[2023-03-17 23:08:31,951] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,951] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg27a05032-ac1b-4215-9955-55590b06f004/dqc_reference
[2023-03-17 23:08:33,132] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,132] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,132] [INFO] Running command: cat /var/lib/cwl/stg43cd4199-9e90-4e12-8b44-77fdef4d03e1/OceanDNA-b479.fa | prodigal -d OceanDNA-b479/cds.fna -a OceanDNA-b479/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:51,175] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:51,175] [INFO] Task started: HMMsearch
[2023-03-17 23:08:51,175] [INFO] Running command: hmmsearch --tblout OceanDNA-b479/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27a05032-ac1b-4215-9955-55590b06f004/dqc_reference/reference_markers.hmm OceanDNA-b479/protein.faa > /dev/null
[2023-03-17 23:08:51,432] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:51,432] [INFO] Found 6/6 markers.
[2023-03-17 23:08:51,458] [INFO] Query marker FASTA was written to OceanDNA-b479/markers.fasta
[2023-03-17 23:08:51,459] [INFO] Task started: Blastn
[2023-03-17 23:08:51,459] [INFO] Running command: blastn -query OceanDNA-b479/markers.fasta -db /var/lib/cwl/stg27a05032-ac1b-4215-9955-55590b06f004/dqc_reference/reference_markers.fasta -out OceanDNA-b479/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:52,245] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:52,248] [INFO] Selected 11 target genomes.
[2023-03-17 23:08:52,249] [INFO] Target genome list was writen to OceanDNA-b479/target_genomes.txt
[2023-03-17 23:08:52,255] [INFO] Task started: fastANI
[2023-03-17 23:08:52,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg43cd4199-9e90-4e12-8b44-77fdef4d03e1/OceanDNA-b479.fa --refList OceanDNA-b479/target_genomes.txt --output OceanDNA-b479/fastani_result.tsv --threads 1
[2023-03-17 23:09:00,001] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:00,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27a05032-ac1b-4215-9955-55590b06f004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:09:00,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27a05032-ac1b-4215-9955-55590b06f004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:09:00,009] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:09:00,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:09:00,010] [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	78.1087	375	922	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.3988	279	922	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.047	220	922	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.9693	155	922	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.0977	74	922	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.6135	93	922	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:09:00,012] [INFO] DFAST Taxonomy check result was written to OceanDNA-b479/tc_result.tsv
[2023-03-17 23:09:00,013] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:09:00,013] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:09:00,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27a05032-ac1b-4215-9955-55590b06f004/dqc_reference/checkm_data
[2023-03-17 23:09:00,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:09:00,069] [INFO] Task started: CheckM
[2023-03-17 23:09:00,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b479/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b479/checkm_input OceanDNA-b479/checkm_result
[2023-03-17 23:09:48,735] [INFO] Task succeeded: CheckM
[2023-03-17 23:09:48,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:09:48,751] [INFO] ===== Completeness check finished =====
[2023-03-17 23:09:48,751] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:09:48,751] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b479/markers.fasta)
[2023-03-17 23:09:48,751] [INFO] Task started: Blastn
[2023-03-17 23:09:48,751] [INFO] Running command: blastn -query OceanDNA-b479/markers.fasta -db /var/lib/cwl/stg27a05032-ac1b-4215-9955-55590b06f004/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b479/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:49,946] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:49,959] [INFO] Selected 18 target genomes.
[2023-03-17 23:09:49,959] [INFO] Target genome list was writen to OceanDNA-b479/target_genomes_gtdb.txt
[2023-03-17 23:09:49,976] [INFO] Task started: fastANI
[2023-03-17 23:09:49,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg43cd4199-9e90-4e12-8b44-77fdef4d03e1/OceanDNA-b479.fa --refList OceanDNA-b479/target_genomes_gtdb.txt --output OceanDNA-b479/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:10:00,427] [INFO] Task succeeded: fastANI
[2023-03-17 23:10:00,437] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:10:00,437] [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_905182555.1	s__Ilumatobacter_A sp905182555	86.6474	609	922	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_018666235.1	s__Ilumatobacter_A sp018666235	78.6015	396	922	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.79	99.78	0.94	0.93	4	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	78.1092	375	922	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	77.6704	318	922	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	77.3991	279	922	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_002711735.1	s__Ilumatobacter_A sp002711735	77.2435	160	922	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.50	99.50	0.82	0.82	2	-
GCF_004364865.1	s__Ilumatobacter fluminis	77.0586	219	922	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480335.1	s__Ilumatobacter_A sp905480335	76.8864	162	922	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	76.8444	181	922	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698945.1	s__Ilumatobacter sp002698945	76.7387	161	922	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015767405.1	s__Sva-07 sp015767405	76.6057	118	922	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Sva-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213625.1	s__UBA668 sp016213625	76.4322	140	922	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213665.1	s__UBA668 sp016213665	76.0623	77	922	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009919275.1	s__F1-20-MAGs119 sp009919275	76.0003	59	922	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-20-MAGs119	95.0	99.53	99.53	0.87	0.87	2	-
GCA_005778215.1	s__UBA668 sp005778215	75.8852	97	922	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.54	99.53	0.90	0.89	3	-
GCA_009701715.1	s__WLJO01 sp009701715	75.8382	71	922	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__WLJO01	95.0	98.34	95.43	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-17 23:10:00,441] [INFO] GTDB search result was written to OceanDNA-b479/result_gtdb.tsv
[2023-03-17 23:10:00,448] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:10:00,455] [INFO] DFAST_QC result json was written to OceanDNA-b479/dqc_result.json
[2023-03-17 23:10:00,455] [INFO] DFAST_QC completed!
[2023-03-17 23:10:00,455] [INFO] Total running time: 0h1m29s