[2023-03-17 07:01:49,025] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,025] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,025] [INFO] DQC Reference Directory: /var/lib/cwl/stgb79dbae3-f4ec-4ca7-aa53-04ba5b20bb6b/dqc_reference
[2023-03-17 07:01:50,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:50,167] [INFO] Task started: Prodigal
[2023-03-17 07:01:50,167] [INFO] Running command: cat /var/lib/cwl/stgc6f39b8e-f811-480d-8de5-c49e097a10ab/OceanDNA-b10709.fa | prodigal -d OceanDNA-b10709/cds.fna -a OceanDNA-b10709/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:02:12,597] [INFO] Task succeeded: Prodigal
[2023-03-17 07:02:12,598] [INFO] Task started: HMMsearch
[2023-03-17 07:02:12,598] [INFO] Running command: hmmsearch --tblout OceanDNA-b10709/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb79dbae3-f4ec-4ca7-aa53-04ba5b20bb6b/dqc_reference/reference_markers.hmm OceanDNA-b10709/protein.faa > /dev/null
[2023-03-17 07:02:12,806] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:02:12,807] [INFO] Found 6/6 markers.
[2023-03-17 07:02:12,826] [INFO] Query marker FASTA was written to OceanDNA-b10709/markers.fasta
[2023-03-17 07:02:12,827] [INFO] Task started: Blastn
[2023-03-17 07:02:12,827] [INFO] Running command: blastn -query OceanDNA-b10709/markers.fasta -db /var/lib/cwl/stgb79dbae3-f4ec-4ca7-aa53-04ba5b20bb6b/dqc_reference/reference_markers.fasta -out OceanDNA-b10709/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:13,400] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:13,401] [INFO] Selected 24 target genomes.
[2023-03-17 07:02:13,401] [INFO] Target genome list was writen to OceanDNA-b10709/target_genomes.txt
[2023-03-17 07:02:13,413] [INFO] Task started: fastANI
[2023-03-17 07:02:13,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f39b8e-f811-480d-8de5-c49e097a10ab/OceanDNA-b10709.fa --refList OceanDNA-b10709/target_genomes.txt --output OceanDNA-b10709/fastani_result.tsv --threads 1
[2023-03-17 07:02:27,290] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:27,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb79dbae3-f4ec-4ca7-aa53-04ba5b20bb6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:27,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb79dbae3-f4ec-4ca7-aa53-04ba5b20bb6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:27,299] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:27,300] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:02:27,300] [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
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	78.8223	398	1091	95	below_threshold
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	77.7442	118	1091	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.2656	162	1091	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.064	182	1091	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.0299	182	1091	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	76.9838	177	1091	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	76.8965	159	1091	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	76.5883	127	1091	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.4744	52	1091	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	76.4232	50	1091	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.4102	55	1091	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	76.3562	119	1091	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.1475	139	1091	95	below_threshold
Kordia zhangzhouensis	strain=MCCC 1A00726	GCA_001005305.1	1620405	1620405	type	True	75.7667	50	1091	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	75.7252	63	1091	95	below_threshold
Kordia periserrulae	strain=DSM 25731	GCA_003054265.1	701523	701523	type	True	75.713	63	1091	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:02:27,300] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10709/tc_result.tsv
[2023-03-17 07:02:27,300] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:27,300] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:27,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb79dbae3-f4ec-4ca7-aa53-04ba5b20bb6b/dqc_reference/checkm_data
[2023-03-17 07:02:27,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:27,305] [INFO] Task started: CheckM
[2023-03-17 07:02:27,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10709/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10709/checkm_input OceanDNA-b10709/checkm_result
[2023-03-17 07:03:23,132] [INFO] Task succeeded: CheckM
[2023-03-17 07:03:23,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:03:23,135] [INFO] ===== Completeness check finished =====
[2023-03-17 07:03:23,135] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:03:23,135] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10709/markers.fasta)
[2023-03-17 07:03:23,135] [INFO] Task started: Blastn
[2023-03-17 07:03:23,135] [INFO] Running command: blastn -query OceanDNA-b10709/markers.fasta -db /var/lib/cwl/stgb79dbae3-f4ec-4ca7-aa53-04ba5b20bb6b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10709/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:03:23,890] [INFO] Task succeeded: Blastn
[2023-03-17 07:03:23,891] [INFO] Selected 16 target genomes.
[2023-03-17 07:03:23,891] [INFO] Target genome list was writen to OceanDNA-b10709/target_genomes_gtdb.txt
[2023-03-17 07:03:24,182] [INFO] Task started: fastANI
[2023-03-17 07:03:24,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f39b8e-f811-480d-8de5-c49e097a10ab/OceanDNA-b10709.fa --refList OceanDNA-b10709/target_genomes_gtdb.txt --output OceanDNA-b10709/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:03:33,058] [INFO] Task succeeded: fastANI
[2023-03-17 07:03:33,067] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:03:33,067] [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_002337605.1	s__Marinirhabdus sp002337605	99.98	1082	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	conclusive
GCA_002707745.1	s__Marinirhabdus sp002707745	80.4873	483	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	99.79	99.79	0.83	0.83	2	-
GCA_002375495.1	s__Marinirhabdus sp002375495	78.8359	347	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_003353425.1	s__Marinirhabdus gelatinilytica	78.8252	399	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011044175.1	s__Marinirhabdus sp011044175	78.1377	348	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746845.1	s__Altibacter lentus	77.7146	120	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	77.3148	210	1091	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	77.2656	162	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364245.1	s__Marixanthomonas sp002364245	77.2446	125	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	77.064	182	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002364215.1	s__Aequorivita sp002364215	76.5961	129	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_001641085.1	s__Aequorivita soesokkakensis	76.5736	128	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_009827225.1	s__SMXJ01 sp009827225	76.4487	73	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129745.1	s__Winogradskyella jejuensis	75.7252	63	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054265.1	s__Kordia periserrulae	75.6973	64	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:03:33,067] [INFO] GTDB search result was written to OceanDNA-b10709/result_gtdb.tsv
[2023-03-17 07:03:33,068] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:03:33,069] [INFO] DFAST_QC result json was written to OceanDNA-b10709/dqc_result.json
[2023-03-17 07:03:33,069] [INFO] DFAST_QC completed!
[2023-03-17 07:03:33,069] [INFO] Total running time: 0h1m44s