[2023-03-18 03:09:33,541] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:33,541] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:33,542] [INFO] DQC Reference Directory: /var/lib/cwl/stgc19a6680-8ed9-44b0-8374-ecc6fca37af6/dqc_reference
[2023-03-18 03:09:34,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:34,689] [INFO] Task started: Prodigal
[2023-03-18 03:09:34,689] [INFO] Running command: cat /var/lib/cwl/stg1284724a-f894-48c4-b31d-3902d2c5f1ce/OceanDNA-b22946.fa | prodigal -d OceanDNA-b22946/cds.fna -a OceanDNA-b22946/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:10:09,625] [INFO] Task succeeded: Prodigal
[2023-03-18 03:10:09,625] [INFO] Task started: HMMsearch
[2023-03-18 03:10:09,626] [INFO] Running command: hmmsearch --tblout OceanDNA-b22946/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc19a6680-8ed9-44b0-8374-ecc6fca37af6/dqc_reference/reference_markers.hmm OceanDNA-b22946/protein.faa > /dev/null
[2023-03-18 03:10:09,995] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:10:09,996] [INFO] Found 6/6 markers.
[2023-03-18 03:10:10,030] [INFO] Query marker FASTA was written to OceanDNA-b22946/markers.fasta
[2023-03-18 03:10:10,031] [INFO] Task started: Blastn
[2023-03-18 03:10:10,031] [INFO] Running command: blastn -query OceanDNA-b22946/markers.fasta -db /var/lib/cwl/stgc19a6680-8ed9-44b0-8374-ecc6fca37af6/dqc_reference/reference_markers.fasta -out OceanDNA-b22946/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:10,603] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:10,603] [INFO] Selected 24 target genomes.
[2023-03-18 03:10:10,604] [INFO] Target genome list was writen to OceanDNA-b22946/target_genomes.txt
[2023-03-18 03:10:10,617] [INFO] Task started: fastANI
[2023-03-18 03:10:10,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg1284724a-f894-48c4-b31d-3902d2c5f1ce/OceanDNA-b22946.fa --refList OceanDNA-b22946/target_genomes.txt --output OceanDNA-b22946/fastani_result.tsv --threads 1
[2023-03-18 03:10:29,534] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:29,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc19a6680-8ed9-44b0-8374-ecc6fca37af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:10:29,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc19a6680-8ed9-44b0-8374-ecc6fca37af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:10:29,539] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:10:29,539] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:10:29,539] [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
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.438	72	1777	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.358	128	1777	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.222	85	1777	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.0157	76	1777	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:10:29,539] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22946/tc_result.tsv
[2023-03-18 03:10:29,539] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:10:29,539] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:10:29,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc19a6680-8ed9-44b0-8374-ecc6fca37af6/dqc_reference/checkm_data
[2023-03-18 03:10:29,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:10:29,547] [INFO] Task started: CheckM
[2023-03-18 03:10:29,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22946/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22946/checkm_input OceanDNA-b22946/checkm_result
[2023-03-18 03:12:09,064] [INFO] Task succeeded: CheckM
[2023-03-18 03:12:09,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:12:09,068] [INFO] ===== Completeness check finished =====
[2023-03-18 03:12:09,068] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:12:09,069] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22946/markers.fasta)
[2023-03-18 03:12:09,070] [INFO] Task started: Blastn
[2023-03-18 03:12:09,070] [INFO] Running command: blastn -query OceanDNA-b22946/markers.fasta -db /var/lib/cwl/stgc19a6680-8ed9-44b0-8374-ecc6fca37af6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22946/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:12:09,803] [INFO] Task succeeded: Blastn
[2023-03-18 03:12:09,804] [INFO] Selected 17 target genomes.
[2023-03-18 03:12:09,804] [INFO] Target genome list was writen to OceanDNA-b22946/target_genomes_gtdb.txt
[2023-03-18 03:12:10,016] [INFO] Task started: fastANI
[2023-03-18 03:12:10,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg1284724a-f894-48c4-b31d-3902d2c5f1ce/OceanDNA-b22946.fa --refList OceanDNA-b22946/target_genomes_gtdb.txt --output OceanDNA-b22946/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:12:26,958] [INFO] Task succeeded: fastANI
[2023-03-18 03:12:26,966] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:12:26,966] [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_002724315.1	s__UBA8437 sp002724315	97.8591	1534	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	conclusive
GCA_003445035.1	s__UBA8437 sp003445035	90.8268	1430	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724415.1	s__UBA8437 sp002724415	79.6979	968	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726205.1	s__GCA-2726205 sp002726205	78.121	650	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__GCA-2726205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861195.1	s__UBA10511 sp903861195	75.4891	81	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__UBA10511	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388505.1	s__MB-PLM-1 sp003388505	75.4356	106	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.3667	127	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699955.1	s__JABISG01 sp018699955	75.328	94	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABISG01	95.0	99.95	99.95	0.96	0.96	3	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.2368	62	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.2242	60	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872645.1	s__SXKJ01 sp016872645	75.1521	71	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935315.1	s__JAFGRD01 sp016935315	75.0465	75	1777	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGRD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:12:26,966] [INFO] GTDB search result was written to OceanDNA-b22946/result_gtdb.tsv
[2023-03-18 03:12:26,967] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:12:26,968] [INFO] DFAST_QC result json was written to OceanDNA-b22946/dqc_result.json
[2023-03-18 03:12:26,968] [INFO] DFAST_QC completed!
[2023-03-18 03:12:26,968] [INFO] Total running time: 0h2m53s