2100	2107	95	conclusive
Pontibacter diazotrophicus	strain=H4X	GCA_003367245.1	1400979	1400979	type	True	88.6321	1586	2107	95	below_threshold
Pontibacter russatus	strain=BT326	GCA_009931655.1	2694929	2694929	type	True	79.1295	761	2107	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	78.4121	527	2107	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_003002015.1	1610492	1610492	type	True	78.369	581	2107	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.3394	498	2107	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_900188175.1	1610492	1610492	type	True	78.3368	589	2107	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	78.1029	473	2107	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	78.0144	496	2107	95	below_threshold
Pontibacter korlensis	strain=X14-1T	GCA_000973725.1	400092	400092	type	True	77.8724	449	2107	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	77.6834	288	2107	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.6076	303	2107	95	below_threshold
Pontibacter roseus	strain=DSM 17521	GCA_000373265.1	336989	336989	type	True	77.5676	384	2107	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	77.5311	332	2107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:12,360] [INFO] DFAST Taxonomy check result was written to GCF_010015475.1_ASM1001547v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:12,360] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:12,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:12,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6df48d3f-ec55-4606-9db9-71f9e4c5a18c/dqc_reference/checkm_data
[2024-01-24 13:36:12,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:12,425] [INFO] Task started: CheckM
[2024-01-24 13:36:12,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010015475.1_ASM1001547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010015475.1_ASM1001547v1_genomic.fna/checkm_input GCF_010015475.1_ASM1001547v1_genomic.fna/checkm_result
[2024-01-24 13:37:35,720] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:35,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,753] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:35,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:35,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010015475.1_ASM1001547v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:35,754] [INFO] Task started: Blastn
[2024-01-24 13:37:35,755] [INFO] Running command: blastn -query GCF_010015475.1_ASM1001547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6df48d3f-ec55-4606-9db9-71f9e4c5a18c/dqc_reference/reference_markers_gtdb.fasta -out GCF_010015475.1_ASM1001547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:36,701] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:36,704] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:36,704] [INFO] Target genome list was writen to GCF_010015475.1_ASM1001547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:36,717] [INFO] Task started: fastANI
[2024-01-24 13:37:36,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c90ce9-63af-4371-b14b-b5ce4b17acd3/GCF_010015475.1_ASM1001547v1_genomic.fna.gz --refList GCF_010015475.1_ASM1001547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010015475.1_ASM1001547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:53,115] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:53,127] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:53,128] [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_010015475.1	s__Pontibacter sp010015475	100.0	2100	2107	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_003367245.1	s__Pontibacter diazotrophicus	88.6029	1590	2107	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	79.1334	763	2107	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	78.5383	549	2107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003585765.1	s__Pontibacter actiniarum	78.4372	531	2107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006385705.1	s__Pontibacter sp006385705	78.3439	498	2107	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	78.3328	589	2107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113285.1	s__Pontibacter chinhatensis	78.1021	473	2107	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	78.0212	404	2107	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	78.0144	496	2107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973725.1	s__Pontibacter korlensis	77.8754	449	2107	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	77.5655	383	2107	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 13:37:53,136] [INFO] GTDB search result was written to GCF_010015475.1_ASM1001547v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:53,138] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:53,147] [INFO] DFAST_QC result json was written to GCF_010015475.1_ASM1001547v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:53,148] [INFO] DFAST_QC completed!
[2024-01-24 13:37:53,148] [INFO] Total running time: 0h2m28s