[2024-01-25 20:04:50,740] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:50,743] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:50,743] [INFO] DQC Reference Directory: /var/lib/cwl/stgb309d9e5-d957-43ae-886f-5d3408051182/dqc_reference
[2024-01-25 20:04:51,919] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:51,920] [INFO] Task started: Prodigal
[2024-01-25 20:04:51,920] [INFO] Running command: gunzip -c /var/lib/cwl/stgbcf41fbd-ac1b-480c-9188-7feb35ad9bcf/GCF_003340495.1_ASM334049v1_genomic.fna.gz | prodigal -d GCF_003340495.1_ASM334049v1_genomic.fna/cds.fna -a GCF_003340495.1_ASM334049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:12,462] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:12,462] [INFO] Task started: HMMsearch
[2024-01-25 20:05:12,463] [INFO] Running command: hmmsearch --tblout GCF_003340495.1_ASM334049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb309d9e5-d957-43ae-886f-5d3408051182/dqc_reference/reference_markers.hmm GCF_003340495.1_ASM334049v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:12,711] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:12,713] [INFO] Found 6/6 markers.
[2024-01-25 20:05:12,758] [INFO] Query marker FASTA was written to GCF_003340495.1_ASM334049v1_genomic.fna/markers.fasta
[2024-01-25 20:05:12,758] [INFO] Task started: Blastn
[2024-01-25 20:05:12,758] [INFO] Running command: blastn -query GCF_003340495.1_ASM334049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb309d9e5-d957-43ae-886f-5d3408051182/dqc_reference/reference_markers.fasta -out GCF_003340495.1_ASM334049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:13,302] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:13,304] [INFO] Selected 15 target genomes.
[2024-01-25 20:05:13,305] [INFO] Target genome list was writen to GCF_003340495.1_ASM334049v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:13,316] [INFO] Task started: fastANI
[2024-01-25 20:05:13,316] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcf41fbd-ac1b-480c-9188-7feb35ad9bcf/GCF_003340495.1_ASM334049v1_genomic.fna.gz --refList GCF_003340495.1_ASM334049v1_genomic.fna/target_genomes.txt --output GCF_003340495.1_ASM334049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:29,414] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:29,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb309d9e5-d957-43ae-886f-5d3408051182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:29,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb309d9e5-d957-43ae-886f-5d3408051182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:29,422] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:05:29,422] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:29,423] [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 pallidiroseus	strain=HMF7616	GCA_003340495.1	2072847	2072847	type	True	100.0	2139	2141	95	conclusive
Adhaeribacter swui	strain=KCTC 52873	GCA_014217805.1	2086471	2086471	type	True	81.4113	1273	2141	95	below_threshold
Adhaeribacter arboris	strain=HMF7605	GCA_003023845.1	2072846	2072846	type	True	79.5693	1060	2141	95	below_threshold
Adhaeribacter radiodurans	strain=KUDC8001	GCA_014075995.1	2745197	2745197	type	True	79.5611	943	2141	95	below_threshold
Adhaeribacter rhizoryzae	strain=DK36	GCA_008629685.1	2607907	2607907	type	True	76.9868	438	2141	95	below_threshold
Adhaeribacter aerolatus	strain=NBRC 106133	GCA_007991635.1	670289	670289	type	True	76.9439	379	2141	95	below_threshold
Adhaeribacter aquaticus	strain=DSM 16391	GCA_000473365.1	299567	299567	type	True	76.5959	204	2141	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	76.3835	81	2141	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	75.1079	59	2141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:29,425] [INFO] DFAST Taxonomy check result was written to GCF_003340495.1_ASM334049v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:29,425] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:29,426] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:29,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb309d9e5-d957-43ae-886f-5d3408051182/dqc_reference/checkm_data
[2024-01-25 20:05:29,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:29,494] [INFO] Task started: CheckM
[2024-01-25 20:05:29,494] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003340495.1_ASM334049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003340495.1_ASM334049v1_genomic.fna/checkm_input GCF_003340495.1_ASM334049v1_genomic.fna/checkm_result
[2024-01-25 20:06:24,991] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:24,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:25,005] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:25,005] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:25,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003340495.1_ASM334049v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:25,006] [INFO] Task started: Blastn
[2024-01-25 20:06:25,006] [INFO] Running command: blastn -query GCF_003340495.1_ASM334049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb309d9e5-d957-43ae-886f-5d3408051182/dqc_reference/reference_markers_gtdb.fasta -out GCF_003340495.1_ASM334049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:25,789] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:25,792] [INFO] Selected 11 target genomes.
[2024-01-25 20:06:25,792] [INFO] Target genome list was writen to GCF_003340495.1_ASM334049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:25,824] [INFO] Task started: fastANI
[2024-01-25 20:06:25,824] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcf41fbd-ac1b-480c-9188-7feb35ad9bcf/GCF_003340495.1_ASM334049v1_genomic.fna.gz --refList GCF_003340495.1_ASM334049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003340495.1_ASM334049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:40,568] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:40,574] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:40,574] [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_003340495.1	s__Adhaeribacter pallidiroseus	100.0	2140	2141	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_014217805.1	s__Adhaeribacter swui	81.4088	1273	2141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014075995.1	s__Adhaeribacter radiodurans	79.5792	945	2141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003023845.1	s__Adhaeribacter arboris	79.5594	1060	2141	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	76.9863	438	2141	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	76.9504	378	2141	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	76.5959	204	2141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:40,575] [INFO] GTDB search result was written to GCF_003340495.1_ASM334049v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:40,576] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:40,578] [INFO] DFAST_QC result json was written to GCF_003340495.1_ASM334049v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:40,578] [INFO] DFAST_QC completed!
[2024-01-25 20:06:40,578] [INFO] Total running time: 0h1m50s