[2024-01-24 15:01:14,935] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:14,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:14,937] [INFO] DQC Reference Directory: /var/lib/cwl/stgcadee298-5583-4b65-900f-cc33fdb10168/dqc_reference
[2024-01-24 15:01:16,138] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:16,139] [INFO] Task started: Prodigal
[2024-01-24 15:01:16,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fa1f928-14ad-49fe-8f57-7e9a31a12f9f/GCF_018271975.1_ASM1827197v1_genomic.fna.gz | prodigal -d GCF_018271975.1_ASM1827197v1_genomic.fna/cds.fna -a GCF_018271975.1_ASM1827197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:41,754] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:41,755] [INFO] Task started: HMMsearch
[2024-01-24 15:01:41,755] [INFO] Running command: hmmsearch --tblout GCF_018271975.1_ASM1827197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcadee298-5583-4b65-900f-cc33fdb10168/dqc_reference/reference_markers.hmm GCF_018271975.1_ASM1827197v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:42,082] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:42,084] [INFO] Found 6/6 markers.
[2024-01-24 15:01:42,130] [INFO] Query marker FASTA was written to GCF_018271975.1_ASM1827197v1_genomic.fna/markers.fasta
[2024-01-24 15:01:42,131] [INFO] Task started: Blastn
[2024-01-24 15:01:42,131] [INFO] Running command: blastn -query GCF_018271975.1_ASM1827197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcadee298-5583-4b65-900f-cc33fdb10168/dqc_reference/reference_markers.fasta -out GCF_018271975.1_ASM1827197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:42,739] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:42,743] [INFO] Selected 15 target genomes.
[2024-01-24 15:01:42,744] [INFO] Target genome list was writen to GCF_018271975.1_ASM1827197v1_genomic.fna/target_genomes.txt
[2024-01-24 15:01:42,755] [INFO] Task started: fastANI
[2024-01-24 15:01:42,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fa1f928-14ad-49fe-8f57-7e9a31a12f9f/GCF_018271975.1_ASM1827197v1_genomic.fna.gz --refList GCF_018271975.1_ASM1827197v1_genomic.fna/target_genomes.txt --output GCF_018271975.1_ASM1827197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:01:56,661] [INFO] Task succeeded: fastANI
[2024-01-24 15:01:56,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcadee298-5583-4b65-900f-cc33fdb10168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:01:56,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcadee298-5583-4b65-900f-cc33fdb10168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:01:56,671] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:01:56,672] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:01:56,672] [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
Carboxylicivirga mesophila	strain=JCM 18290	GCA_018271975.1	1166478	1166478	type	True	100.0	1841	1845	95	conclusive
Carboxylicivirga sediminis	strain=JR1	GCA_018156225.1	2006564	2006564	type	True	93.3497	1589	1845	95	below_threshold
Carboxylicivirga marina	strain=N1Y132	GCA_016612505.1	2800988	2800988	type	True	79.1827	534	1845	95	below_threshold
Carboxylicivirga linearis	strain=FB218	GCA_018271995.1	1628157	1628157	type	True	77.4522	224	1845	95	below_threshold
Labilibacter marinus	strain=Y11	GCA_001659685.2	1477105	1477105	type	True	76.5325	79	1845	95	below_threshold
Saccharicrinis aurantiacus	strain=HQYD1	GCA_001660705.2	1849719	1849719	type	True	75.9474	76	1845	95	below_threshold
Saccharicrinis carchari	strain=DSM 27040	GCA_900182605.1	1168039	1168039	type	True	75.8598	63	1845	95	below_threshold
Marinifilum breve	strain=JC075	GCA_003202155.1	2184082	2184082	type	True	75.7893	64	1845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:01:56,674] [INFO] DFAST Taxonomy check result was written to GCF_018271975.1_ASM1827197v1_genomic.fna/tc_result.tsv
[2024-01-24 15:01:56,675] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:01:56,675] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:01:56,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcadee298-5583-4b65-900f-cc33fdb10168/dqc_reference/checkm_data
[2024-01-24 15:01:56,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:01:56,749] [INFO] Task started: CheckM
[2024-01-24 15:01:56,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018271975.1_ASM1827197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018271975.1_ASM1827197v1_genomic.fna/checkm_input GCF_018271975.1_ASM1827197v1_genomic.fna/checkm_result
[2024-01-24 15:03:09,853] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:09,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:09,881] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:09,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:09,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018271975.1_ASM1827197v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:09,883] [INFO] Task started: Blastn
[2024-01-24 15:03:09,883] [INFO] Running command: blastn -query GCF_018271975.1_ASM1827197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcadee298-5583-4b65-900f-cc33fdb10168/dqc_reference/reference_markers_gtdb.fasta -out GCF_018271975.1_ASM1827197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:10,764] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:10,767] [INFO] Selected 9 target genomes.
[2024-01-24 15:03:10,767] [INFO] Target genome list was writen to GCF_018271975.1_ASM1827197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:10,775] [INFO] Task started: fastANI
[2024-01-24 15:03:10,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fa1f928-14ad-49fe-8f57-7e9a31a12f9f/GCF_018271975.1_ASM1827197v1_genomic.fna.gz --refList GCF_018271975.1_ASM1827197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018271975.1_ASM1827197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:20,818] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:20,825] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:20,826] [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_018271975.1	s__Carboxylicivirga mesophila	100.0	1841	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018156225.1	s__Carboxylicivirga sediminis	93.3497	1589	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612505.1	s__Carboxylicivirga sp016612505	79.2089	532	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097485.1	s__Carboxylicivirga sp007097485	78.4653	462	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429115.1	s__Carboxylicivirga sp002429115	78.4457	351	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018271995.1	s__Carboxylicivirga linearis	77.4665	224	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877885.1	s__Saccharicrinis sediminis	76.2644	120	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:20,827] [INFO] GTDB search result was written to GCF_018271975.1_ASM1827197v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:20,828] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:20,831] [INFO] DFAST_QC result json was written to GCF_018271975.1_ASM1827197v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:20,831] [INFO] DFAST_QC completed!
[2024-01-24 15:03:20,831] [INFO] Total running time: 0h2m6s