[2024-01-24 13:55:57,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:57,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:57,965] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbe6ba30-15b2-4760-ae18-46a91482df3a/dqc_reference
[2024-01-24 13:55:59,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:59,177] [INFO] Task started: Prodigal
[2024-01-24 13:55:59,177] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5386fec-2111-4739-a60b-f1a59d9bb7d0/GCF_008087665.1_ASM808766v1_genomic.fna.gz | prodigal -d GCF_008087665.1_ASM808766v1_genomic.fna/cds.fna -a GCF_008087665.1_ASM808766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:25,948] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:25,949] [INFO] Task started: HMMsearch
[2024-01-24 13:56:25,949] [INFO] Running command: hmmsearch --tblout GCF_008087665.1_ASM808766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbe6ba30-15b2-4760-ae18-46a91482df3a/dqc_reference/reference_markers.hmm GCF_008087665.1_ASM808766v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:26,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:26,288] [INFO] Found 6/6 markers.
[2024-01-24 13:56:26,341] [INFO] Query marker FASTA was written to GCF_008087665.1_ASM808766v1_genomic.fna/markers.fasta
[2024-01-24 13:56:26,341] [INFO] Task started: Blastn
[2024-01-24 13:56:26,341] [INFO] Running command: blastn -query GCF_008087665.1_ASM808766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbe6ba30-15b2-4760-ae18-46a91482df3a/dqc_reference/reference_markers.fasta -out GCF_008087665.1_ASM808766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:26,930] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:26,935] [INFO] Selected 21 target genomes.
[2024-01-24 13:56:26,935] [INFO] Target genome list was writen to GCF_008087665.1_ASM808766v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:26,961] [INFO] Task started: fastANI
[2024-01-24 13:56:26,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5386fec-2111-4739-a60b-f1a59d9bb7d0/GCF_008087665.1_ASM808766v1_genomic.fna.gz --refList GCF_008087665.1_ASM808766v1_genomic.fna/target_genomes.txt --output GCF_008087665.1_ASM808766v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:47,993] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:47,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbe6ba30-15b2-4760-ae18-46a91482df3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:47,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbe6ba30-15b2-4760-ae18-46a91482df3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:48,007] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:56:48,007] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:48,008] [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
Mariniblastus fucicola	strain=FC18	GCA_008087665.1	980251	980251	type	True	100.0	2190	2190	95	conclusive
Mariniblastus fucicola	strain=FC18	GCA_001642875.1	980251	980251	type	True	99.974	2149	2190	95	conclusive
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	76.0889	52	2190	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.9418	58	2190	95	below_threshold
Rosistilla oblonga	strain=CA51	GCA_007751715.1	2527990	2527990	type	True	75.8747	52	2190	95	below_threshold
Rosistilla ulvae	strain=EC9	GCA_007741475.1	1930277	1930277	type	True	75.7858	53	2190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:48,009] [INFO] DFAST Taxonomy check result was written to GCF_008087665.1_ASM808766v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:48,010] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:48,010] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:48,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbe6ba30-15b2-4760-ae18-46a91482df3a/dqc_reference/checkm_data
[2024-01-24 13:56:48,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:48,072] [INFO] Task started: CheckM
[2024-01-24 13:56:48,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008087665.1_ASM808766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008087665.1_ASM808766v1_genomic.fna/checkm_input GCF_008087665.1_ASM808766v1_genomic.fna/checkm_result
[2024-01-24 13:58:03,701] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:03,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:03,732] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:03,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:03,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008087665.1_ASM808766v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:03,733] [INFO] Task started: Blastn
[2024-01-24 13:58:03,733] [INFO] Running command: blastn -query GCF_008087665.1_ASM808766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbe6ba30-15b2-4760-ae18-46a91482df3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008087665.1_ASM808766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:04,517] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:04,520] [INFO] Selected 25 target genomes.
[2024-01-24 13:58:04,520] [INFO] Target genome list was writen to GCF_008087665.1_ASM808766v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:04,537] [INFO] Task started: fastANI
[2024-01-24 13:58:04,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5386fec-2111-4739-a60b-f1a59d9bb7d0/GCF_008087665.1_ASM808766v1_genomic.fna.gz --refList GCF_008087665.1_ASM808766v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008087665.1_ASM808766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:32,574] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:32,581] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:32,581] [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_008087665.1	s__Mariniblastus fucicola	100.0	2190	2190	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Mariniblastus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_007859835.1	s__Novipirellula sp007859835	77.2287	52	2190	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192335.1	s__Rhodopirellula rubra	76.8746	54	2190	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCF_000196115.1	s__Rhodopirellula baltica	76.1035	53	2190	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	-
GCF_009618275.1	s__Roseimaritima sp009618275	75.9186	59	2190	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007751715.1	s__Rosistilla oblonga	75.8747	52	2190	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	97.20	97.20	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:32,583] [INFO] GTDB search result was written to GCF_008087665.1_ASM808766v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:32,583] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:32,586] [INFO] DFAST_QC result json was written to GCF_008087665.1_ASM808766v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:32,587] [INFO] DFAST_QC completed!
[2024-01-24 13:58:32,587] [INFO] Total running time: 0h2m35s