[2023-03-15 04:45:50,540] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:45:50,541] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:45:50,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a68cdda-b170-4d65-acb7-7a7dd9a1f63d/dqc_reference
[2023-03-15 04:45:51,709] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:45:51,709] [INFO] Task started: Prodigal
[2023-03-15 04:45:51,709] [INFO] Running command: cat /var/lib/cwl/stgb98aeb11-59c7-48ff-979b-0603a94fa317/OceanDNA-b22490.fa | prodigal -d OceanDNA-b22490/cds.fna -a OceanDNA-b22490/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:46:26,828] [INFO] Task succeeded: Prodigal
[2023-03-15 04:46:26,829] [INFO] Task started: HMMsearch
[2023-03-15 04:46:26,829] [INFO] Running command: hmmsearch --tblout OceanDNA-b22490/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a68cdda-b170-4d65-acb7-7a7dd9a1f63d/dqc_reference/reference_markers.hmm OceanDNA-b22490/protein.faa > /dev/null
[2023-03-15 04:46:27,121] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:46:27,121] [INFO] Found 6/6 markers.
[2023-03-15 04:46:27,172] [INFO] Query marker FASTA was written to OceanDNA-b22490/markers.fasta
[2023-03-15 04:46:27,173] [INFO] Task started: Blastn
[2023-03-15 04:46:27,173] [INFO] Running command: blastn -query OceanDNA-b22490/markers.fasta -db /var/lib/cwl/stg7a68cdda-b170-4d65-acb7-7a7dd9a1f63d/dqc_reference/reference_markers.fasta -out OceanDNA-b22490/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:46:27,711] [INFO] Task succeeded: Blastn
[2023-03-15 04:46:27,718] [INFO] Selected 24 target genomes.
[2023-03-15 04:46:27,718] [INFO] Target genome list was writen to OceanDNA-b22490/target_genomes.txt
[2023-03-15 04:46:27,734] [INFO] Task started: fastANI
[2023-03-15 04:46:27,734] [INFO] Running command: fastANI --query /var/lib/cwl/stgb98aeb11-59c7-48ff-979b-0603a94fa317/OceanDNA-b22490.fa --refList OceanDNA-b22490/target_genomes.txt --output OceanDNA-b22490/fastani_result.tsv --threads 1
[2023-03-15 04:46:53,774] [INFO] Task succeeded: fastANI
[2023-03-15 04:46:53,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a68cdda-b170-4d65-acb7-7a7dd9a1f63d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:46:53,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a68cdda-b170-4d65-acb7-7a7dd9a1f63d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:46:53,784] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:46:53,784] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:46:53,784] [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
Novipirellula artificiosorum	strain=Poly41	GCA_007860135.1	2528016	2528016	type	True	76.1287	62	1853	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	75.8275	80	1853	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	75.7631	60	1853	95	below_threshold
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	75.7602	79	1853	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	75.6966	65	1853	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	75.6507	54	1853	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	75.5608	62	1853	95	below_threshold
Rubripirellula obstinata	strain=LF1	GCA_008374075.1	406547	406547	type	True	75.5523	68	1853	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	75.5373	69	1853	95	below_threshold
Roseiconus lacunae	strain=JC635	GCA_008312935.1	2605694	2605694	type	True	75.514	52	1853	95	below_threshold
Rubripirellula amarantea	strain=Pla22	GCA_007859865.1	2527999	2527999	type	True	75.5075	55	1853	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	75.5049	57	1853	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	75.3899	64	1853	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	75.359	56	1853	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:46:53,788] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22490/tc_result.tsv
[2023-03-15 04:46:53,790] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:46:53,790] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:46:53,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a68cdda-b170-4d65-acb7-7a7dd9a1f63d/dqc_reference/checkm_data
[2023-03-15 04:46:53,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:46:53,807] [INFO] Task started: CheckM
[2023-03-15 04:46:53,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22490/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22490/checkm_input OceanDNA-b22490/checkm_result
[2023-03-15 04:48:20,850] [INFO] Task succeeded: CheckM
[2023-03-15 04:48:20,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:48:20,929] [INFO] ===== Completeness check finished =====
[2023-03-15 04:48:20,929] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:48:20,929] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22490/markers.fasta)
[2023-03-15 04:48:20,930] [INFO] Task started: Blastn
[2023-03-15 04:48:20,930] [INFO] Running command: blastn -query OceanDNA-b22490/markers.fasta -db /var/lib/cwl/stg7a68cdda-b170-4d65-acb7-7a7dd9a1f63d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22490/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:48:21,666] [INFO] Task succeeded: Blastn
[2023-03-15 04:48:21,669] [INFO] Selected 24 target genomes.
[2023-03-15 04:48:21,669] [INFO] Target genome list was writen to OceanDNA-b22490/target_genomes_gtdb.txt
[2023-03-15 04:48:21,689] [INFO] Task started: fastANI
[2023-03-15 04:48:21,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgb98aeb11-59c7-48ff-979b-0603a94fa317/OceanDNA-b22490.fa --refList OceanDNA-b22490/target_genomes_gtdb.txt --output OceanDNA-b22490/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:48:48,398] [INFO] Task succeeded: fastANI
[2023-03-15 04:48:48,407] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:48:48,408] [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_002712845.1	s__Rubripirellula sp002712845	77.7608	179	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862205.1	s__Rubripirellula sp002862205	77.497	433	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003513555.1	s__Rubripirellula sp003513555	77.2899	317	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689655.1	s__Rubripirellula sp002689655	77.252	345	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	100.00	100.00	0.98	0.98	2	-
GCA_002690925.1	s__Rubripirellula sp002690925	77.0035	310	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270065.1	s__Rubripirellula sp012270065	76.783	283	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	98.24	98.24	0.95	0.95	2	-
GCF_007754155.1	s__Stieleria neptunia	75.7631	60	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860125.1	s__Rubripirellula tenax	75.7602	79	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752935.1	s__Crateriforma conspicua	75.6507	54	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_008629675.1	s__Stieleria nitratireducens	75.5608	62	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642955.1	s__Rubripirellula obstinata	75.5373	69	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	99.93	99.93	1.00	1.00	2	-
GCF_008312935.1	s__Stieleria lacunae	75.514	52	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007859865.1	s__Rubripirellula amarantea	75.5075	55	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027925.1	s__Rhodopirellula islandica	75.5049	57	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860045.1	s__Stieleria varia	75.3899	64	1853	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:48:48,409] [INFO] GTDB search result was written to OceanDNA-b22490/result_gtdb.tsv
[2023-03-15 04:48:48,410] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:48:48,413] [INFO] DFAST_QC result json was written to OceanDNA-b22490/dqc_result.json
[2023-03-15 04:48:48,413] [INFO] DFAST_QC completed!
[2023-03-15 04:48:48,413] [INFO] Total running time: 0h2m58s