[2023-03-18 00:15:08,421] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:15:08,422] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:15:08,423] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1353726-2e36-4353-ad0a-4bb3784e1209/dqc_reference
[2023-03-18 00:15:09,524] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:15:09,524] [INFO] Task started: Prodigal
[2023-03-18 00:15:09,524] [INFO] Running command: cat /var/lib/cwl/stgd08fea1c-9847-4bb0-9625-0701008de0a5/OceanDNA-b37578.fa | prodigal -d OceanDNA-b37578/cds.fna -a OceanDNA-b37578/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:15:33,015] [INFO] Task succeeded: Prodigal
[2023-03-18 00:15:33,015] [INFO] Task started: HMMsearch
[2023-03-18 00:15:33,016] [INFO] Running command: hmmsearch --tblout OceanDNA-b37578/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1353726-2e36-4353-ad0a-4bb3784e1209/dqc_reference/reference_markers.hmm OceanDNA-b37578/protein.faa > /dev/null
[2023-03-18 00:15:33,226] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:15:33,227] [INFO] Found 6/6 markers.
[2023-03-18 00:15:33,249] [INFO] Query marker FASTA was written to OceanDNA-b37578/markers.fasta
[2023-03-18 00:15:33,250] [INFO] Task started: Blastn
[2023-03-18 00:15:33,250] [INFO] Running command: blastn -query OceanDNA-b37578/markers.fasta -db /var/lib/cwl/stgc1353726-2e36-4353-ad0a-4bb3784e1209/dqc_reference/reference_markers.fasta -out OceanDNA-b37578/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:15:33,982] [INFO] Task succeeded: Blastn
[2023-03-18 00:15:33,994] [INFO] Selected 21 target genomes.
[2023-03-18 00:15:33,995] [INFO] Target genome list was writen to OceanDNA-b37578/target_genomes.txt
[2023-03-18 00:15:34,009] [INFO] Task started: fastANI
[2023-03-18 00:15:34,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgd08fea1c-9847-4bb0-9625-0701008de0a5/OceanDNA-b37578.fa --refList OceanDNA-b37578/target_genomes.txt --output OceanDNA-b37578/fastani_result.tsv --threads 1
[2023-03-18 00:15:48,839] [INFO] Task succeeded: fastANI
[2023-03-18 00:15:48,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1353726-2e36-4353-ad0a-4bb3784e1209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:15:48,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1353726-2e36-4353-ad0a-4bb3784e1209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:15:48,852] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:15:48,853] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:15:48,853] [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
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	81.3924	817	1220	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	81.148	819	1220	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	78.1158	330	1220	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	77.8891	330	1220	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.7552	320	1220	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.6192	295	1220	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	77.4554	298	1220	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.1484	261	1220	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.8491	204	1220	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.7602	159	1220	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.7429	156	1220	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.6845	158	1220	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.293	85	1220	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	76.2865	92	1220	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.1754	92	1220	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	76.0848	88	1220	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	76.0605	81	1220	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	75.938	64	1220	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.8602	104	1220	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.8471	106	1220	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	75.6388	51	1220	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:15:48,861] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37578/tc_result.tsv
[2023-03-18 00:15:48,862] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:15:48,862] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:15:48,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1353726-2e36-4353-ad0a-4bb3784e1209/dqc_reference/checkm_data
[2023-03-18 00:15:48,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:15:48,868] [INFO] Task started: CheckM
[2023-03-18 00:15:48,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37578/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37578/checkm_input OceanDNA-b37578/checkm_result
[2023-03-18 00:16:47,918] [INFO] Task succeeded: CheckM
[2023-03-18 00:16:47,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:16:47,978] [INFO] ===== Completeness check finished =====
[2023-03-18 00:16:47,978] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:16:47,978] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37578/markers.fasta)
[2023-03-18 00:16:47,979] [INFO] Task started: Blastn
[2023-03-18 00:16:47,980] [INFO] Running command: blastn -query OceanDNA-b37578/markers.fasta -db /var/lib/cwl/stgc1353726-2e36-4353-ad0a-4bb3784e1209/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37578/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:16:49,291] [INFO] Task succeeded: Blastn
[2023-03-18 00:16:49,292] [INFO] Selected 10 target genomes.
[2023-03-18 00:16:49,292] [INFO] Target genome list was writen to OceanDNA-b37578/target_genomes_gtdb.txt
[2023-03-18 00:16:49,301] [INFO] Task started: fastANI
[2023-03-18 00:16:49,301] [INFO] Running command: fastANI --query /var/lib/cwl/stgd08fea1c-9847-4bb0-9625-0701008de0a5/OceanDNA-b37578.fa --refList OceanDNA-b37578/target_genomes_gtdb.txt --output OceanDNA-b37578/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:16:57,499] [INFO] Task succeeded: fastANI
[2023-03-18 00:16:57,506] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:16:57,507] [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_002414665.1	s__Haliea sp002414665	99.8584	1165	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	conclusive
GCA_002416125.1	s__Haliea sp002416125	90.341	1014	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCF_000423125.1	s__Haliea salexigens	81.3905	818	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCF_003719295.1	s__Haliea alexandrii	81.1397	820	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692965.1	s__NZNC01 sp002692965	78.4148	372	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCA_002699145.1	s__Halioglobus sp002699145	77.9136	288	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_010669285.1	s__Kineobactrum salinum	77.8991	329	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	77.7504	322	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.6938	367	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	76.9134	197	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:16:57,507] [INFO] GTDB search result was written to OceanDNA-b37578/result_gtdb.tsv
[2023-03-18 00:16:57,507] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:16:57,509] [INFO] DFAST_QC result json was written to OceanDNA-b37578/dqc_result.json
[2023-03-18 00:16:57,509] [INFO] DFAST_QC completed!
[2023-03-18 00:16:57,509] [INFO] Total running time: 0h1m49s