[2023-03-16 01:12:29,292] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:12:29,294] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:12:29,294] [INFO] DQC Reference Directory: /var/lib/cwl/stg40e5ac7a-6a3e-4f7a-8171-8b472cd93dd0/dqc_reference
[2023-03-16 01:12:30,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:12:30,461] [INFO] Task started: Prodigal
[2023-03-16 01:12:30,462] [INFO] Running command: cat /var/lib/cwl/stg2e9cda08-149f-4f69-bf41-792d117c216a/OceanDNA-b9709.fa | prodigal -d OceanDNA-b9709/cds.fna -a OceanDNA-b9709/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:12:48,873] [INFO] Task succeeded: Prodigal
[2023-03-16 01:12:48,873] [INFO] Task started: HMMsearch
[2023-03-16 01:12:48,873] [INFO] Running command: hmmsearch --tblout OceanDNA-b9709/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40e5ac7a-6a3e-4f7a-8171-8b472cd93dd0/dqc_reference/reference_markers.hmm OceanDNA-b9709/protein.faa > /dev/null
[2023-03-16 01:12:49,075] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:12:49,075] [INFO] Found 6/6 markers.
[2023-03-16 01:12:49,097] [INFO] Query marker FASTA was written to OceanDNA-b9709/markers.fasta
[2023-03-16 01:12:49,098] [INFO] Task started: Blastn
[2023-03-16 01:12:49,098] [INFO] Running command: blastn -query OceanDNA-b9709/markers.fasta -db /var/lib/cwl/stg40e5ac7a-6a3e-4f7a-8171-8b472cd93dd0/dqc_reference/reference_markers.fasta -out OceanDNA-b9709/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:12:49,709] [INFO] Task succeeded: Blastn
[2023-03-16 01:12:49,711] [INFO] Selected 18 target genomes.
[2023-03-16 01:12:49,712] [INFO] Target genome list was writen to OceanDNA-b9709/target_genomes.txt
[2023-03-16 01:12:49,761] [INFO] Task started: fastANI
[2023-03-16 01:12:49,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e9cda08-149f-4f69-bf41-792d117c216a/OceanDNA-b9709.fa --refList OceanDNA-b9709/target_genomes.txt --output OceanDNA-b9709/fastani_result.tsv --threads 1
[2023-03-16 01:12:59,556] [INFO] Task succeeded: fastANI
[2023-03-16 01:12:59,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40e5ac7a-6a3e-4f7a-8171-8b472cd93dd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:12:59,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40e5ac7a-6a3e-4f7a-8171-8b472cd93dd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:12:59,567] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:12:59,568] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 01:12:59,568] [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
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	84.2359	694	900	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	80.8072	554	900	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.2623	197	900	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.1872	199	900	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.7727	148	900	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.7665	139	900	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	76.7429	110	900	95	below_threshold
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	76.732	132	900	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.7026	180	900	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.7008	123	900	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	76.6945	110	900	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.6739	143	900	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	76.5034	111	900	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	76.4873	111	900	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	76.4198	149	900	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.1298	72	900	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.1141	85	900	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	75.9267	70	900	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 01:12:59,571] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9709/tc_result.tsv
[2023-03-16 01:12:59,571] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:12:59,571] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:12:59,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40e5ac7a-6a3e-4f7a-8171-8b472cd93dd0/dqc_reference/checkm_data
[2023-03-16 01:12:59,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:12:59,578] [INFO] Task started: CheckM
[2023-03-16 01:12:59,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9709/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9709/checkm_input OceanDNA-b9709/checkm_result
[2023-03-16 01:13:46,760] [INFO] Task succeeded: CheckM
[2023-03-16 01:13:46,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:13:46,765] [INFO] ===== Completeness check finished =====
[2023-03-16 01:13:46,766] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:13:46,766] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9709/markers.fasta)
[2023-03-16 01:13:46,766] [INFO] Task started: Blastn
[2023-03-16 01:13:46,766] [INFO] Running command: blastn -query OceanDNA-b9709/markers.fasta -db /var/lib/cwl/stg40e5ac7a-6a3e-4f7a-8171-8b472cd93dd0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9709/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:13:47,630] [INFO] Task succeeded: Blastn
[2023-03-16 01:13:47,632] [INFO] Selected 7 target genomes.
[2023-03-16 01:13:47,632] [INFO] Target genome list was writen to OceanDNA-b9709/target_genomes_gtdb.txt
[2023-03-16 01:13:47,851] [INFO] Task started: fastANI
[2023-03-16 01:13:47,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e9cda08-149f-4f69-bf41-792d117c216a/OceanDNA-b9709.fa --refList OceanDNA-b9709/target_genomes_gtdb.txt --output OceanDNA-b9709/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:13:52,398] [INFO] Task succeeded: fastANI
[2023-03-16 01:13:52,403] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 01:13:52,403] [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_002360635.1	s__Marixanthomonas sp002360635	99.9869	895	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	conclusive
GCA_002364245.1	s__Marixanthomonas sp002364245	90.7074	420	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	90.7012	743	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	84.2359	694	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003095375.1	s__Marixanthomonas sp003095375	80.8072	554	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	76.7026	180	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346335.1	s__Aequorivita sinensis	76.6739	143	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-16 01:13:52,403] [INFO] GTDB search result was written to OceanDNA-b9709/result_gtdb.tsv
[2023-03-16 01:13:52,403] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:13:52,406] [INFO] DFAST_QC result json was written to OceanDNA-b9709/dqc_result.json
[2023-03-16 01:13:52,406] [INFO] DFAST_QC completed!
[2023-03-16 01:13:52,406] [INFO] Total running time: 0h1m23s