[2024-01-24 15:06:36,715] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg55d29375-0cd0-4be9-a3f7-cfad10c65b13/dqc_reference
[2024-01-24 15:06:38,158] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,159] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,160] [INFO] Running command: gunzip -c /var/lib/cwl/stg4118ce4a-c67b-4025-a1af-54a3d71d54dc/GCF_003054055.1_ASM305405v1_genomic.fna.gz | prodigal -d GCF_003054055.1_ASM305405v1_genomic.fna/cds.fna -a GCF_003054055.1_ASM305405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:07:06,397] [INFO] Task succeeded: Prodigal
[2024-01-24 15:07:06,398] [INFO] Task started: HMMsearch
[2024-01-24 15:07:06,398] [INFO] Running command: hmmsearch --tblout GCF_003054055.1_ASM305405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55d29375-0cd0-4be9-a3f7-cfad10c65b13/dqc_reference/reference_markers.hmm GCF_003054055.1_ASM305405v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:07:06,705] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:07:06,707] [INFO] Found 6/6 markers.
[2024-01-24 15:07:06,761] [INFO] Query marker FASTA was written to GCF_003054055.1_ASM305405v1_genomic.fna/markers.fasta
[2024-01-24 15:07:06,761] [INFO] Task started: Blastn
[2024-01-24 15:07:06,761] [INFO] Running command: blastn -query GCF_003054055.1_ASM305405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55d29375-0cd0-4be9-a3f7-cfad10c65b13/dqc_reference/reference_markers.fasta -out GCF_003054055.1_ASM305405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:07,526] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:07,530] [INFO] Selected 11 target genomes.
[2024-01-24 15:07:07,531] [INFO] Target genome list was writen to GCF_003054055.1_ASM305405v1_genomic.fna/target_genomes.txt
[2024-01-24 15:07:07,536] [INFO] Task started: fastANI
[2024-01-24 15:07:07,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg4118ce4a-c67b-4025-a1af-54a3d71d54dc/GCF_003054055.1_ASM305405v1_genomic.fna.gz --refList GCF_003054055.1_ASM305405v1_genomic.fna/target_genomes.txt --output GCF_003054055.1_ASM305405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:22,585] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:22,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55d29375-0cd0-4be9-a3f7-cfad10c65b13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:22,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55d29375-0cd0-4be9-a3f7-cfad10c65b13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:22,602] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:07:22,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:22,602] [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 mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	100.0	1729	1730	95	conclusive
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	92.0234	1480	1730	95	below_threshold
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	83.7105	1154	1730	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	81.9792	995	1730	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	80.4188	860	1730	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	80.3912	867	1730	95	below_threshold
Pontibacter oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	79.3566	639	1730	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.6623	591	1730	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	78.2176	474	1730	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	78.0278	379	1730	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	77.9209	365	1730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:22,604] [INFO] DFAST Taxonomy check result was written to GCF_003054055.1_ASM305405v1_genomic.fna/tc_result.tsv
[2024-01-24 15:07:22,605] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:22,605] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:22,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55d29375-0cd0-4be9-a3f7-cfad10c65b13/dqc_reference/checkm_data
[2024-01-24 15:07:22,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:22,658] [INFO] Task started: CheckM
[2024-01-24 15:07:22,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003054055.1_ASM305405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003054055.1_ASM305405v1_genomic.fna/checkm_input GCF_003054055.1_ASM305405v1_genomic.fna/checkm_result
[2024-01-24 15:08:35,125] [INFO] Task succeeded: CheckM
[2024-01-24 15:08:35,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:08:35,148] [INFO] ===== Completeness check finished =====
[2024-01-24 15:08:35,149] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:08:35,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003054055.1_ASM305405v1_genomic.fna/markers.fasta)
[2024-01-24 15:08:35,150] [INFO] Task started: Blastn
[2024-01-24 15:08:35,150] [INFO] Running command: blastn -query GCF_003054055.1_ASM305405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55d29375-0cd0-4be9-a3f7-cfad10c65b13/dqc_reference/reference_markers_gtdb.fasta -out GCF_003054055.1_ASM305405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:08:36,039] [INFO] Task succeeded: Blastn
[2024-01-24 15:08:36,043] [INFO] Selected 6 target genomes.
[2024-01-24 15:08:36,044] [INFO] Target genome list was writen to GCF_003054055.1_ASM305405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:08:36,065] [INFO] Task started: fastANI
[2024-01-24 15:08:36,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg4118ce4a-c67b-4025-a1af-54a3d71d54dc/GCF_003054055.1_ASM305405v1_genomic.fna.gz --refList GCF_003054055.1_ASM305405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003054055.1_ASM305405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:08:47,718] [INFO] Task succeeded: fastANI
[2024-01-24 15:08:47,727] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:08:47,728] [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_003054055.1	s__Pontibacter mucosus	100.0	1729	1730	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_900113285.1	s__Pontibacter chinhatensis	92.0234	1480	1730	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	83.7088	1156	1730	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	81.9899	994	1730	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	80.4236	859	1730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003576375.1	s__Pontibacter oryzae	79.3619	637	1730	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 15:08:47,729] [INFO] GTDB search result was written to GCF_003054055.1_ASM305405v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:08:47,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:08:47,733] [INFO] DFAST_QC result json was written to GCF_003054055.1_ASM305405v1_genomic.fna/dqc_result.json
[2024-01-24 15:08:47,733] [INFO] DFAST_QC completed!
[2024-01-24 15:08:47,733] [INFO] Total running time: 0h2m11s