[2024-01-24 13:48:59,722] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,725] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,725] [INFO] DQC Reference Directory: /var/lib/cwl/stgab4205be-a870-46ce-a6d3-a828721bb0bd/dqc_reference
[2024-01-24 13:49:01,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,105] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg91478919-0ab8-45ba-a0e1-a67272d6dfd9/GCF_000314935.1_ASM31493v1_genomic.fna.gz | prodigal -d GCF_000314935.1_ASM31493v1_genomic.fna/cds.fna -a GCF_000314935.1_ASM31493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:13,977] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:13,978] [INFO] Task started: HMMsearch
[2024-01-24 13:49:13,978] [INFO] Running command: hmmsearch --tblout GCF_000314935.1_ASM31493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab4205be-a870-46ce-a6d3-a828721bb0bd/dqc_reference/reference_markers.hmm GCF_000314935.1_ASM31493v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:14,295] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:14,297] [INFO] Found 6/6 markers.
[2024-01-24 13:49:14,354] [INFO] Query marker FASTA was written to GCF_000314935.1_ASM31493v1_genomic.fna/markers.fasta
[2024-01-24 13:49:14,354] [INFO] Task started: Blastn
[2024-01-24 13:49:14,354] [INFO] Running command: blastn -query GCF_000314935.1_ASM31493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab4205be-a870-46ce-a6d3-a828721bb0bd/dqc_reference/reference_markers.fasta -out GCF_000314935.1_ASM31493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:15,083] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:15,088] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:15,088] [INFO] Target genome list was writen to GCF_000314935.1_ASM31493v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:15,132] [INFO] Task started: fastANI
[2024-01-24 13:49:15,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg91478919-0ab8-45ba-a0e1-a67272d6dfd9/GCF_000314935.1_ASM31493v1_genomic.fna.gz --refList GCF_000314935.1_ASM31493v1_genomic.fna/target_genomes.txt --output GCF_000314935.1_ASM31493v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:30,772] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:30,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab4205be-a870-46ce-a6d3-a828721bb0bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:30,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab4205be-a870-46ce-a6d3-a828721bb0bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:30,783] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:30,783] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:30,783] [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
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	83.26	1023	1844	95	below_threshold
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	80.8493	701	1844	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	78.1092	131	1844	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.9825	154	1844	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	77.8777	145	1844	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	77.7544	167	1844	95	below_threshold
Alteromonas sediminis	strain=U0105	GCA_003820355.1	2259342	2259342	type	True	77.6474	53	1844	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	77.6344	164	1844	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	77.5206	106	1844	95	below_threshold
Glaciecola nitratireducens	strain=FR1064	GCA_000226565.1	300231	300231	type	True	76.9856	68	1844	95	below_threshold
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	76.8312	92	1844	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:30,785] [INFO] DFAST Taxonomy check result was written to GCF_000314935.1_ASM31493v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:30,785] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:30,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:30,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab4205be-a870-46ce-a6d3-a828721bb0bd/dqc_reference/checkm_data
[2024-01-24 13:49:30,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:30,845] [INFO] Task started: CheckM
[2024-01-24 13:49:30,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000314935.1_ASM31493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000314935.1_ASM31493v1_genomic.fna/checkm_input GCF_000314935.1_ASM31493v1_genomic.fna/checkm_result
[2024-01-24 13:50:12,388] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:12,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:12,411] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:12,412] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:12,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000314935.1_ASM31493v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:12,413] [INFO] Task started: Blastn
[2024-01-24 13:50:12,413] [INFO] Running command: blastn -query GCF_000314935.1_ASM31493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab4205be-a870-46ce-a6d3-a828721bb0bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000314935.1_ASM31493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:13,509] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:13,512] [INFO] Selected 8 target genomes.
[2024-01-24 13:50:13,512] [INFO] Target genome list was writen to GCF_000314935.1_ASM31493v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:13,535] [INFO] Task started: fastANI
[2024-01-24 13:50:13,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg91478919-0ab8-45ba-a0e1-a67272d6dfd9/GCF_000314935.1_ASM31493v1_genomic.fna.gz --refList GCF_000314935.1_ASM31493v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000314935.1_ASM31493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:22,378] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:22,397] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:22,397] [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
GCA_000314955.1	s__Paraglaciecola chathamensis	98.3743	1549	1844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.24	97.58	0.90	0.88	8	conclusive
GCF_009906955.1	s__Paraglaciecola mesophila_A	89.8748	1425	1844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315015.1	s__Paraglaciecola mesophila	83.2609	1023	1844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.29	98.05	0.87	0.80	4	-
GCF_000014225.1	s__Paraglaciecola atlantica_A	81.5968	989	1844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315055.1	s__Paraglaciecola polaris	80.8411	703	1844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796745.1	s__Paraglaciecola sp009796745	79.7694	651	1844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378905.1	s__Paraglaciecola sp011378905	79.6754	669	1844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197995.1	s__Aliiglaciecola sp007197995	77.5769	88	1844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliiglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:22,400] [INFO] GTDB search result was written to GCF_000314935.1_ASM31493v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:22,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:22,405] [INFO] DFAST_QC result json was written to GCF_000314935.1_ASM31493v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:22,405] [INFO] DFAST_QC completed!
[2024-01-24 13:50:22,405] [INFO] Total running time: 0h1m23s