[2023-03-16 03:47:32,866] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,866] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,866] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb485657-79e8-409d-bc81-8eed28b2c48e/dqc_reference
[2023-03-16 03:47:34,539] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,540] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,540] [INFO] Running command: cat /var/lib/cwl/stg4f389e14-11e1-4107-98d4-aabd3765aabf/OceanDNA-b584.fa | prodigal -d OceanDNA-b584/cds.fna -a OceanDNA-b584/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:47,184] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:47,184] [INFO] Task started: HMMsearch
[2023-03-16 03:47:47,184] [INFO] Running command: hmmsearch --tblout OceanDNA-b584/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb485657-79e8-409d-bc81-8eed28b2c48e/dqc_reference/reference_markers.hmm OceanDNA-b584/protein.faa > /dev/null
[2023-03-16 03:47:47,432] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:47,432] [INFO] Found 6/6 markers.
[2023-03-16 03:47:47,461] [INFO] Query marker FASTA was written to OceanDNA-b584/markers.fasta
[2023-03-16 03:47:47,461] [INFO] Task started: Blastn
[2023-03-16 03:47:47,461] [INFO] Running command: blastn -query OceanDNA-b584/markers.fasta -db /var/lib/cwl/stgcb485657-79e8-409d-bc81-8eed28b2c48e/dqc_reference/reference_markers.fasta -out OceanDNA-b584/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:48,060] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:48,061] [INFO] Selected 30 target genomes.
[2023-03-16 03:47:48,061] [INFO] Target genome list was writen to OceanDNA-b584/target_genomes.txt
[2023-03-16 03:47:48,076] [INFO] Task started: fastANI
[2023-03-16 03:47:48,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f389e14-11e1-4107-98d4-aabd3765aabf/OceanDNA-b584.fa --refList OceanDNA-b584/target_genomes.txt --output OceanDNA-b584/fastani_result.tsv --threads 1
[2023-03-16 03:48:07,382] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:07,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb485657-79e8-409d-bc81-8eed28b2c48e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:07,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb485657-79e8-409d-bc81-8eed28b2c48e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:07,386] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:07,386] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:07,386] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.4681	55	373	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.8923	55	373	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:07,386] [INFO] DFAST Taxonomy check result was written to OceanDNA-b584/tc_result.tsv
[2023-03-16 03:48:07,386] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:07,386] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:07,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb485657-79e8-409d-bc81-8eed28b2c48e/dqc_reference/checkm_data
[2023-03-16 03:48:07,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:07,409] [INFO] Task started: CheckM
[2023-03-16 03:48:07,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b584/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b584/checkm_input OceanDNA-b584/checkm_result
[2023-03-16 03:48:36,968] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:36,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 18.32%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:36,971] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:36,971] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:36,971] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b584/markers.fasta)
[2023-03-16 03:48:36,971] [INFO] Task started: Blastn
[2023-03-16 03:48:36,972] [INFO] Running command: blastn -query OceanDNA-b584/markers.fasta -db /var/lib/cwl/stgcb485657-79e8-409d-bc81-8eed28b2c48e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b584/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:37,911] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:37,912] [INFO] Selected 24 target genomes.
[2023-03-16 03:48:37,912] [INFO] Target genome list was writen to OceanDNA-b584/target_genomes_gtdb.txt
[2023-03-16 03:48:38,091] [INFO] Task started: fastANI
[2023-03-16 03:48:38,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f389e14-11e1-4107-98d4-aabd3765aabf/OceanDNA-b584.fa --refList OceanDNA-b584/target_genomes_gtdb.txt --output OceanDNA-b584/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:48,399] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:48,409] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:48:48,409] [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_016845305.1	s__UBA9410 sp016845305	78.1713	167	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727895.1	s__UBA9410 sp002727895	77.8009	110	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_002346745.1	s__S20-B6 sp002346745	77.7643	163	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_002699725.1	s__S20-B6 sp002699725	77.6678	127	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.58	98.41	0.87	0.86	3	-
GCA_014239855.1	s__UBA9410 sp014239855	77.5763	143	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381945.1	s__S20-B6 sp014381945	77.5556	132	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002329075.1	s__S20-B6 sp002329075	77.5483	150	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.53	97.43	0.90	0.85	7	-
GCA_015658775.1	s__UBA3125 sp015658775	77.4492	116	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.89	98.89	0.81	0.81	2	-
GCA_012961035.1	s__UBA9410 sp012961035	77.3175	118	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_014237715.1	s__UBA9410 sp014237715	77.2114	122	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_002365325.1	s__UBA3125 sp002365325	77.0875	69	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.82	97.98	0.79	0.76	7	-
GCA_014240365.1	s__UBA9410 sp014240365	76.9283	99	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	-
GCA_014381745.1	s__UBA3125 sp014381745	76.7761	82	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.87	99.86	0.97	0.96	3	-
GCA_003541675.1	s__UBA9410 sp003541675	76.7597	60	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697065.1	s__J010 sp003697065	76.2806	60	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	76.2448	56	373	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:48:48,409] [INFO] GTDB search result was written to OceanDNA-b584/result_gtdb.tsv
[2023-03-16 03:48:48,409] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:48,410] [INFO] DFAST_QC result json was written to OceanDNA-b584/dqc_result.json
[2023-03-16 03:48:48,411] [INFO] DFAST_QC completed!
[2023-03-16 03:48:48,411] [INFO] Total running time: 0h1m16s