[2023-03-18 00:53:42,874] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,874] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,874] [INFO] DQC Reference Directory: /var/lib/cwl/stgee3209e6-4acd-40ef-a100-ef89fb42d6b1/dqc_reference
[2023-03-18 00:53:44,408] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:44,409] [INFO] Task started: Prodigal
[2023-03-18 00:53:44,409] [INFO] Running command: cat /var/lib/cwl/stg31cba14c-4f94-41b7-a753-6b14ff375b26/OceanDNA-b36577.fa | prodigal -d OceanDNA-b36577/cds.fna -a OceanDNA-b36577/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:54:05,294] [INFO] Task succeeded: Prodigal
[2023-03-18 00:54:05,294] [INFO] Task started: HMMsearch
[2023-03-18 00:54:05,295] [INFO] Running command: hmmsearch --tblout OceanDNA-b36577/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee3209e6-4acd-40ef-a100-ef89fb42d6b1/dqc_reference/reference_markers.hmm OceanDNA-b36577/protein.faa > /dev/null
[2023-03-18 00:54:05,493] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:54:05,494] [INFO] Found 6/6 markers.
[2023-03-18 00:54:05,513] [INFO] Query marker FASTA was written to OceanDNA-b36577/markers.fasta
[2023-03-18 00:54:05,514] [INFO] Task started: Blastn
[2023-03-18 00:54:05,514] [INFO] Running command: blastn -query OceanDNA-b36577/markers.fasta -db /var/lib/cwl/stgee3209e6-4acd-40ef-a100-ef89fb42d6b1/dqc_reference/reference_markers.fasta -out OceanDNA-b36577/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:06,278] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:06,279] [INFO] Selected 13 target genomes.
[2023-03-18 00:54:06,279] [INFO] Target genome list was writen to OceanDNA-b36577/target_genomes.txt
[2023-03-18 00:54:06,286] [INFO] Task started: fastANI
[2023-03-18 00:54:06,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg31cba14c-4f94-41b7-a753-6b14ff375b26/OceanDNA-b36577.fa --refList OceanDNA-b36577/target_genomes.txt --output OceanDNA-b36577/fastani_result.tsv --threads 1
[2023-03-18 00:54:15,957] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:15,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee3209e6-4acd-40ef-a100-ef89fb42d6b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:15,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee3209e6-4acd-40ef-a100-ef89fb42d6b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:15,966] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:15,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:54:15,966] [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
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	94.6947	946	1092	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	81.7456	663	1092	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	81.5135	633	1092	95	below_threshold
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	80.7469	616	1092	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	80.5725	555	1092	95	below_threshold
Alcanivorax borkumensis	strain=SK2	GCA_000009365.1	59754	59754	type	True	79.365	415	1092	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	78.2821	334	1092	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	78.0702	363	1092	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	78.0643	314	1092	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	78.0497	336	1092	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.3623	202	1092	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.5999	69	1092	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:54:15,966] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36577/tc_result.tsv
[2023-03-18 00:54:15,966] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:15,966] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:15,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee3209e6-4acd-40ef-a100-ef89fb42d6b1/dqc_reference/checkm_data
[2023-03-18 00:54:15,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:15,971] [INFO] Task started: CheckM
[2023-03-18 00:54:15,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36577/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36577/checkm_input OceanDNA-b36577/checkm_result
[2023-03-18 00:55:08,704] [INFO] Task succeeded: CheckM
[2023-03-18 00:55:08,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:55:08,711] [INFO] ===== Completeness check finished =====
[2023-03-18 00:55:08,711] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:55:08,711] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36577/markers.fasta)
[2023-03-18 00:55:08,713] [INFO] Task started: Blastn
[2023-03-18 00:55:08,713] [INFO] Running command: blastn -query OceanDNA-b36577/markers.fasta -db /var/lib/cwl/stgee3209e6-4acd-40ef-a100-ef89fb42d6b1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36577/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:55:10,086] [INFO] Task succeeded: Blastn
[2023-03-18 00:55:10,087] [INFO] Selected 10 target genomes.
[2023-03-18 00:55:10,087] [INFO] Target genome list was writen to OceanDNA-b36577/target_genomes_gtdb.txt
[2023-03-18 00:55:10,097] [INFO] Task started: fastANI
[2023-03-18 00:55:10,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg31cba14c-4f94-41b7-a753-6b14ff375b26/OceanDNA-b36577.fa --refList OceanDNA-b36577/target_genomes_gtdb.txt --output OceanDNA-b36577/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:55:18,650] [INFO] Task succeeded: fastANI
[2023-03-18 00:55:18,657] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:55:18,657] [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_002706085.1	s__Alcanivorax sp002706085	99.6388	1047	1092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.88	0.86	0.86	2	conclusive
GCF_003597125.1	s__Alcanivorax profundi	94.7136	945	1092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.31	99.31	0.96	0.96	2	-
GCA_017794965.1	s__Alcanivorax sp017794965	82.1849	706	1092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756665.1	s__Alcanivorax nanhaiticus	81.7166	666	1092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882945.1	s__Alcanivorax sp009882945	81.5603	654	1092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601165.1	s__Alcanivorax sediminis	81.5121	633	1092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107995.1	s__Alcanivorax sp900107995	80.7996	641	1092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCF_000756655.1	s__Alcanivorax jadensis	80.7566	615	1092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCF_000300995.1	s__Alcanivorax hongdengensis	80.5724	555	1092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762765.1	s__Alcanivorax sp014762765	80.3236	568	1092	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:55:18,657] [INFO] GTDB search result was written to OceanDNA-b36577/result_gtdb.tsv
[2023-03-18 00:55:18,657] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:55:18,659] [INFO] DFAST_QC result json was written to OceanDNA-b36577/dqc_result.json
[2023-03-18 00:55:18,659] [INFO] DFAST_QC completed!
[2023-03-18 00:55:18,659] [INFO] Total running time: 0h1m36s