[2023-06-19 13:14:08,021] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:14:08,030] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:14:08,030] [INFO] DQC Reference Directory: /var/lib/cwl/stga7386318-d924-4449-b776-bc10e6158f0f/dqc_reference
[2023-06-19 13:14:09,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:14:09,565] [INFO] Task started: Prodigal
[2023-06-19 13:14:09,565] [INFO] Running command: gunzip -c /var/lib/cwl/stg19041bf5-8a10-4ced-a554-88aa1a464e01/GCA_013203845.1_ASM1320384v1_genomic.fna.gz | prodigal -d GCA_013203845.1_ASM1320384v1_genomic.fna/cds.fna -a GCA_013203845.1_ASM1320384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:14:31,195] [INFO] Task succeeded: Prodigal
[2023-06-19 13:14:31,195] [INFO] Task started: HMMsearch
[2023-06-19 13:14:31,195] [INFO] Running command: hmmsearch --tblout GCA_013203845.1_ASM1320384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7386318-d924-4449-b776-bc10e6158f0f/dqc_reference/reference_markers.hmm GCA_013203845.1_ASM1320384v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:14:31,642] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:14:31,643] [INFO] Found 6/6 markers.
[2023-06-19 13:14:31,721] [INFO] Query marker FASTA was written to GCA_013203845.1_ASM1320384v1_genomic.fna/markers.fasta
[2023-06-19 13:14:31,721] [INFO] Task started: Blastn
[2023-06-19 13:14:31,721] [INFO] Running command: blastn -query GCA_013203845.1_ASM1320384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7386318-d924-4449-b776-bc10e6158f0f/dqc_reference/reference_markers.fasta -out GCA_013203845.1_ASM1320384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:14:32,363] [INFO] Task succeeded: Blastn
[2023-06-19 13:14:32,367] [INFO] Selected 25 target genomes.
[2023-06-19 13:14:32,367] [INFO] Target genome list was writen to GCA_013203845.1_ASM1320384v1_genomic.fna/target_genomes.txt
[2023-06-19 13:14:32,374] [INFO] Task started: fastANI
[2023-06-19 13:14:32,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg19041bf5-8a10-4ced-a554-88aa1a464e01/GCA_013203845.1_ASM1320384v1_genomic.fna.gz --refList GCA_013203845.1_ASM1320384v1_genomic.fna/target_genomes.txt --output GCA_013203845.1_ASM1320384v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:14:57,116] [INFO] Task succeeded: fastANI
[2023-06-19 13:14:57,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7386318-d924-4449-b776-bc10e6158f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:14:57,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7386318-d924-4449-b776-bc10e6158f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:14:57,126] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:14:57,126] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:14:57,126] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.1676	87	2457	95	below_threshold
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	75.1042	70	2457	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	74.949	60	2457	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:14:57,128] [INFO] DFAST Taxonomy check result was written to GCA_013203845.1_ASM1320384v1_genomic.fna/tc_result.tsv
[2023-06-19 13:14:57,129] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:14:57,129] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:14:57,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7386318-d924-4449-b776-bc10e6158f0f/dqc_reference/checkm_data
[2023-06-19 13:14:57,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:14:57,210] [INFO] Task started: CheckM
[2023-06-19 13:14:57,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013203845.1_ASM1320384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013203845.1_ASM1320384v1_genomic.fna/checkm_input GCA_013203845.1_ASM1320384v1_genomic.fna/checkm_result
[2023-06-19 13:16:00,804] [INFO] Task succeeded: CheckM
[2023-06-19 13:16:00,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.91%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:16:00,835] [INFO] ===== Completeness check finished =====
[2023-06-19 13:16:00,836] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:16:00,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013203845.1_ASM1320384v1_genomic.fna/markers.fasta)
[2023-06-19 13:16:00,837] [INFO] Task started: Blastn
[2023-06-19 13:16:00,837] [INFO] Running command: blastn -query GCA_013203845.1_ASM1320384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7386318-d924-4449-b776-bc10e6158f0f/dqc_reference/reference_markers_gtdb.fasta -out GCA_013203845.1_ASM1320384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:16:01,632] [INFO] Task succeeded: Blastn
[2023-06-19 13:16:01,637] [INFO] Selected 26 target genomes.
[2023-06-19 13:16:01,637] [INFO] Target genome list was writen to GCA_013203845.1_ASM1320384v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:16:01,673] [INFO] Task started: fastANI
[2023-06-19 13:16:01,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg19041bf5-8a10-4ced-a554-88aa1a464e01/GCA_013203845.1_ASM1320384v1_genomic.fna.gz --refList GCA_013203845.1_ASM1320384v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013203845.1_ASM1320384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:16:26,612] [INFO] Task succeeded: fastANI
[2023-06-19 13:16:26,632] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:16:26,633] [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_013203845.1	s__JABMPE01 sp013203845	100.0	2419	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016779365.1	s__JABMPE01 sp016779365	79.5942	571	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124895.1	s__JABMPE01 sp016124895	76.5563	335	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242525.1	s__Schlesneria sp018242525	75.745	53	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299185.1	s__AM-0621 sp900299185	75.2144	70	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__AM-0621	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.1701	87	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778115.1	s__SXKJ01 sp005778115	75.1066	68	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.84	99.84	0.89	0.89	2	-
GCF_001983935.1	s__Fuerstia marisgermanicae	75.1042	70	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235885.1	s__JACRIH01 sp016235885	74.9804	54	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACRIH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113665.1	s__Planctomicrobium piriforme	74.9653	58	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696385.1	s__J052 sp003696385	74.898	64	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__J052	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:16:26,635] [INFO] GTDB search result was written to GCA_013203845.1_ASM1320384v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:16:26,636] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:16:26,640] [INFO] DFAST_QC result json was written to GCA_013203845.1_ASM1320384v1_genomic.fna/dqc_result.json
[2023-06-19 13:16:26,641] [INFO] DFAST_QC completed!
[2023-06-19 13:16:26,641] [INFO] Total running time: 0h2m19s