[2023-03-17 09:05:02,535] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,535] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,536] [INFO] DQC Reference Directory: /var/lib/cwl/stge9588ce2-e2fb-48d3-b905-53632396b5d1/dqc_reference
[2023-03-17 09:05:03,734] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,734] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,734] [INFO] Running command: cat /var/lib/cwl/stg413b181e-3717-44db-8ef0-0327d859538e/OceanDNA-b35229.fa | prodigal -d OceanDNA-b35229/cds.fna -a OceanDNA-b35229/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:05:23,758] [INFO] Task succeeded: Prodigal
[2023-03-17 09:05:23,759] [INFO] Task started: HMMsearch
[2023-03-17 09:05:23,759] [INFO] Running command: hmmsearch --tblout OceanDNA-b35229/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9588ce2-e2fb-48d3-b905-53632396b5d1/dqc_reference/reference_markers.hmm OceanDNA-b35229/protein.faa > /dev/null
[2023-03-17 09:05:23,971] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:05:23,971] [INFO] Found 6/6 markers.
[2023-03-17 09:05:23,992] [INFO] Query marker FASTA was written to OceanDNA-b35229/markers.fasta
[2023-03-17 09:05:23,993] [INFO] Task started: Blastn
[2023-03-17 09:05:23,993] [INFO] Running command: blastn -query OceanDNA-b35229/markers.fasta -db /var/lib/cwl/stge9588ce2-e2fb-48d3-b905-53632396b5d1/dqc_reference/reference_markers.fasta -out OceanDNA-b35229/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:24,668] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:24,669] [INFO] Selected 21 target genomes.
[2023-03-17 09:05:24,669] [INFO] Target genome list was writen to OceanDNA-b35229/target_genomes.txt
[2023-03-17 09:05:24,712] [INFO] Task started: fastANI
[2023-03-17 09:05:24,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg413b181e-3717-44db-8ef0-0327d859538e/OceanDNA-b35229.fa --refList OceanDNA-b35229/target_genomes.txt --output OceanDNA-b35229/fastani_result.tsv --threads 1
[2023-03-17 09:05:39,873] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:39,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9588ce2-e2fb-48d3-b905-53632396b5d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:05:39,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9588ce2-e2fb-48d3-b905-53632396b5d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:05:39,884] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:05:39,884] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:05:39,885] [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
Psychromonas arctica	strain=DSM 14288	GCA_000482725.1	168275	168275	type	True	82.253	795	1265	95	below_threshold
Psychromonas ossibalaenae	strain=JAMM 0738	GCA_000381745.1	444922	444922	type	True	78.6087	195	1265	95	below_threshold
Psychromonas aquimarina	strain=ATCC BAA-1526	GCA_000428725.1	444919	444919	type	True	78.3381	202	1265	95	below_threshold
Psychromonas hadalis	strain=ATCC BAA-638	GCA_000420245.1	211669	211669	type	True	78.2767	236	1265	95	below_threshold
Psychromonas ingrahamii	strain=37	GCA_000015285.1	357794	357794	type	True	78.1398	220	1265	95	below_threshold
Psychromonas antarctica	strain=DSM 10704	GCA_022267535.1	67573	67573	type	True	77.5523	228	1265	95	below_threshold
Photobacterium indicum	strain=ATCC 19614	GCA_003026215.1	81447	81447	type	True	76.7173	64	1265	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	76.383	56	1265	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	76.3285	59	1265	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	76.256	60	1265	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	76.2225	50	1265	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.2216	58	1265	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	76.2137	50	1265	95	below_threshold
Pseudoalteromonas ostreae	strain=hOe-66	GCA_018069805.1	2774154	2774154	type	True	76.187	66	1265	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	76.0482	53	1265	95	below_threshold
Shewanella glacialimarina	strain=TZS-4	GCA_020511155.1	2590884	2590884	type	True	76.0052	57	1265	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:05:39,885] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35229/tc_result.tsv
[2023-03-17 09:05:39,885] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:05:39,885] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:05:39,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9588ce2-e2fb-48d3-b905-53632396b5d1/dqc_reference/checkm_data
[2023-03-17 09:05:39,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:05:39,891] [INFO] Task started: CheckM
[2023-03-17 09:05:39,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35229/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35229/checkm_input OceanDNA-b35229/checkm_result
[2023-03-17 09:06:29,428] [INFO] Task succeeded: CheckM
[2023-03-17 09:06:29,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:06:29,431] [INFO] ===== Completeness check finished =====
[2023-03-17 09:06:29,431] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:06:29,431] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35229/markers.fasta)
[2023-03-17 09:06:29,432] [INFO] Task started: Blastn
[2023-03-17 09:06:29,432] [INFO] Running command: blastn -query OceanDNA-b35229/markers.fasta -db /var/lib/cwl/stge9588ce2-e2fb-48d3-b905-53632396b5d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35229/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:06:30,484] [INFO] Task succeeded: Blastn
[2023-03-17 09:06:30,485] [INFO] Selected 6 target genomes.
[2023-03-17 09:06:30,485] [INFO] Target genome list was writen to OceanDNA-b35229/target_genomes_gtdb.txt
[2023-03-17 09:06:30,520] [INFO] Task started: fastANI
[2023-03-17 09:06:30,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg413b181e-3717-44db-8ef0-0327d859538e/OceanDNA-b35229.fa --refList OceanDNA-b35229/target_genomes_gtdb.txt --output OceanDNA-b35229/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:06:35,743] [INFO] Task succeeded: fastANI
[2023-03-17 09:06:35,748] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:06:35,748] [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
GCF_000470315.2	s__Psychromonas sp000470315	82.7109	792	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828855.1	s__Psychromonas sp009828855	82.6801	788	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	98.96	98.96	0.95	0.95	2	-
GCF_000482725.1	s__Psychromonas arctica	82.2541	797	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	98.18	98.18	0.89	0.89	2	-
GCF_011378715.1	s__Psychromonas sp011378715	82.0177	791	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004376845.1	s__Psychromonas sp004376845	80.7777	533	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318165.1	s__Psychromonas sp003318165	80.1457	519	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:06:35,748] [INFO] GTDB search result was written to OceanDNA-b35229/result_gtdb.tsv
[2023-03-17 09:06:35,748] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:06:35,750] [INFO] DFAST_QC result json was written to OceanDNA-b35229/dqc_result.json
[2023-03-17 09:06:35,750] [INFO] DFAST_QC completed!
[2023-03-17 09:06:35,750] [INFO] Total running time: 0h1m33s