[2023-03-16 23:35:12,971] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:12,971] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:12,971] [INFO] DQC Reference Directory: /var/lib/cwl/stg00f728d5-a21f-4b81-afd6-3747bf672204/dqc_reference
[2023-03-16 23:35:14,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,100] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,100] [INFO] Running command: cat /var/lib/cwl/stg182303e2-9102-49fc-a05a-d84d2c35e81e/OceanDNA-b22840.fa | prodigal -d OceanDNA-b22840/cds.fna -a OceanDNA-b22840/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:53,274] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:53,275] [INFO] Task started: HMMsearch
[2023-03-16 23:35:53,275] [INFO] Running command: hmmsearch --tblout OceanDNA-b22840/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00f728d5-a21f-4b81-afd6-3747bf672204/dqc_reference/reference_markers.hmm OceanDNA-b22840/protein.faa > /dev/null
[2023-03-16 23:35:53,551] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:53,552] [INFO] Found 6/6 markers.
[2023-03-16 23:35:53,591] [INFO] Query marker FASTA was written to OceanDNA-b22840/markers.fasta
[2023-03-16 23:35:53,591] [INFO] Task started: Blastn
[2023-03-16 23:35:53,591] [INFO] Running command: blastn -query OceanDNA-b22840/markers.fasta -db /var/lib/cwl/stg00f728d5-a21f-4b81-afd6-3747bf672204/dqc_reference/reference_markers.fasta -out OceanDNA-b22840/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:54,132] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:54,133] [INFO] Selected 27 target genomes.
[2023-03-16 23:35:54,133] [INFO] Target genome list was writen to OceanDNA-b22840/target_genomes.txt
[2023-03-16 23:35:54,149] [INFO] Task started: fastANI
[2023-03-16 23:35:54,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg182303e2-9102-49fc-a05a-d84d2c35e81e/OceanDNA-b22840.fa --refList OceanDNA-b22840/target_genomes.txt --output OceanDNA-b22840/fastani_result.tsv --threads 1
[2023-03-16 23:36:18,355] [INFO] Task succeeded: fastANI
[2023-03-16 23:36:18,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00f728d5-a21f-4b81-afd6-3747bf672204/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:36:18,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00f728d5-a21f-4b81-afd6-3747bf672204/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:36:18,361] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:36:18,361] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:36:18,361] [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
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	75.4725	74	2160	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.3947	122	2160	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	75.215	66	2160	95	below_threshold
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	75.1197	55	2160	95	below_threshold
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	75.106	85	2160	95	below_threshold
Thalassoroseus pseudoceratinae	strain=JC658	GCA_011634775.1	2713176	2713176	type	True	74.9767	50	2160	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:36:18,361] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22840/tc_result.tsv
[2023-03-16 23:36:18,362] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:36:18,362] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:36:18,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00f728d5-a21f-4b81-afd6-3747bf672204/dqc_reference/checkm_data
[2023-03-16 23:36:18,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:36:18,371] [INFO] Task started: CheckM
[2023-03-16 23:36:18,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22840/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22840/checkm_input OceanDNA-b22840/checkm_result
[2023-03-16 23:37:53,207] [INFO] Task succeeded: CheckM
[2023-03-16 23:37:53,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.84%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:37:53,218] [INFO] ===== Completeness check finished =====
[2023-03-16 23:37:53,218] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:37:53,219] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22840/markers.fasta)
[2023-03-16 23:37:53,220] [INFO] Task started: Blastn
[2023-03-16 23:37:53,220] [INFO] Running command: blastn -query OceanDNA-b22840/markers.fasta -db /var/lib/cwl/stg00f728d5-a21f-4b81-afd6-3747bf672204/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22840/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:37:53,962] [INFO] Task succeeded: Blastn
[2023-03-16 23:37:53,966] [INFO] Selected 22 target genomes.
[2023-03-16 23:37:53,966] [INFO] Target genome list was writen to OceanDNA-b22840/target_genomes_gtdb.txt
[2023-03-16 23:37:54,641] [INFO] Task started: fastANI
[2023-03-16 23:37:54,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg182303e2-9102-49fc-a05a-d84d2c35e81e/OceanDNA-b22840.fa --refList OceanDNA-b22840/target_genomes_gtdb.txt --output OceanDNA-b22840/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:38:17,194] [INFO] Task succeeded: fastANI
[2023-03-16 23:38:17,202] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:38:17,202] [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_016779365.1	s__JABMPE01 sp016779365	80.898	611	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203845.1	s__JABMPE01 sp013203845	79.7368	1075	2160	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	76.2624	320	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795105.1	s__Rubinisphaera sp017795105	75.6406	66	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778115.1	s__SXKJ01 sp005778115	75.5133	89	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.84	99.84	0.89	0.89	2	-
GCF_000165715.2	s__Rubinisphaera brasiliensis	75.4399	60	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.4367	116	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872645.1	s__SXKJ01 sp016872645	75.3052	69	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299185.1	s__AM-0621 sp900299185	75.2622	74	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__AM-0621	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235885.1	s__JACRIH01 sp016235885	75.1557	63	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACRIH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903840265.1	s__Schlesneria sp903840265	75.1514	64	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.98	99.98	0.97	0.97	3	-
GCF_007748155.1	s__Gimesia panareensis	75.1334	54	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	96.61	95.86	0.91	0.90	3	-
GCF_001983935.1	s__Fuerstia marisgermanicae	75.0979	86	2160	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:38:17,204] [INFO] GTDB search result was written to OceanDNA-b22840/result_gtdb.tsv
[2023-03-16 23:38:17,206] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:38:17,208] [INFO] DFAST_QC result json was written to OceanDNA-b22840/dqc_result.json
[2023-03-16 23:38:17,209] [INFO] DFAST_QC completed!
[2023-03-16 23:38:17,209] [INFO] Total running time: 0h3m4s