[2023-03-16 10:20:34,896] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,896] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,896] [INFO] DQC Reference Directory: /var/lib/cwl/stg4282d576-3957-44a8-b334-1948d1e9bda9/dqc_reference
[2023-03-16 10:20:36,138] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:36,138] [INFO] Task started: Prodigal
[2023-03-16 10:20:36,138] [INFO] Running command: cat /var/lib/cwl/stgaf8c07f1-43ad-4d50-bac4-fc2628a9a4be/OceanDNA-b39139.fa | prodigal -d OceanDNA-b39139/cds.fna -a OceanDNA-b39139/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:21:02,557] [INFO] Task succeeded: Prodigal
[2023-03-16 10:21:02,557] [INFO] Task started: HMMsearch
[2023-03-16 10:21:02,557] [INFO] Running command: hmmsearch --tblout OceanDNA-b39139/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4282d576-3957-44a8-b334-1948d1e9bda9/dqc_reference/reference_markers.hmm OceanDNA-b39139/protein.faa > /dev/null
[2023-03-16 10:21:02,836] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:21:02,836] [INFO] Found 6/6 markers.
[2023-03-16 10:21:02,863] [INFO] Query marker FASTA was written to OceanDNA-b39139/markers.fasta
[2023-03-16 10:21:02,864] [INFO] Task started: Blastn
[2023-03-16 10:21:02,864] [INFO] Running command: blastn -query OceanDNA-b39139/markers.fasta -db /var/lib/cwl/stg4282d576-3957-44a8-b334-1948d1e9bda9/dqc_reference/reference_markers.fasta -out OceanDNA-b39139/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:04,095] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:04,096] [INFO] Selected 14 target genomes.
[2023-03-16 10:21:04,096] [INFO] Target genome list was writen to OceanDNA-b39139/target_genomes.txt
[2023-03-16 10:21:04,106] [INFO] Task started: fastANI
[2023-03-16 10:21:04,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf8c07f1-43ad-4d50-bac4-fc2628a9a4be/OceanDNA-b39139.fa --refList OceanDNA-b39139/target_genomes.txt --output OceanDNA-b39139/fastani_result.tsv --threads 1
[2023-03-16 10:21:16,290] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:16,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4282d576-3957-44a8-b334-1948d1e9bda9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:21:16,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4282d576-3957-44a8-b334-1948d1e9bda9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:21:16,300] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:21:16,300] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:21:16,300] [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
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	86.9576	971	1380	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	83.9369	877	1380	95	below_threshold
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	83.3732	878	1380	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	83.2534	867	1380	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	82.8779	822	1380	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	81.5025	723	1380	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.8198	642	1380	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	80.3175	628	1380	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.0532	563	1380	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	80.0094	569	1380	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.6924	509	1380	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	79.6244	550	1380	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	79.2792	372	1380	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	79.1644	514	1380	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:21:16,301] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39139/tc_result.tsv
[2023-03-16 10:21:16,301] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:21:16,301] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:21:16,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4282d576-3957-44a8-b334-1948d1e9bda9/dqc_reference/checkm_data
[2023-03-16 10:21:16,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:21:16,308] [INFO] Task started: CheckM
[2023-03-16 10:21:16,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39139/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39139/checkm_input OceanDNA-b39139/checkm_result
[2023-03-16 10:22:21,062] [INFO] Task succeeded: CheckM
[2023-03-16 10:22:21,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:22:21,066] [INFO] ===== Completeness check finished =====
[2023-03-16 10:22:21,066] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:22:21,067] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39139/markers.fasta)
[2023-03-16 10:22:21,068] [INFO] Task started: Blastn
[2023-03-16 10:22:21,068] [INFO] Running command: blastn -query OceanDNA-b39139/markers.fasta -db /var/lib/cwl/stg4282d576-3957-44a8-b334-1948d1e9bda9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39139/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:22:22,252] [INFO] Task succeeded: Blastn
[2023-03-16 10:22:22,253] [INFO] Selected 13 target genomes.
[2023-03-16 10:22:22,253] [INFO] Target genome list was writen to OceanDNA-b39139/target_genomes_gtdb.txt
[2023-03-16 10:22:22,262] [INFO] Task started: fastANI
[2023-03-16 10:22:22,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf8c07f1-43ad-4d50-bac4-fc2628a9a4be/OceanDNA-b39139.fa --refList OceanDNA-b39139/target_genomes_gtdb.txt --output OceanDNA-b39139/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:22:33,352] [INFO] Task succeeded: fastANI
[2023-03-16 10:22:33,360] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:22:33,363] [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_002707215.1	s__Marinobacter sp002707215	98.9404	640	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003441595.1	s__Marinobacter sp003441595	92.7267	1076	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744735.1	s__Marinobacter guineae	86.9347	973	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045555.1	s__Marinobacter subterrani	83.9216	880	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	83.5753	897	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCA_003030785.1	s__Marinobacter sp003030785	83.5262	561	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650915.1	s__Marinobacter sp001650915	83.4619	901	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_002933275.1	s__Marinobacter maroccanus	83.3736	878	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008107725.1	s__Marinobacter sp008107725	82.97	884	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188435.1	s__Marinobacter sp900188435	82.9279	844	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188315.1	s__Marinobacter sp900188315	82.725	799	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.8497	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	81.5119	722	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	80.8263	642	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:22:33,363] [INFO] GTDB search result was written to OceanDNA-b39139/result_gtdb.tsv
[2023-03-16 10:22:33,364] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:22:33,365] [INFO] DFAST_QC result json was written to OceanDNA-b39139/dqc_result.json
[2023-03-16 10:22:33,365] [INFO] DFAST_QC completed!
[2023-03-16 10:22:33,365] [INFO] Total running time: 0h1m58s