[2023-03-15 10:34:48,003] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:34:48,015] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:34:48,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg333db952-94fd-4ead-9578-a708edd57072/dqc_reference
[2023-03-15 10:34:49,423] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:34:49,423] [INFO] Task started: Prodigal
[2023-03-15 10:34:49,423] [INFO] Running command: cat /var/lib/cwl/stgf12c893c-1b8f-4b2c-acf8-41b757ba43cf/OceanDNA-b488.fa | prodigal -d OceanDNA-b488/cds.fna -a OceanDNA-b488/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:35:08,957] [INFO] Task succeeded: Prodigal
[2023-03-15 10:35:08,957] [INFO] Task started: HMMsearch
[2023-03-15 10:35:08,957] [INFO] Running command: hmmsearch --tblout OceanDNA-b488/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg333db952-94fd-4ead-9578-a708edd57072/dqc_reference/reference_markers.hmm OceanDNA-b488/protein.faa > /dev/null
[2023-03-15 10:35:09,153] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:35:09,153] [INFO] Found 6/6 markers.
[2023-03-15 10:35:09,282] [INFO] Query marker FASTA was written to OceanDNA-b488/markers.fasta
[2023-03-15 10:35:09,282] [INFO] Task started: Blastn
[2023-03-15 10:35:09,282] [INFO] Running command: blastn -query OceanDNA-b488/markers.fasta -db /var/lib/cwl/stg333db952-94fd-4ead-9578-a708edd57072/dqc_reference/reference_markers.fasta -out OceanDNA-b488/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:35:09,931] [INFO] Task succeeded: Blastn
[2023-03-15 10:35:09,974] [INFO] Selected 17 target genomes.
[2023-03-15 10:35:09,974] [INFO] Target genome list was writen to OceanDNA-b488/target_genomes.txt
[2023-03-15 10:35:09,983] [INFO] Task started: fastANI
[2023-03-15 10:35:09,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12c893c-1b8f-4b2c-acf8-41b757ba43cf/OceanDNA-b488.fa --refList OceanDNA-b488/target_genomes.txt --output OceanDNA-b488/fastani_result.tsv --threads 1
[2023-03-15 10:35:24,040] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:24,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg333db952-94fd-4ead-9578-a708edd57072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:35:24,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg333db952-94fd-4ead-9578-a708edd57072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:35:24,048] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:35:24,048] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:35:24,048] [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
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	78.373	370	981	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	78.0499	276	981	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.2427	230	981	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.9798	183	981	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.4409	104	981	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.2316	92	981	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	75.5276	55	981	95	below_threshold
Longispora fulva	strain=NBRC 105670	GCA_016862835.1	619741	619741	type	True	75.0591	55	981	95	below_threshold
Longispora fulva	strain=DSM 45356	GCA_015751905.1	619741	619741	type	True	75.0591	55	981	95	below_threshold
Actinoplanes ferrugineus	strain=NBRC 15555	GCA_016862195.1	113564	113564	type	True	74.997	60	981	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:35:24,064] [INFO] DFAST Taxonomy check result was written to OceanDNA-b488/tc_result.tsv
[2023-03-15 10:35:24,094] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:35:24,094] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:35:24,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg333db952-94fd-4ead-9578-a708edd57072/dqc_reference/checkm_data
[2023-03-15 10:35:24,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:35:24,131] [INFO] Task started: CheckM
[2023-03-15 10:35:24,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b488/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b488/checkm_input OceanDNA-b488/checkm_result
[2023-03-15 10:36:39,473] [INFO] Task succeeded: CheckM
[2023-03-15 10:36:39,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:36:39,516] [INFO] ===== Completeness check finished =====
[2023-03-15 10:36:39,516] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:36:39,516] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b488/markers.fasta)
[2023-03-15 10:36:39,517] [INFO] Task started: Blastn
[2023-03-15 10:36:39,518] [INFO] Running command: blastn -query OceanDNA-b488/markers.fasta -db /var/lib/cwl/stg333db952-94fd-4ead-9578-a708edd57072/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b488/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:36:40,542] [INFO] Task succeeded: Blastn
[2023-03-15 10:36:40,618] [INFO] Selected 11 target genomes.
[2023-03-15 10:36:40,618] [INFO] Target genome list was writen to OceanDNA-b488/target_genomes_gtdb.txt
[2023-03-15 10:36:41,043] [INFO] Task started: fastANI
[2023-03-15 10:36:41,043] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12c893c-1b8f-4b2c-acf8-41b757ba43cf/OceanDNA-b488.fa --refList OceanDNA-b488/target_genomes_gtdb.txt --output OceanDNA-b488/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:36:48,186] [INFO] Task succeeded: fastANI
[2023-03-15 10:36:48,193] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:36:48,193] [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_018666235.1	s__Ilumatobacter_A sp018666235	99.7702	940	981	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.79	99.78	0.94	0.93	4	conclusive
GCA_002711735.1	s__Ilumatobacter_A sp002711735	86.0145	523	981	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.50	99.50	0.82	0.82	2	-
GCA_905182555.1	s__Ilumatobacter_A sp905182555	79.0541	338	981	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	78.3625	371	981	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	78.2027	343	981	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	78.0486	276	981	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213745.1	s__JABSQH01 sp013213745	77.1678	218	981	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480335.1	s__Ilumatobacter_A sp905480335	77.1283	199	981	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697065.1	s__J010 sp003697065	76.0453	60	981	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377505.1	s__WHTX01 sp009377505	75.7413	65	981	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CAIXPF01;g__WHTX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:36:48,212] [INFO] GTDB search result was written to OceanDNA-b488/result_gtdb.tsv
[2023-03-15 10:36:48,268] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:36:48,291] [INFO] DFAST_QC result json was written to OceanDNA-b488/dqc_result.json
[2023-03-15 10:36:48,291] [INFO] DFAST_QC completed!
[2023-03-15 10:36:48,291] [INFO] Total running time: 0h2m0s