[2023-03-18 20:40:39,434] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,435] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c3f36c2-8499-4ce1-a1ae-e6fb37e01249/dqc_reference
[2023-03-18 20:40:41,218] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,219] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,219] [INFO] Running command: cat /var/lib/cwl/stgc4453d80-c525-4ed5-810d-f46a27a6060d/OceanDNA-b33388.fa | prodigal -d OceanDNA-b33388/cds.fna -a OceanDNA-b33388/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:41:12,499] [INFO] Task succeeded: Prodigal
[2023-03-18 20:41:12,499] [INFO] Task started: HMMsearch
[2023-03-18 20:41:12,499] [INFO] Running command: hmmsearch --tblout OceanDNA-b33388/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c3f36c2-8499-4ce1-a1ae-e6fb37e01249/dqc_reference/reference_markers.hmm OceanDNA-b33388/protein.faa > /dev/null
[2023-03-18 20:41:12,848] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:41:12,849] [INFO] Found 6/6 markers.
[2023-03-18 20:41:12,880] [INFO] Query marker FASTA was written to OceanDNA-b33388/markers.fasta
[2023-03-18 20:41:12,880] [INFO] Task started: Blastn
[2023-03-18 20:41:12,880] [INFO] Running command: blastn -query OceanDNA-b33388/markers.fasta -db /var/lib/cwl/stg2c3f36c2-8499-4ce1-a1ae-e6fb37e01249/dqc_reference/reference_markers.fasta -out OceanDNA-b33388/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:13,801] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:13,802] [INFO] Selected 20 target genomes.
[2023-03-18 20:41:13,802] [INFO] Target genome list was writen to OceanDNA-b33388/target_genomes.txt
[2023-03-18 20:41:13,809] [INFO] Task started: fastANI
[2023-03-18 20:41:13,809] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4453d80-c525-4ed5-810d-f46a27a6060d/OceanDNA-b33388.fa --refList OceanDNA-b33388/target_genomes.txt --output OceanDNA-b33388/fastani_result.tsv --threads 1
[2023-03-18 20:41:38,492] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:38,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c3f36c2-8499-4ce1-a1ae-e6fb37e01249/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:38,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c3f36c2-8499-4ce1-a1ae-e6fb37e01249/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:38,504] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:38,504] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:38,504] [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
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	82.4861	1009	1643	95	below_threshold
Massilia psychrophila	strain=CGMCC 1.15196	GCA_014641415.1	1603353	1603353	type	True	82.2243	900	1643	95	below_threshold
Massilia psychrophila	strain=JCM 30813	GCA_002760665.1	1603353	1603353	type	True	82.1786	898	1643	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	81.5648	962	1643	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	81.1208	757	1643	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	81.1163	940	1643	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	81.1017	891	1643	95	below_threshold
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	81.0979	925	1643	95	below_threshold
Massilia polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	81.0539	775	1643	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	81.0438	918	1643	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	80.7781	849	1643	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	80.7685	768	1643	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	80.6754	899	1643	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	80.6657	951	1643	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	80.5409	847	1643	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.5228	850	1643	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	80.4692	820	1643	95	below_threshold
Massilia arenae	strain=GEM5	GCA_008014745.1	2603288	2603288	type	True	80.431	844	1643	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	80.2513	785	1643	95	below_threshold
Massilia aurea	strain=JCM 13879	GCA_024753205.1	373040	373040	type	True	79.6289	727	1643	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:38,504] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33388/tc_result.tsv
[2023-03-18 20:41:38,505] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:38,505] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:38,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c3f36c2-8499-4ce1-a1ae-e6fb37e01249/dqc_reference/checkm_data
[2023-03-18 20:41:38,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:38,566] [INFO] Task started: CheckM
[2023-03-18 20:41:38,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33388/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33388/checkm_input OceanDNA-b33388/checkm_result
[2023-03-18 20:42:52,989] [INFO] Task succeeded: CheckM
[2023-03-18 20:42:52,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 20:42:52,993] [INFO] ===== Completeness check finished =====
[2023-03-18 20:42:52,993] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:42:52,993] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33388/markers.fasta)
[2023-03-18 20:42:52,994] [INFO] Task started: Blastn
[2023-03-18 20:42:52,994] [INFO] Running command: blastn -query OceanDNA-b33388/markers.fasta -db /var/lib/cwl/stg2c3f36c2-8499-4ce1-a1ae-e6fb37e01249/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33388/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:42:54,781] [INFO] Task succeeded: Blastn
[2023-03-18 20:42:54,781] [INFO] Selected 20 target genomes.
[2023-03-18 20:42:54,782] [INFO] Target genome list was writen to OceanDNA-b33388/target_genomes_gtdb.txt
[2023-03-18 20:42:54,819] [INFO] Task started: fastANI
[2023-03-18 20:42:54,819] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4453d80-c525-4ed5-810d-f46a27a6060d/OceanDNA-b33388.fa --refList OceanDNA-b33388/target_genomes_gtdb.txt --output OceanDNA-b33388/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:43:18,569] [INFO] Task succeeded: fastANI
[2023-03-18 20:43:18,581] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:43:18,581] [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_002760655.1	s__Massilia eurypsychrophila	82.4682	1010	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760665.1	s__Massilia psychrophila	82.1662	901	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003953935.1	s__Massilia atriviolacea	81.5708	961	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428015.1	s__Massilia sp002428015	81.5684	810	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003484545.1	s__Massilia sp003484545	81.4379	561	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590855.1	s__Massilia sp003590855	81.1182	756	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752675.1	s__Massilia violaceinigra	81.1167	889	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003520365.1	s__Massilia sp003520365	81.1064	559	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682065.1	s__Massilia rubra	81.1039	924	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCF_011682145.1	s__Massilia mucilaginosa	81.0696	945	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682175.1	s__Massilia frigida	81.0678	915	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927275.1	s__Massilia sp012927275	81.0623	774	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682045.1	s__Massilia aquatica	81.0292	949	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382345.1	s__Massilia niastensis	80.7898	844	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003011895.2	s__Massilia glaciei	80.7694	768	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007115.1	s__Massilia sp002007115	80.7488	867	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017582745.1	s__Massilia oculi	80.5081	843	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.07	95.07	0.86	0.86	2	-
GCF_900129765.1	s__Massilia sp900129765	80.0368	727	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127655.1	s__Janthinobacterium sp002127655	79.9019	776	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0774	99.99	99.99	0.99	0.99	4	-
GCA_014841595.1	s__Massilia sp014841595	79.6893	736	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	98.42	98.38	0.96	0.95	4	-
--------------------------------------------------------------------------------
[2023-03-18 20:43:18,581] [INFO] GTDB search result was written to OceanDNA-b33388/result_gtdb.tsv
[2023-03-18 20:43:18,581] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:43:18,583] [INFO] DFAST_QC result json was written to OceanDNA-b33388/dqc_result.json
[2023-03-18 20:43:18,584] [INFO] DFAST_QC completed!
[2023-03-18 20:43:18,584] [INFO] Total running time: 0h2m39s