[2023-03-16 13:57:23,576] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:57:23,576] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:57:23,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg865493cf-e745-4ae0-b9bc-45a8ab1d72dd/dqc_reference
[2023-03-16 13:57:26,814] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:57:26,815] [INFO] Task started: Prodigal
[2023-03-16 13:57:26,815] [INFO] Running command: cat /var/lib/cwl/stg851a81e6-4242-4b0a-bbd7-f20d552305a4/OceanDNA-b1820.fa | prodigal -d OceanDNA-b1820/cds.fna -a OceanDNA-b1820/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:57:49,944] [INFO] Task succeeded: Prodigal
[2023-03-16 13:57:49,944] [INFO] Task started: HMMsearch
[2023-03-16 13:57:49,944] [INFO] Running command: hmmsearch --tblout OceanDNA-b1820/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg865493cf-e745-4ae0-b9bc-45a8ab1d72dd/dqc_reference/reference_markers.hmm OceanDNA-b1820/protein.faa > /dev/null
[2023-03-16 13:57:50,175] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:57:50,175] [INFO] Found 6/6 markers.
[2023-03-16 13:57:50,205] [INFO] Query marker FASTA was written to OceanDNA-b1820/markers.fasta
[2023-03-16 13:57:50,207] [INFO] Task started: Blastn
[2023-03-16 13:57:50,207] [INFO] Running command: blastn -query OceanDNA-b1820/markers.fasta -db /var/lib/cwl/stg865493cf-e745-4ae0-b9bc-45a8ab1d72dd/dqc_reference/reference_markers.fasta -out OceanDNA-b1820/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:57:51,165] [INFO] Task succeeded: Blastn
[2023-03-16 13:57:51,166] [INFO] Selected 27 target genomes.
[2023-03-16 13:57:51,166] [INFO] Target genome list was writen to OceanDNA-b1820/target_genomes.txt
[2023-03-16 13:57:51,186] [INFO] Task started: fastANI
[2023-03-16 13:57:51,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg851a81e6-4242-4b0a-bbd7-f20d552305a4/OceanDNA-b1820.fa --refList OceanDNA-b1820/target_genomes.txt --output OceanDNA-b1820/fastani_result.tsv --threads 1
[2023-03-16 13:58:29,370] [INFO] Task succeeded: fastANI
[2023-03-16 13:58:29,370] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg865493cf-e745-4ae0-b9bc-45a8ab1d72dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 13:58:29,370] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg865493cf-e745-4ae0-b9bc-45a8ab1d72dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 13:58:29,380] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 13:58:29,380] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 13:58:29,381] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.6934	126	766	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.4733	118	766	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.282	137	766	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.1795	112	766	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.1326	79	766	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.0984	96	766	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.9148	116	766	95	below_threshold
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	75.2961	55	766	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	75.2163	65	766	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	75.1971	65	766	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	75.1227	59	766	95	below_threshold
Fodinicola acaciae	strain=GKU 173	GCA_010993745.1	2681555	2681555	type	True	75.0929	58	766	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	75.0926	69	766	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	75.0722	70	766	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 13:58:29,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1820/tc_result.tsv
[2023-03-16 13:58:29,381] [INFO] ===== Taxonomy check completed =====
[2023-03-16 13:58:29,381] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:58:29,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg865493cf-e745-4ae0-b9bc-45a8ab1d72dd/dqc_reference/checkm_data
[2023-03-16 13:58:29,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:58:29,387] [INFO] Task started: CheckM
[2023-03-16 13:58:29,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1820/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1820/checkm_input OceanDNA-b1820/checkm_result
[2023-03-16 13:59:09,386] [INFO] Task succeeded: CheckM
[2023-03-16 13:59:09,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 13:59:09,389] [INFO] ===== Completeness check finished =====
[2023-03-16 13:59:09,389] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:59:09,389] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1820/markers.fasta)
[2023-03-16 13:59:09,390] [INFO] Task started: Blastn
[2023-03-16 13:59:09,390] [INFO] Running command: blastn -query OceanDNA-b1820/markers.fasta -db /var/lib/cwl/stg865493cf-e745-4ae0-b9bc-45a8ab1d72dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1820/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:59:10,307] [INFO] Task succeeded: Blastn
[2023-03-16 13:59:10,308] [INFO] Selected 12 target genomes.
[2023-03-16 13:59:10,308] [INFO] Target genome list was writen to OceanDNA-b1820/target_genomes_gtdb.txt
[2023-03-16 13:59:10,704] [INFO] Task started: fastANI
[2023-03-16 13:59:10,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg851a81e6-4242-4b0a-bbd7-f20d552305a4/OceanDNA-b1820.fa --refList OceanDNA-b1820/target_genomes_gtdb.txt --output OceanDNA-b1820/fastani_result_gtdb.tsv --threads 1
[2023-03-16 13:59:18,173] [INFO] Task succeeded: fastANI
[2023-03-16 13:59:18,181] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 13:59:18,181] [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_002729125.1	s__UBA11606 sp002729125	99.9613	723	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.78	99.78	0.92	0.92	2	conclusive
GCA_002694825.1	s__UBA11606 sp002694825	91.8832	640	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	97.28	96.77	0.84	0.81	7	-
GCA_002699625.1	s__UBA11606 sp002699625	91.4309	564	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845585.1	s__UBA11606 sp016845585	78.1341	287	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480195.1	s__UBA11606 sp905480195	78.0766	271	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937405.1	s__UBA11606 sp009937405	76.9634	129	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.36	99.36	0.86	0.86	2	-
GCA_003697065.1	s__J010 sp003697065	76.7854	145	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002375.1	s__JABDJW01 sp013002375	76.7586	104	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SHLQ01;g__JABDJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003231645.1	s__SZUA-87 sp003231645	76.6251	145	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__SZUA-87	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716005.1	s__JADJXE01 sp016716005	76.1885	84	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JADJXE01;g__JADJXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698945.1	s__Ilumatobacter sp002698945	75.9785	83	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888325.1	s__AC-14 sp005888325	75.8693	83	766	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__AC-14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 13:59:18,182] [INFO] GTDB search result was written to OceanDNA-b1820/result_gtdb.tsv
[2023-03-16 13:59:18,182] [INFO] ===== GTDB Search completed =====
[2023-03-16 13:59:18,185] [INFO] DFAST_QC result json was written to OceanDNA-b1820/dqc_result.json
[2023-03-16 13:59:18,185] [INFO] DFAST_QC completed!
[2023-03-16 13:59:18,185] [INFO] Total running time: 0h1m55s