[2024-01-24 14:47:08,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,457] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,457] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f823755-ef1e-468c-903d-e0834651cb44/dqc_reference
[2024-01-24 14:47:09,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,908] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg9043242d-9364-497f-b5cb-eeef3dca1a2e/GCF_003023845.1_ASM302384v1_genomic.fna.gz | prodigal -d GCF_003023845.1_ASM302384v1_genomic.fna/cds.fna -a GCF_003023845.1_ASM302384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:37,430] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:37,430] [INFO] Task started: HMMsearch
[2024-01-24 14:47:37,430] [INFO] Running command: hmmsearch --tblout GCF_003023845.1_ASM302384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f823755-ef1e-468c-903d-e0834651cb44/dqc_reference/reference_markers.hmm GCF_003023845.1_ASM302384v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:37,832] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:37,833] [INFO] Found 6/6 markers.
[2024-01-24 14:47:37,888] [INFO] Query marker FASTA was written to GCF_003023845.1_ASM302384v1_genomic.fna/markers.fasta
[2024-01-24 14:47:37,888] [INFO] Task started: Blastn
[2024-01-24 14:47:37,888] [INFO] Running command: blastn -query GCF_003023845.1_ASM302384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f823755-ef1e-468c-903d-e0834651cb44/dqc_reference/reference_markers.fasta -out GCF_003023845.1_ASM302384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:38,595] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:38,598] [INFO] Selected 13 target genomes.
[2024-01-24 14:47:38,599] [INFO] Target genome list was writen to GCF_003023845.1_ASM302384v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:38,608] [INFO] Task started: fastANI
[2024-01-24 14:47:38,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg9043242d-9364-497f-b5cb-eeef3dca1a2e/GCF_003023845.1_ASM302384v1_genomic.fna.gz --refList GCF_003023845.1_ASM302384v1_genomic.fna/target_genomes.txt --output GCF_003023845.1_ASM302384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:55,715] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:55,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f823755-ef1e-468c-903d-e0834651cb44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:55,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f823755-ef1e-468c-903d-e0834651cb44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:55,724] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:55,725] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:55,725] [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
Adhaeribacter arboris	strain=HMF7605	GCA_003023845.1	2072846	2072846	type	True	100.0	2415	2415	95	conclusive
Adhaeribacter radiodurans	strain=KUDC8001	GCA_014075995.1	2745197	2745197	type	True	81.7404	1495	2415	95	below_threshold
Adhaeribacter pallidiroseus	strain=HMF7616	GCA_003340495.1	2072847	2072847	type	True	79.5192	1052	2415	95	below_threshold
Adhaeribacter swui	strain=KCTC 52873	GCA_014217805.1	2086471	2086471	type	True	79.4843	1018	2415	95	below_threshold
Adhaeribacter rhizoryzae	strain=DK36	GCA_008629685.1	2607907	2607907	type	True	77.006	402	2415	95	below_threshold
Adhaeribacter aerolatus	strain=NBRC 106133	GCA_007991635.1	670289	670289	type	True	76.8365	356	2415	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	76.0746	80	2415	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	75.8848	55	2415	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	75.8747	81	2415	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	75.7988	69	2415	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:55,727] [INFO] DFAST Taxonomy check result was written to GCF_003023845.1_ASM302384v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:55,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:55,728] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:55,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f823755-ef1e-468c-903d-e0834651cb44/dqc_reference/checkm_data
[2024-01-24 14:47:55,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:55,802] [INFO] Task started: CheckM
[2024-01-24 14:47:55,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003023845.1_ASM302384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003023845.1_ASM302384v1_genomic.fna/checkm_input GCF_003023845.1_ASM302384v1_genomic.fna/checkm_result
[2024-01-24 14:49:06,203] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:06,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:06,227] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:06,228] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:06,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003023845.1_ASM302384v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:06,228] [INFO] Task started: Blastn
[2024-01-24 14:49:06,229] [INFO] Running command: blastn -query GCF_003023845.1_ASM302384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f823755-ef1e-468c-903d-e0834651cb44/dqc_reference/reference_markers_gtdb.fasta -out GCF_003023845.1_ASM302384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:07,054] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:07,057] [INFO] Selected 9 target genomes.
[2024-01-24 14:49:07,057] [INFO] Target genome list was writen to GCF_003023845.1_ASM302384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:07,064] [INFO] Task started: fastANI
[2024-01-24 14:49:07,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg9043242d-9364-497f-b5cb-eeef3dca1a2e/GCF_003023845.1_ASM302384v1_genomic.fna.gz --refList GCF_003023845.1_ASM302384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003023845.1_ASM302384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:19,238] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:19,245] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:19,245] [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_003023845.1	s__Adhaeribacter arboris	100.0	2414	2415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014075995.1	s__Adhaeribacter radiodurans	81.7356	1497	2415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217805.1	s__Adhaeribacter swui	79.5156	1016	2415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340495.1	s__Adhaeribacter pallidiroseus	79.4862	1053	2415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629685.1	s__Adhaeribacter rhizoryzae	77.0114	401	2415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991635.1	s__Adhaeribacter aerolatus	76.8424	355	2415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473365.1	s__Adhaeribacter aquaticus	76.6364	214	2415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:19,246] [INFO] GTDB search result was written to GCF_003023845.1_ASM302384v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:19,247] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:19,250] [INFO] DFAST_QC result json was written to GCF_003023845.1_ASM302384v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:19,250] [INFO] DFAST_QC completed!
[2024-01-24 14:49:19,250] [INFO] Total running time: 0h2m11s