[2023-03-18 07:06:22,032] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:22,032] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:22,032] [INFO] DQC Reference Directory: /var/lib/cwl/stg650727af-105f-438b-b5fe-90db9dacce3f/dqc_reference
[2023-03-18 07:06:23,286] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:23,286] [INFO] Task started: Prodigal
[2023-03-18 07:06:23,286] [INFO] Running command: cat /var/lib/cwl/stg45868c88-aca7-42db-97ed-5ad36257be46/OceanDNA-b22926.fa | prodigal -d OceanDNA-b22926/cds.fna -a OceanDNA-b22926/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:54,607] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:54,608] [INFO] Task started: HMMsearch
[2023-03-18 07:06:54,608] [INFO] Running command: hmmsearch --tblout OceanDNA-b22926/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg650727af-105f-438b-b5fe-90db9dacce3f/dqc_reference/reference_markers.hmm OceanDNA-b22926/protein.faa > /dev/null
[2023-03-18 07:06:54,893] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:54,894] [INFO] Found 6/6 markers.
[2023-03-18 07:06:54,927] [INFO] Query marker FASTA was written to OceanDNA-b22926/markers.fasta
[2023-03-18 07:06:54,928] [INFO] Task started: Blastn
[2023-03-18 07:06:54,928] [INFO] Running command: blastn -query OceanDNA-b22926/markers.fasta -db /var/lib/cwl/stg650727af-105f-438b-b5fe-90db9dacce3f/dqc_reference/reference_markers.fasta -out OceanDNA-b22926/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:55,471] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:55,472] [INFO] Selected 30 target genomes.
[2023-03-18 07:06:55,472] [INFO] Target genome list was writen to OceanDNA-b22926/target_genomes.txt
[2023-03-18 07:06:55,488] [INFO] Task started: fastANI
[2023-03-18 07:06:55,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg45868c88-aca7-42db-97ed-5ad36257be46/OceanDNA-b22926.fa --refList OceanDNA-b22926/target_genomes.txt --output OceanDNA-b22926/fastani_result.tsv --threads 1
[2023-03-18 07:07:21,921] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:21,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg650727af-105f-438b-b5fe-90db9dacce3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:07:21,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg650727af-105f-438b-b5fe-90db9dacce3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:07:21,927] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:07:21,928] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:07:21,928] [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	75.687	136	1655	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.3752	97	1655	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.3033	94	1655	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	75.2668	101	1655	95	below_threshold
Roseimaritima ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	74.8865	59	1655	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	74.8729	55	1655	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	74.6942	65	1655	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	74.6123	81	1655	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	74.5864	69	1655	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:07:21,928] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22926/tc_result.tsv
[2023-03-18 07:07:21,928] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:07:21,928] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:07:21,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg650727af-105f-438b-b5fe-90db9dacce3f/dqc_reference/checkm_data
[2023-03-18 07:07:21,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:07:21,935] [INFO] Task started: CheckM
[2023-03-18 07:07:21,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22926/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22926/checkm_input OceanDNA-b22926/checkm_result
[2023-03-18 07:08:45,757] [INFO] Task succeeded: CheckM
[2023-03-18 07:08:45,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:08:45,761] [INFO] ===== Completeness check finished =====
[2023-03-18 07:08:45,761] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:08:45,761] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22926/markers.fasta)
[2023-03-18 07:08:45,762] [INFO] Task started: Blastn
[2023-03-18 07:08:45,762] [INFO] Running command: blastn -query OceanDNA-b22926/markers.fasta -db /var/lib/cwl/stg650727af-105f-438b-b5fe-90db9dacce3f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22926/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:08:46,543] [INFO] Task succeeded: Blastn
[2023-03-18 07:08:46,544] [INFO] Selected 22 target genomes.
[2023-03-18 07:08:46,544] [INFO] Target genome list was writen to OceanDNA-b22926/target_genomes_gtdb.txt
[2023-03-18 07:08:47,059] [INFO] Task started: fastANI
[2023-03-18 07:08:47,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg45868c88-aca7-42db-97ed-5ad36257be46/OceanDNA-b22926.fa --refList OceanDNA-b22926/target_genomes_gtdb.txt --output OceanDNA-b22926/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:09:06,217] [INFO] Task succeeded: fastANI
[2023-03-18 07:09:06,225] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:09:06,225] [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_003445035.1	s__UBA8437 sp003445035	80.7811	1071	1655	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724315.1	s__UBA8437 sp002724315	80.1211	1030	1655	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	-
GCA_002724415.1	s__UBA8437 sp002724415	79.6862	980	1655	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	78.2843	669	1655	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__GCA-2726205	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.7036	132	1655	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	75.4933	95	1655	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABISG01	95.0	99.95	99.95	0.96	0.96	3	-
GCA_009691905.1	s__SIAF01 sp009691905	75.3895	97	1655	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__SIAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.3834	96	1655	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935315.1	s__JAFGRD01 sp016935315	75.3561	76	1655	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGRD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124895.1	s__JABMPE01 sp016124895	75.3239	96	1655	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	75.3216	65	1655	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872645.1	s__SXKJ01 sp016872645	75.229	69	1655	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200145.1	s__JACQFH01 sp016200145	75.2234	119	1655	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACQFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464385.1	s__Ga0077550 sp001464385	74.7444	83	1655	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:09:06,225] [INFO] GTDB search result was written to OceanDNA-b22926/result_gtdb.tsv
[2023-03-18 07:09:06,225] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:09:06,227] [INFO] DFAST_QC result json was written to OceanDNA-b22926/dqc_result.json
[2023-03-18 07:09:06,227] [INFO] DFAST_QC completed!
[2023-03-18 07:09:06,227] [INFO] Total running time: 0h2m44s