[2023-03-14 12:25:41,529] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,529] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d5df943-7ad2-4405-b471-187177b24166/dqc_reference
[2023-03-14 12:25:42,821] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,822] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,822] [INFO] Running command: cat /var/lib/cwl/stg5e7b7c4b-f851-4a59-97ad-bcf411c1284c/OceanDNA-b22496.fa | prodigal -d OceanDNA-b22496/cds.fna -a OceanDNA-b22496/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:26:17,891] [INFO] Task succeeded: Prodigal
[2023-03-14 12:26:17,891] [INFO] Task started: HMMsearch
[2023-03-14 12:26:17,891] [INFO] Running command: hmmsearch --tblout OceanDNA-b22496/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d5df943-7ad2-4405-b471-187177b24166/dqc_reference/reference_markers.hmm OceanDNA-b22496/protein.faa > /dev/null
[2023-03-14 12:26:18,204] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:26:18,204] [INFO] Found 6/6 markers.
[2023-03-14 12:26:18,248] [INFO] Query marker FASTA was written to OceanDNA-b22496/markers.fasta
[2023-03-14 12:26:18,250] [INFO] Task started: Blastn
[2023-03-14 12:26:18,250] [INFO] Running command: blastn -query OceanDNA-b22496/markers.fasta -db /var/lib/cwl/stg6d5df943-7ad2-4405-b471-187177b24166/dqc_reference/reference_markers.fasta -out OceanDNA-b22496/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:18,796] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:18,797] [INFO] Selected 26 target genomes.
[2023-03-14 12:26:18,797] [INFO] Target genome list was writen to OceanDNA-b22496/target_genomes.txt
[2023-03-14 12:26:18,815] [INFO] Task started: fastANI
[2023-03-14 12:26:18,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e7b7c4b-f851-4a59-97ad-bcf411c1284c/OceanDNA-b22496.fa --refList OceanDNA-b22496/target_genomes.txt --output OceanDNA-b22496/fastani_result.tsv --threads 1
[2023-03-14 12:26:46,252] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:46,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d5df943-7ad2-4405-b471-187177b24166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:26:46,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d5df943-7ad2-4405-b471-187177b24166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:26:46,262] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:26:46,263] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:26:46,263] [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
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	76.1305	108	1769	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	75.9088	124	1769	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	75.8343	84	1769	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	75.7802	78	1769	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	75.7217	119	1769	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	75.6668	125	1769	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	75.6413	90	1769	95	below_threshold
Rosistilla ulvae	strain=EC9	GCA_007741475.1	1930277	1930277	type	True	75.5507	61	1769	95	below_threshold
Rhodopirellula solitaria	strain=CA85	GCA_007859855.1	2527987	2527987	type	True	75.5435	64	1769	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	75.5349	85	1769	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	75.5054	82	1769	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	75.4739	72	1769	95	below_threshold
Roseiconus lacunae	strain=JC635	GCA_008312935.1	2605694	2605694	type	True	75.4498	73	1769	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.4454	62	1769	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	75.4289	66	1769	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	75.2975	79	1769	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:26:46,263] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22496/tc_result.tsv
[2023-03-14 12:26:46,263] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:26:46,263] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:26:46,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d5df943-7ad2-4405-b471-187177b24166/dqc_reference/checkm_data
[2023-03-14 12:26:46,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:26:46,272] [INFO] Task started: CheckM
[2023-03-14 12:26:46,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22496/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22496/checkm_input OceanDNA-b22496/checkm_result
[2023-03-14 12:28:12,732] [INFO] Task succeeded: CheckM
[2023-03-14 12:28:12,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.65%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:28:12,737] [INFO] ===== Completeness check finished =====
[2023-03-14 12:28:12,737] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:28:12,737] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22496/markers.fasta)
[2023-03-14 12:28:12,738] [INFO] Task started: Blastn
[2023-03-14 12:28:12,739] [INFO] Running command: blastn -query OceanDNA-b22496/markers.fasta -db /var/lib/cwl/stg6d5df943-7ad2-4405-b471-187177b24166/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22496/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:28:13,498] [INFO] Task succeeded: Blastn
[2023-03-14 12:28:13,499] [INFO] Selected 29 target genomes.
[2023-03-14 12:28:13,499] [INFO] Target genome list was writen to OceanDNA-b22496/target_genomes_gtdb.txt
[2023-03-14 12:28:13,524] [INFO] Task started: fastANI
[2023-03-14 12:28:13,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e7b7c4b-f851-4a59-97ad-bcf411c1284c/OceanDNA-b22496.fa --refList OceanDNA-b22496/target_genomes_gtdb.txt --output OceanDNA-b22496/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:28:46,618] [INFO] Task succeeded: fastANI
[2023-03-14 12:28:46,629] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:28:46,630] [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	76.793	63	1769	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	76.5586	128	1769	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	76.1929	112	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	100.00	100.00	0.98	0.98	2	-
GCF_007860125.1	s__Rubripirellula tenax	76.1305	108	1769	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	76.1092	106	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741535.1	s__Rubripirellula sp007741535	75.9212	123	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338295.1	s__Rhodopirellula europaea	75.7802	78	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCA_007753675.1	s__Stieleria sp007753675	75.748	130	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860175.1	s__Rubripirellula reticaptiva	75.7234	119	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754155.1	s__Stieleria neptunia	75.6668	125	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	75.6482	118	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192335.1	s__Rhodopirellula rubra	75.6413	90	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCA_007741555.1	s__K23-9 sp007741555	75.6085	79	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__K23-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741475.1	s__Rosistilla sp007741475	75.5507	61	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859855.1	s__Rhodopirellula solitaria	75.5435	64	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027925.1	s__Rhodopirellula islandica	75.5349	85	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002727185.1	s__Rhodopirellula bahusiensis	75.4919	83	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312935.1	s__Stieleria lacunae	75.4498	73	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000346505.1	s__Rhodopirellula sallentina	75.4289	66	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196115.1	s__Rhodopirellula baltica	75.2975	79	1769	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	-
--------------------------------------------------------------------------------
[2023-03-14 12:28:46,630] [INFO] GTDB search result was written to OceanDNA-b22496/result_gtdb.tsv
[2023-03-14 12:28:46,630] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:28:46,632] [INFO] DFAST_QC result json was written to OceanDNA-b22496/dqc_result.json
[2023-03-14 12:28:46,632] [INFO] DFAST_QC completed!
[2023-03-14 12:28:46,632] [INFO] Total running time: 0h3m5s